AGBT 2012 Tweets Day 3

17 Feb 2012

(Day 1, Day 2, Day 3, Day 4)

AGBT has been low on announcements so far. As Dan Koboldt says people are now a bit more focused on how to interpret all that lovely data they've been generating. Probably no bad thing, but that's not what we want from AGBT. We want buzz, hype, outrageous marketing statements and speculation on the future of sequencing.

Today my prayers may be answered ... all eyes will be on Clive Brown and Oxford Nanopore at 11:40am local (4:40pm GMT).

Scientific agenda

9:00-9:35 am, Keynote Speaker: Rick Myers, HudsonAlpha Institute for Biotechnology, “Genetics and Epigenetics of Human Gene Regulation”
9:35-10:05 am, Tom Gingeras, Cold Spring Harbor Laboratory, “Important Lessons from Complex Genomes”
10:05-10:25 am, Geoffrey Smith, Illumina Cambridge Ltd., “The Miseq DNA Sequencing Platform and Application in Clinical Microbiology”
11:00-11:20 am, Joseph Boland, National Cancer Institute, “Exome Sequencing on the PGM: Exome in a Day”
11:20-11:40 am, Richard Roberts, New England Biolabs, “Characterization of DNA Methyltransferase Specificities Using Single-Molecule, Real-Time DNA Sequencing”
11:40 am-12:00 pm, Clive Brown, Oxford Nanopore Technologies, “Single Molecule ‘Strand’ Sequencing Using Protein Nanopores and Scalable Electronic Devices”
12:15-2:15 pm, Pacific Biosciences Workshop
2:15-2:35 pm, Illumina, Inc., Elliott Margulies, “From Sample to Answer: Fast and Accurate Genome Sequencing for the Clinic”
2:35-2:55 pm, Caliper a Perkin Elmer Company, Kevin Hrusovsky, “Next Generation Technologies Enabling a Revolution in Medicine”
2:55-3:15 pm, Complete Genomics, Carlos Bustamante, Stanford University, “Population Genetic Inference in the Personal Era”
3:15-3:35 pm, RainDance Technologies, Andy Watson, “Recent Publication Successes: The Power of RainDance Targeted Sequencing”
3:35-3:55 pm, Advanced Analytical, Steve Siembieda, “Fragment Analyzer™- Streamlining Quality and Quantity Analysis of Nucleic Acids”
3:55-4:15 pm, NuGen Technologies, Inc., Elaine Mardis, Washington University School of Medicine, “Simplifying Genomic Sample Preparation with Digital Microfluidics”

Evening session topics

Cancer and Transcriptomes (Michael Metzker, Baylor College of Medicine, Chair)
Genome Biology (Steven Jones, British Columbia Cancer Agency, Chair)
Computational Biology (Mike Zody, Broad Institute of MIT and Harvard, Chair)

Most popular tweets
(34) nanopore: Introducing the MinION, a nanopore sequencer the size of a USB stick. Works just like GridION, but smaller #AGBT
(22) pathogenomenick: Oxford Nanopore megaton announcement: Why do you need a machine? exclusive interview on my blog! http://t.co/tJxQit9T #AGBT
(22) kbradnam: Reactions to @nanopore news. Biologists: cheer. Bioinformaticians: groan. System admins: weep. #AGBT
(20) bioitworld: Full story on Oxford @nanopore stunning presentation from CTO Clive Brown at #AGBT http://t.co/VNvCxLQN
(17) Copenhagenomics: Here's a spy photo from a projected sequencing center, planned to open in early 2013: http://t.co/BjaSNe1P #AGBT
(17) Matt_Francis: #AGBT obi-wan:I felt a great disturbance in the force, as if a million #illumina investors cried out in pain #oxford #Nanopore
(13) nanopore: of course! RT @kbradnam: @nanopore release also reveals that MinION syncs with iTunes, acts as a 3G modem, and has a fresh lemon scent #AGBT
(13) genomesunzipped: Making sequencing simpler with nanopores: Our take on the new Oxford @Nanopore machines #AGBT http://t.co/cjrQX1db
(12) kbradnam: Things to tell your grandchildren: "and we used to work in large buildings called sequencing centers" #AGBT
(10) pathogenomenick: The full Oxford Nanopore press release up here http://t.co/JnJHjsD4 #AGBT
(9) genetics_blog: If looking through the #AGBT tag is too daunting, @pathogenomenick is doing a fine job summarizing at http://t.co/CWWf79Yi. Thank you sir
(9) pathogenomenick: I've embedded all the nanopore videos on the blog here http://t.co/rhBpP9XS #AGBT
(9) acdarby: I am a bit worried that my computer does not have enough USB ports to turn it into a sequencing lab #AGBT @nanopore!
(7) girlscientist: Rich Roberts plays to crowd by asking if some of money being spent on DNA sequencing could instead be used figuring out what genes do. #AGBT
(6) girlscientist: Myers: analysis of DNA methylation in family shows genetics have strong effect, http://t.co/TxLlZIle #AGBT
(6) ElementoLab: #AGBT Tom Gingeras: extremely low copy number transcripts in 1 cell type can be highly expressed in another cell type
(6) timjph: New sequencers announced at #AGBT by Oxford Nanopore; one USB sized @pathogenomenick: full press release here http://t.co/fYNWJYEf #AGBT
(5) ElementoLab: #AGBT Tom Gingeras: intergenic regions migth be much smaller than currently thought, genes might massively overlap
(5) girlscientist: Eric Green asks Geoffrey Smith of Illumina the $1M question: where do you actually see MiSeq's being deployed? A: in clinics, we hope #AGBT
(5) bmahersciwriter: RT @girlscientist: Eric Green asks Illumina the $1M question: where do you actually see MiSeq's being deployed? A: in clinics, we hope #AGBT
(5) Massgenomics: Joseph Boland on IonTorrent PGM "Exome in a Day". Sure, if you ignore the fact that hybridization takes 3 days. #AGBT.
(5) deannachurch: RR: There is a lot of money being spent on sequencing- it would be nice to see some of that spent on understanding what genes do. #AGBT
(5) Copenhagenomics: Richard Roberts: "Can we use a fraction of the $$$ we spend on sequencing, to actually find out what the genes are doing?" #applause #AGBT
(5) ElementoLab: #AGBT Clive Brown: RNA can be DIRECTLY read using nanopores - no cDNA
(5) notSoJunkDNA: So, it's for real? DNA sequencer the size of a USB key: http://t.co/VSOyO4WD #AGBT (via @nanopore )
(5) illumina: Loman and Robison on #AGBT big news, the MiniIon http://t.co/EUYEpp1d and http://t.co/iGRNR6gq
(5) leonidkruglyak: Great problem to have: "how will 100kb+ reads change your research?" http://t.co/5A6wlkfc #AGBT
(5) SEQanswers: Realists: spit take. @kbradnam: Reactions to @nanopore news. Biologists: cheer. Bioinformaticians: groan. System admins: weep. #AGBT
(5) kbradnam: Warning to all employees of @Nanopore. If you carry any 'regular' USB flash drives on you, prepare to be mugged by rabid genomicists #AGBT
(4) girlscientist: Come tweet my talk at 730 tonight #AGBT, Salon E/F: you will learn about the awesome power of immunogenomics (*hype included w/no charge)!

5 - 6am EST
+5m archivist84: Question to those at #AGBT - After we sort the #datadeluge will we have to tackle an #informationinundation ???
+9m t_basi: Nice blog that even I can understand: #AGBT Marco Island Never Gets Old http://t.co/QrvhInBo
+25m lucamartins12: @begandara p mlk agbt vai aloprar
+34m ewanbirney: I went past 1000 followers yesterday - no doubt to AGBT - am and now at the round number of 1011. Welcome!
+47m pathogenomenick: #AGBT day 3 tweets kick off here http://t.co/RfDEXv7H - today's the big one!

6 - 7am EST
+4m omespeak: RT @pathogenomenick All of the #AGBT day 2 tweets are available at http://t.co/1XkWv6XH
+5m pathogenomenick: A bit of info on GnuBIO and Lasergen announcements http://t.co/wmy0taIZ #AGBT - both sound pretty interesting!
+19m mcaccamo: RT @GenomeAnalysis: if you are at #AGBT remember at 16:30 - 18:00 today Rob Davey will be presenting MISO - An Open Source LIMS - Poster 71
+29m hiro_h: AGBT tweets 2012 (1) http://t.co/Gn5LFZMN

7 - 8am EST
+7m pascal_biotech: Good report on AGBT 2012 Day 1: Clinical Annotation and Fierce Competition http://t.co/shuHIlKH #agbt
+11m engawa_02: AGBT tweets 2012 (1) http://t.co/AaFMlZYq
+21m girlscientist: Come tweet my talk at 730 tonight #AGBT, Salon E/F: you will learn about the awesome power of immunogenomics (*hype included w/no charge)!

8 - 9am EST
+24m Copenhagenomics: RT @rforsberg: Europe also has a genomics conference inspired by #AGBT - it's called @Copenhagenomics - http://t.co/FJrXPacO #CPHx
+24m illumina: New blog post from Live at #AGBT http://t.co/isP5PzDn
+39m GenomeScience: via @girlscientist at #AGBT Good q at @PacBio event: who's going to pay for the storage of data we all want to generate?
+45m illumina: On Facebook? Check out pictures from #AGBT on our page. http://t.co/dQC1dUKE
+59m omespeak: RT @illumina: New blog post from Live at #AGBT http://t.co/f8Cn91ky

9 - 10am EST
+0m fluidigm: Suite 285 at #AGBT, last day for drop in discussions, 9am -5pm, Single-Cell Gene Expression, Targeted Resequencing and more>o
+0m omespeak: We had GnuBio and LaserGen announcing new sequencing machines last night. Today, Oxford Nanopore makes big announcement. #AGBT preview
+1m EdgeBio: Good Morning! Here are some more live updates via @dgaalaas on some of the talks from Life Tech and GNUbio #AGBT http://t.co/yQV86960
+3m djschlesinger: First talk of morning session: Rick Myers from HudsonAlpha talking about genetics and epigenetics of gene regulation #AGBT
+3m deannachurch: Good morning! Up first Rick Myers on genetics and epigenetics of human gene regulation. #AGBT
+3m CompleteGenomic: Come see Steve Lincoln, our VP of scientific apps, present on our assembly process in the #AGBT Complete Suite today at 10:30 am
+5m bffo: RM has been working on transcription gene regulation for 30 years ... Should be a great talk! #agbt
+5m girlscientist: Day 2 of #AGBT starts with Rick Myers of @HudsonAlpha. That's my boss up there, so I expect only good tweets from y'all.
+5m bioinfosm: #agbt tweeps, wassup with the tweetup; when and where? #anotherParty
+6m girlscientist: .@bioinfosm #AGBT tweetup is in hotel lobby bar at 9:30ish after sessions end tonight.
+7m bffo: C U all there! RT @girlscientist: .@bioinfosm #AGBT tweetup is in hotel lobby bar at 9:30ish after sessions end tonight.
+9m girlscientist: R Myers echoes theme of meeting: you learn a lot more when you integrate a number of different data types, as in ENCODE. #AGBT
+9m ElementoLab: #AGBT Rick Myers: we will learn a lot by integrating interactome, transcriptome, methylome and allelic variation
+12m bffo: RM:Encode neophytes should look at the guide paper, from PLoS Biology paper http://t.co/gvTjRKCf #AGBT
+14m illumina: Rick Myers, HudsonAlpha Inst, Encode: Integrate data from interactome, transcriptome, methylome with allelic variation #AGBT
+14m ElementoLab: #AGBT Rick Myers: has performed ChIP-seq for ~80 transcription factors in many cell lines for ENCODE
+14m deannachurch: RM: analyzed over 80 transcription factors as part of ENCODE #AGBT
+15m dgaalaas: Good morning. Rick Myers from Hudson Alpha talking ENCODE and ChIP-Seq at #AGBT
+16m illumina: Myers: NSRF is almost exclusively a repressor, binds ~2000 sites. Could not find NRSF binding site upstr of neuro D, until ChIP-Seq #AGBT
+16m deannachurch: RM: by integrating binding data with variation data they can find both allele biased ans allele specific binding. #AGBT
+17m ElementoLab: #AGBT Rick Myers: found a lot of allele-specific binding
+17m finchtalk: #AGBT Rick Meyers on the gene regulation and the ENCODE project. Allele specific expression is wide spread.
+18m illumina: Myers: ChIP-seq on over 80 TFs many cell lines. Allele specific occupancy of protein on DNA & only G allele bound by GABP #AGBT
+19m ElementoLab: #AGBT Rick Myers: have developed transposon mediated method to make RNA-seq libraries, Gertz et al, 2012, Genome Research
+19m ElementoLab: #AGBT Rick Myers: can work with very small quantities of RNA, down to 1ng
+20m girlscientist: Myers: recent paper on transposase-mediated construction of RNA-seq libraries, in @genomeresearch: http://t.co/1lpB7JY0 #AGBT
+20m finchtalk: #AGBT RM on RNA-seq, alignment and gene models are an unsolved problem. Transposon based "shearing" improves lib prep.
+20m illumina: Myers: w/RNA-seq 40M reads gives 40 reads for 1 kb. really really sensitive #AGBT
+21m omespeak: Rick Myers mentions difficulty of sequencing methylation using bisulfite (too expensive now). Perhaps nanopores will change that? #AGBT
+21m illumina: Myers RNA seq library contruction by transposon hopping, much more easier and quite sensitive only 10 pg mRNA #AGBT
+21m rnomics: RT @finchtalk: #AGBT RM on #RNA-seq, alignment and gene models are an unsolved problem.... http://t.co/ZJtnjjfa #rnomics-bioscience @MyEN
+22m ElementoLab: #AGBT Rick Myers: did RRBS on 82 cell lines and tissues for ENCODE, clearly cell lines massively hypermethylated compared to tissues
+22m GenomeBiology: DNA methylation profiling of 82 cell lines and tissues on encode project. RM #agbt
+23m illumina: Myers: DNA methylation, whole genome bisulfite expensive. Compromise = RRBS, w/ Illumina 450k array. Very sensitive, quantitative #AGBT
+23m EpicentreBio: RT @pathogenomenick: #AGBT blog-post round-up http://t.co/p3yUQSPV
+23m girlscientist: Myers: analysis of DNA methylation in family shows genetics have strong effect, http://t.co/TxLlZIle #AGBT
+23m NCBI: This afternoon at Poster 59, @deannachurch will discuss the impact of structural variation on genome assembly. #AGBT http://t.co/1Kj0Xmpy
+24m deannachurch: RM: genetics has a strong affect on methylation patterns. #AGBT
+24m EpicentreBio: RT @illumina: On Facebook? Check out pictures from #AGBT on our page. http://t.co/nnwjLErU
+24m ElementoLab: #AGBT Rick Myers: 92% allele specific methylation is genetic, 8% is imprinting
+26m illumina: Myers: Genetics has a strong effect on methylation patterns, 8% allele-specific imprinting, 92% was genetic #AGBT
+26m ElementoLab: #AGBT Rick Myers: in clinical trial of anti-DR5 antibody in breast cancer, methylation at 114 CpGs is associated w response to therapy
+26m girlscientist: RT @NCBI: This afternoon at Poster 59, @deannachurch will discuss the impact of structural variation on genome assembly. #AGBT
+27m Massgenomics: Good lineup at #AGBT this morning: Rick Myers (HudsonAlpha), Tom Gingeras (CSHL), Geoffrey Smith (Illumina), then much-needed coffee.
+27m GenomeRef: Com to poster 59 this afternoon at #AGBT to see what we are up to with the reference assembly. #AGBT
+27m omespeak: "correlation between methylation and gene expression depends on location of CpG" Rick Myers #AGBT
+27m iontorrent: Rick Myers, Hudson Alpha, shows 114 CpGs associated with response to antibody therapy. #AGBT
+27m illumina: Myers: Correlation of methylation and gene expression depends on location of CpG #AGBT
+28m westr: +1 RT @girlscientist: Myers: analysis of DNA methylation in family shows genetics have strong effect, http://t.co/hgCK8IX7 #AGBT #pm101
+28m ElementoLab: #AGBT Rick Myers: methylation near TSSs negatively correlates w gene expression
+29m ElementoLab: #AGBT Rick Myers: gene body methylation positively correlates w gene expression EXCEPT when CpG islands in gene bodies are methylated
+30m NCBI: Tonight at 9:30 in Salon G, NCBI's Eugene Yaschenko will talk about new NGS data compression strategies. #AGBT http:http://t.co/1Kj0Xmpy
+30m ElementoLab: #AGBT Rick Myers: these gene body CGI are typically enhancers, and need to be unmethylated for gene to be transcribed
+31m NCBI: Tonight at 9:30 in Salon G, NCBI's Eugene Yaschenko will talk about new NGS data compression strategies. #AGBT http://t.co/1Kj0Xmpy
+32m GenomeBiology: Genetics meets genomics when variants correlate with phenotype RM #agbt
+32m CompleteGenomic: Great roundtable discussion this morning with Carlos Bustamante of Stanford U at #AGBT http://t.co/7fcXmUAy
+33m Gavin_Oliver: # AGBT Will keep you up to date on Oxford Nanopore announcements here: http://t.co/Rk184B0R
+33m maureen_mack: Good morning @Personal_RX_WI friends at #agbt. What's on the agenda for today?
+36m deannachurch: Now up Tom Ginger as on important lessons from complex genomes. #AGBT
+36m CRIgenomics: #ONT are talkng today at #AGBT, anyone want to place a bet on the type and number of genomes they have sequenced?
+36m bioinfosm: a real fun video (not sure of the facts yet) from #ionTorrent on homopolymer comparisons with #illumina = http://t.co/TcAfFaYQ #agbt #ngs
+36m ElementoLab: #AGBT Tom Gingeras: lessons learned from complex genomes
+37m girlscientist: Like that Tom Gingeras's computer had a calendar reminder pop up: "Your Talk = Now." #AGBT
+38m Personal_RX_WI: Day 3 #AGBT Genomic Studies and New Tech. Looking forward to Oxford Nanopore single molecule seq talk late morning. Stay tuned. . .
+38m omespeak: RT @CRIgenomics: #ONT are talkng today at #AGBT, anyone want to place a bet on the type and number of genomes they have sequenced?
+38m obahcall: Tom Hudson on lessons learned from ENCODE and modENCODE #AGBT
+40m obahcall: Tom Gingeras on lessons learned from ENCODE and modENCODE #AGBT
+40m deannachurch: TG: over 51,000 genic regions 40.5% protein coding, over 161,000 transcripts. #AGBT
+40m KamounLab: Nanopores or NanoBores? RT @Gavin_Oliver # AGBT Will keep you up to date on Oxford Nanopore announcements here: http://t.co/vbSoAWYJ
+41m deannachurch: TG: genes don't have a single control region- they have multiple. #AGBT
+42m bioinfosm: TG: 51k genes, 8 transcripts/gene on avg, 40% are protein coding; alt start could be anywhere; promoters embedded in introns as well! #agbt
+42m illumina: Gingeras, Lessons learned from complex genomes. 8 transcripts per gene locus more than half are non-coding. #AGBT
+42m bffo: RM: fEffects of sequence variation on differential allelic transcription factor occupancy & gene expression. http://t.co/qdAf8OxO #AGBT
+42m finchtalk: #AGBT Tom Gingeras on the transcriptomes: the rule, genes have multiple control points. The exception is 1 gene 1 transcript
+43m ElementoLab: #AGBT Tom Gingeras: it is critical to think that most genes have multiple transcription initiation sites
+43m michaelgrr: presentation from Oxford @nanopore at the Advances in Genome Biology and Technology (#AGBT) conf coming up at 11.40am (EST) / 4.40pm (GMT).
+43m illumina: Gingeras: Number of genes increased 41% since 2004, number of transcripts increased 52% since 2008 #AGBT
+43m timjph: Lots of GRCh37 patches for one! RT @GenomeRef: poster 59 if you're at #AGBT to see what GRC is up to with the reference assembly
+46m bioinfosm: #agbt TG: thats a fun term i learnt 'irreproducibility detection rate IDR'
+46m bioinfosm: #agbt, sorry the term is from TG, but comment is mine :)
+47m genome_gov: Signing on from the Advances in Genome Biology and Technology Conference in Marco Island, FL. Day 2 of talks. #AGBT
+47m illumina: Gingeras: cellular addresses RNA for localization: cytoplasmic, nuclear (nucleoli, nucleoplasm, chromatin) #AGBT
+47m westr: Would like to hear more about it: RT @iontorrent Rick Myers, Hudson Alpha, shows 114 CpGs associated with response to antibody therapy #AGBT
+48m ElementoLab: #AGBT Tom Gingeras: how do you know low read cnt is background or real transcription? irreproducibility detection rate (IDR) (Bickel et al)
+48m westr: RT @deannachurch: TG: over 51,000 genic regions 40.5% protein coding, over 161,000 transcripts. #AGBT // Includes ncRNA genes #pm101
+49m Massgenomics: Tom Gingeras: 80% of the genome covered by primary transcripts (90.7% of exons, 79.3% of introns, 35.5% of intergenic seqs) #AGBT.
+49m ElementoLab: #AGBT Tom Gingeras: found up to 15K NOVEL multi exon transcripts in intergenic regions, 8K antisense
+50m westr: NB! RT @ElementoLab: #AGBT Tom Gingeras: it is critical to think that most genes have multiple transcription initiation sites #pm101
+50m girlscientist: Gingeras: A very large portion of the genome is appearing in the RNA space as unspliced transcript, very often polyA- and antisense. #AGBT
+51m ElementoLab: #AGBT Tom Gingeras: (that was based on RNA-seq in 15 cell lines)
+51m NEBiolabs: Hear Rich Roberts, NEB CSO, speak at 11:20 in the Plenary Session at #AGBT. http://t.co/4LcUZpwW
+51m CRIgenomics: #AGBT Tom Gingeras IDR analysis (Li et al 2011). Statistics for two replicates, I know a lot of biologists who will say two is enough!
+52m ElementoLab: #AGBT Tom Gingeras: intergenic regions migth be much smaller than currently thought, genes might massively overlap
+52m iontorrent: @westr #AGBT cool stuff! He is going into publication now. Stay tuned.
+53m girlscientist: Gingeras elaborating on previous intriguing suggestions that the amount of transcription seen means we need to redefine "gene." #AGBT
+53m bongopondit: Actually finding it easier to follow these genomics-heavy talks through the summaries on Twitter (my background is not in genomics). #AGBT
+53m bioinfosm: #agbt have not heard of STAR; TG: rna-seq reads mapped using STAR
+53m CRIgenomics: Illumina previewed 687bp reads at #AGBT, no wonder Roche are circling. 25M on MiSeq coming soon...
+55m illumina: Illumina Talk: MiSeq DNA Seq Platform and Application in Clinical Microbiology -- starts in 10 min, Island Ballroom #AGBT
+55m ClaireAinsworth: This v cool. MT @girlscientist: Gingeras elaborating on suggestions that amount of transcription seen = we need to redefine "gene." #AGBT
+55m bongopondit: Missed this news earlier. 687bps! Holy moly! MT @CRIgenomics: Illumina previewed 687bp reads at #AGBT,
+56m iontorrent: For ea category of genes w/ 2 isoforms, both will be expressed in cells. Minor/alt isoforms seen in specific compartments -T Gingeras #AGBT
+56m omespeak: Missed this news earlier. 687bps! Holy moly! MT @CRIgenomics: Illumina previewed 687bp reads at #AGBT,
+56m girlscientist: Gingeras: most genes have multiple isoforms expressed - and these isoforms are each located in specific compartments of the cell. #AGBT
+56m illumina: Gingeras: More than half of 247,685 unannotated single exome transcripts are intergenic and antisense #AGBT
+57m ElementoLab: #AGBT Tom Gingeras: in a given cell, most isoforms of a given gene are expressed, whether the gene has 2 isoforms or 10+
+57m illumina: Gingeras: Reduction of intergenic region sizes, <10,000 bp due to the discovery of more transcripts #AGBT
+57m Massgenomics: Tom Gingeras did a 454 run looking for novel unannotated GTAG junction seqs. What was that "50% false neg rate for RNA-seq?" about? #AGBT
+57m PacBio: #AGBT PacBio Workshop today at 12:15 in Palms Ballroom. Speakers incl. Erich Jarvis (Duke), Paul Hagerman (UC Davis), Matt Waldor (Harvard)
+58m bioinfosm: #agbt Gingeras: fate of most long ncRNA is small RNA - confirmed by conservation analysis phastCons
+58m illumina: Gingreas: an indivl cell w/ multiple isoforms, some dominant & the minor ones only in specific cell compartments. Incredible! #AGBT

10 - 11am EST
+2m illumina: Gingeras: Drospolia snoRNA, only 25-30% are capped full length, and 20-40% uncapped,= a specific processing site w/ends conserved! #AGBT
+5m omespeak: Genomics papers are the new high-energy physics papers (50+ authors). #AGBT
+6m ElementoLab: #AGBT Tom Gingeras: extremely low copy number transcripts in 1 cell type can be highly expressed in another cell type
+7m illumina: Gingeras: Transcript low copy can be a std feature in one cell but can change by 5 orders of magnitude in another cell type #AGBT
+8m ElementoLab: #AGBT Tom Gingeras: low copy number transcripts tend to be nuclear, but in specific compartments
+8m bioinfosm: if one were to spread out all the sessions (partying being the major part) at #AGBT to sequential events; it would be a month long affair!
+10m genome_gov: Now up - Geoffrey Smith: "The Miseq DNA Sequencing Platform and Application in Clinical Microbiology" #AGBT
+11m dgaalaas: Geoffrey Smith of ILMN talking MiSeq in clinical microbiology #AGBT
+11m ElementoLab: #AGBT Geoffrey Smith: using the Miseq for clinical microbiology applications
+12m dgaalaas: Uh-oh...just got the no-tweet disclaimer for this talk #AGBT
+15m NGSman: @dgaalaas #agbt There's always one
+15m bffo: GS from Illumina "under review, no tweet" is a very lame excuse that is becoming very bogus ... #badexcuse #verylame #agbt
+17m froggleston: GS: Can short turnaround time sequencing be applied to a clinical setting? I have sneaky feeling this will be a leading question. #agbt
+20m irondiet: OpGen Demonstrates Whole Human Chromosome Mapping Capabilities at 2012 AGBT ...: OpGen, Inc., a whole-genome ana... http://t.co/pB9ka95g
+22m mbcf: #AGBT finch and Duck. Tod lunches with RD http://t.co/Kiozg8Rq
+24m stuka: I'm feeling lonely w/ everyone @ retreats or #AGBT, so I think I throw a few hundred thousands jobs into the cluster so I can get some email
+27m Personal_RX_WI: #AGBT @illumina MiSeqused to track antibiotic resistant bacteria in hospitals. Clinical 2 day turn around time.
+28m CRIgenomics: #AGBT: Some lovely examples of the impact of sequencing on clincal microbiology by Geoff Smith. Look out for publications coming soon...
+31m girlscientist: Eric Green asks Geoffrey Smith of Illumina the $1M question: where do you actually see MiSeq's being deployed? A: in clinics, we hope #AGBT
+33m bmahersciwriter: RT @girlscientist: Eric Green asks Illumina the $1M question: where do you actually see MiSeq's being deployed? A: in clinics, we hope #AGBT
+36m girlscientist: Judging by the questions, people are intensely curious about issues surrounding use of MiSeq in clinics. Validation? Translation? #AGBT
+40m CompleteGenomic: Heres another chance to see Jason Laramie presenting on family-based studies, today at the #AGBT Complete Suite at 1:00 pm
+44m assemblathon: RT @djschlesinger: Schwartz: De novo assembly capabilities has not kept pace with increasing volumes of sequencing data #AGBT
+48m EpicentreBio: MT @girlscientist: EG asks GS of Illumina the $1M question: where do you actually see MiSeq's being deployed? A: in clinics, we hope #AGBT
+50m ScienceAdvBoard: RT @illumina: Myers: Correlation of methylation and gene expression depends on location of CpG #AGBT
+59m djschlesinger: Joseph Boland from NCI up next to discuss exome sequencing on the Ion PGM #AGBT

11 - 12pm EST
+0m DNASTARInc: Are you at #AGBT? Come see us at our poster featuring our #GWAS workflow today from 4:30-6:00 pm
http://t.co/7Bx7e75b
+4m EdgeBio: #AGBT Joe Boland from NCI talking about exome sequencing on the ion torrent
+4m girlscientist: Strap in for the lightning round on new technologies #AGBT Starting off with Ion Torrent and the PGM.
+4m nanopore: Wow, busy in here #AGBT
+5m deannachurch: Joseph Boland up after the break- talking about exome sequencing using the PGM. #AGBT
+6m dgaalaas: Welcome back to #agbt . Joe Boland talking about generating an Exome in a day on the PGM
+6m ElementoLab: #AGBT Joseph Boland: exome sequencing on the PGM: exome in a day
+7m deannachurch: JB: now routinely getting 250bp reads- up from 100bp reads in Q1. "Length does matter" #AGBT
+7m Massgenomics: Next up: Joseph Boland (NCI) on PGM exomes, Richard Roberts (NE bioLabs) on single-mol seq, Clive Brown of Oxford Nanopore! #AGBT
+7m omespeak: Second session of morning underway, most anticipated probably the last one from Clive Owen Of Oxford Nano. #AGBT
+8m iontorrent: within the span of one year with PGM: went from simply looking at barcode diversity to now, exome sequencing -Joe Boland #AGBT
+9m deannachurch: JB: Every 6-8 days producing 24-36 exomes on HiSeq but not a lot of flexibility in getting new samples in pipeline. PGM provides flex. #AGBT
+9m omespeak: Also, final plug for this blog-post on nanopore technology till it becomes irrelevant in about an hour: http://t.co/v331AKmW #AGBT
+9m djschlesinger: Boland: lab produces 24-36 exomes every 6-8 days #AGBT
+9m girlscientist: Boland singing praises of PGM for, among other things, meeting reviewer requests in two weeks. Hmmm. #AGBT
+9m finchtalk: #AGBT Joe Boland: exome in a day on the ion pgm. Uses, data fast for paper resubmission, impending site visits, fill pedigree gaps, backup
+9m dgaalaas: Exomes on a PGM gives Joe flexibility - main platform is HiSeq2000 #agbt
+10m EdgeBio: #AGBT Boland: first PGM arrived in Jan '11, first exome data generated by Nov
+10m dgaalaas: Joe currently generating an Exome on PGM via sequence across4-5 chips #agbt
+11m omespeak: Gah, bad typo ......meant Clive Brown of Oxford of course, not Owen. #AGBT
+14m EdgeBio: RT @dgaalaas: Joe currently generating an Exome on PGM via sequence across4-5 chips #agbt
+15m froggleston: @omespeak although I now look foolish as I can't seem to spell 'agbt'.
+15m AdamKraut: NCI showing impressive evolution of the PGM over the past year. Towards 'Exome in a Day' #AGBT
+15m EdgeBio: #AGBT Joe Boland: found that 5Gb/exome was the sweet spot
+16m omespeak: Second session of morning underway, most anticipated probably the last one from Clive Brown Of Oxford Nano. #AGBT
+16m Massgenomics: Joseph Boland on IonTorrent PGM "Exome in a Day". Sure, if you ignore the fact that hybridization takes 3 days. #AGBT.
+16m NEBiolabs: Rich Roberts "Characterization of DNA Methyltransferase Specificities Using Single-Molecule, Real-Time DNA Sequencing" NOW! #AGBT
+18m girlscientist: Boland and lab generated "exome in a day" after 5 days sample prep, if I read slide correctly. #AGBT
+18m bioinfosm: #agbt Boland's talk - am not sure if he defined the 'target region' that is referred in the talk
+19m Copenhagenomics: My guess: Most people at #AGBT are waiting for Oxford Nanopore's presentation... Are they going to present a game changer?
+19m ElementoLab: #AGBT Joseph Boland: can do exome in a day but with 6 machines
+20m CRIgenomics: The #ONT website is closed for maintenance, expect it to reopen just after Clive Browns talk later this morning at #AGBT
+20m omespeak: RT @CRIgenomics: The #ONT website is closed for maintenance, expect it to reopen just after Clive Browns talk later this morning at #AGBT
+22m girlscientist: Boland final conclusion: he needs to go back to school for bioinformatics. Don't we all? #AGBT
+23m salisburymw: How fast is tech advancing? J Boland: "This time next year this is going to seem prehistoric.". #agbt
+24m genome_gov: Up now: Rich Roberts NEB "Characterization of DNA Methyltransferase Specificities using Single-Molecule, Real-time DNA Sequencing" #AGBT
+24m froggleston: Borland: Interesting exome-in-a-day PGM talk. Were the pictures of kids the current staff mugshots? Child labour. Tut tut. #agbt
+24m deannachurch: Rich Roberts is up next talking about DNA methyltransferase specificities using single molecule sequencing. #AGBT
+25m girlscientist: Rich Roberts plays to crowd by asking if some of money being spent on DNA sequencing could instead be used figuring out what genes do. #AGBT
+25m djschlesinger: Richard Roberts from NEB talking about characterizing of DNA methyltransferase specificities using a PacBio #AGBT
+25m omespeak: Applause for Richard Roberts for saying fraction of money spent on sequencing should be spent on biology. #AGBT
+25m chrisfall: RT @GenomicsIo RT @girlscientist: Boland and lab generated "exome in a day" after 5 days sample prep, if I read slide correctly. #AGBT
+25m GenomeBiology: Spend some of the money used for sequencing genomes on finding out what genomes actually do. Richard roberts (NEB) #agbt
+25m deannachurch: RR: There is a lot of money being spent on sequencing- it would be nice to see some of that spent on understanding what genes do. #AGBT
+26m froggleston: Roberts: Lots of money spent on sequencing, and would be good to see the same amount spent on gene function studies. Cue clapping. #agbt
+26m Massgenomics: Richard Roberts hits the theme of the meeting: it would be nice to start spending some money figuring out what genes do. #AGBT
+26m djschlesinger: Roberts: a lot of money being spent on sequencing, what about money being spent on determining what it all means biologically? #AGBT
+27m ElementoLab: #AGBT Richard Roberts: we don't know the specificities of DNA methyltransferases (unlike for restriction enzymes)
+27m girlscientist: Can report that this is the first slide talk at #AGBT or perhaps ever I've seen with slides in vertical dimension. Am fixated on it. #AGBT
+27m Copenhagenomics: Richard Roberts: "Can we use a fraction of the $$$ we spend on sequencing, to actually find out what the genes are doing?" #applause #AGBT
+27m CRIgenomics: Rich Roberts NEB at #AGBT: can we spend a small fraction of the $$$ going into NGS on finding out what the genes do! Function rocks!
+30m Massgenomics: Was it fair when I asked about sensitivity of PGM exome-in-a-day sequencing? I worry that they found 10 of 16 cancer variants (62.5%). #AGBT
+31m ElementoLab: #AGBT Richard Roberts: use PacBio to show that EcoKDAM also recognizes also GATC sites, eg GACC
+32m girlscientist: #AGBT RT @jimcollins: @girlscientist I for one welcome our new exome overlords
+32m ElementoLab: #AGBT Richard Roberts: (I meant non-GATC sites) ... non-GATC sites might be due to high over-expression of methyltransferse
+33m Symbionticism: Rich Roberta of NEB shows PacBio detects methylated Cs due to slower sequencing through these bps in comparison to normal bps. Cool. #AGBT
+34m obahcall: New technologies session at #AGBT Joseph Boland just spoke on exome seq in a day (plus sample prep days) using PGM
+34m ElementoLab: #AGBT Richard Roberts: used PacBio SMRT seq to identify DNA motifs methylated by methyltransferases
+35m EdgeBio: A special thank you for all of our new followers! Stay tuned for more EdgeBio at #AGBT updates #FF
+35m drgitlin: @girlscientist when does AGBT registration usually happen? Need to make sure I'm approved to go beforehand.
+35m illumina: Richard Roberts, NEB, Characterization of DNA methyltrasferases specifcity using singe-iolecule real-time DNA sequencing #AGBT
+36m obahcall: Rich Roberts on char DNA methyltransferase specifities using PacBio #AGBT
+36m finchtalk: #AGBT Richard Roberts: e.coli methylases. Methylase free strains, plasmids, restriction enzymes, and pacbio to see specific target sites.
+38m CRIgenomics: How many labs name instruments after Star Wars characters? #AGBT Jo Boland has Yoda, Vader, Boba, etc. We have R2D2, et al...what about you?
+38m froggleston: Roberts: Lovely slides. No text. Easy to follow and back up his talk. Portrait a bit weird though. #refreshingchange #agbt
+39m ElementoLab: #AGBT Richard Roberts: found a methyltransferase that can methylate almost all As in the E coli genome ! it's M.ecoGI
+39m liveinsymbiosis: @Symbionticism That's cool. How much slower? #AGBT
+39m archivist84: So @nanopore are up soon at #AGBT
+39m girlscientist: Roberts: turns out E. coli can live with most of its genomic adenines methylated, as revealed by PacBio methylation sequencing. #AGBT
+41m DailyScan: Sequencing Takes a Clinical Bent at #AGBT http://t.co/k6QbldL2
+42m omespeak: 'ome' alert: Methylome. #AGBT
+42m froggleston: Roberts: Desire to see production of whole genome with accompanying methylation pattern as standard #agbt
+42m AdamKraut: Clive Brown from @nanopore up next. Wait for it. #AGBT
+42m RainDanceTech: Join us today at the RainDance #AGBT Workshop; 3:15pm in the Island Ballroom. Andy Watson will be discussing recent customer publications.
+43m djschlesinger: Clive Brown from Oxford Nanopore up next, he's been pacing back and forth for the past 10 minutes. Anticipations are high. #AGBT
+44m deannachurch: Clive Brown from ONT up next- standing room only in here. #AGBT #anticipation
+44m Copenhagenomics: Clive Brown from Oxford @Nanopore coming up now at #AGBT - perhaps the most anticipated presentation this year... Game changer coming up?
+44m EdgeBio: #AGBT much anticipated talk from Oxford Nanopore up next
+44m obahcall: More applications discussed by Eric Schadt in session tonight (thats after @girlscientist talk) #AGBT
+44m CRIgenomics: #ONT #AGBT...here it comes.
+44m finchtalk: #AGBT next up Clive Brown from Oxford Nanopore, a highly anticipated presentation. BTW, HDF is at the core of their data management.
+45m drgitlin: With the tweets and the fact that @nanopore's website is down, I'm getting the feeling that #AGBT is channeling Steve Jobs and Apple today.
+45m omespeak: Well, here it is. #nanopore #agbt
+46m dgaalaas: Clive Brown from Oxford Nanopore on deck here #agbt
+46m obahcall: Clive Brown Oxford Nanopore talk starting now at #AGBT
+46m deannachurch: CB: 2 hour talk in 17 minutes. #AGBT #go
+46m dgaalaas: Currently using protein nanopores #agbt
+46m ElementoLab: #AGBT Clive Brown: Nanopore sequencing
+46m omespeak: I will be mostly taking notes, so not much tweeting here. Will do summary later. #agbt
+46m t_basi: Breath baited. RT @omespeak: Well, here it is. #nanopore #agbt
+46m Symbionticism: Next up clive brown on oxford nanopore sequencing. #AGBT
+47m djschlesinger: Brown: this talk usually takes 2 hours, but I'll try to get it down to 17 minutes #AGBT
+47m nanopore: Nanopore sensing 101: current through nanopore, molecules interacting with nanopore generate characteristic disruptions, I/D molecule #AGBT
+47m Copenhagenomics: CB, @Nanopore "We have spent the last two years developing our own chemistry" #AGBT
+47m dgaalaas: Have developed their own proprietary chemistry - 400 bases per second #agbt
+48m djschlesinger: Brown: giving s brief overview of Nanopores and strand sequencing, nothing new yet #AGBT
+48m deannachurch: CB: attach a hairpin to the strand so you can sequence one strand then flip around and sequence the other. #AGBT
+48m CRIgenomics: #ONT Hungry Hippos at #AGBT
+48m dgaalaas: Enzyme feeds sense &antisense through custom Nanopore #agbt
+48m graveley: Holy cow - Oxford Nanopore @dgaalaas: Have developed their own proprietary chemistry - 400 bases per second #agbt
+48m UK_Biomek: No pressure on you @nanopore for #AGBT , but it seems like the whole of bio-twitter is expecting something earth-shattering...
+48m froggleston: Brown: Hungry Hippos. I knew it! #agbt
+49m dgaalaas: No fixed runtime - just refresh solution #agbt
+49m djschlesinger: Brown: no attachment of DNA, all free flowing, sequence read in real time, only requirement for sample prep is dsDNA have 5' overhang #AGBT
+50m dgaalaas: Sensor can handle 1000bps #agbt
+50m Copenhagenomics: CB, @Nanopore "ASIC is the core. Can do 1000bps. Cameras can't do that." #AGBT
+50m dgaalaas: Can do parallel sensing - multiplexing using an ASIC #agbt
+51m djschlesinger: Brown: alternative sample prep methods have been tried #AGBT
+51m finchtalk: #AGBT CB uses enzymes to pull DNA through pores, or block movement. over 160 tested. Measurement onASIC (app spec. integrated circuit)
+51m ElementoLab: #AGBT Clive Brown: only dsDNA with 5' overhang is needed
+51m AdamKraut: @nanopore uses ASICs, no fixed run time, capable of 1000bps #AGBT
+51m djschlesinger: Brown: membranes in sensor chip are very stable #AGBT
+52m illumina: Brown: ONT #AGBT Application Specific Integrated circuits instead of cameras
+52m notSoJunkDNA: Can do, or actually DO? @dgaalaas: Have developed their own proprietary chemistry - 400 bases per second #agbt
+52m girlscientist: Brown of Oxford Nanopore at light speed through their technology. Many comparative asides of how superior to current methods. #AGBT
+53m nanopore: Oxford Nanopore has engineered+screened >1,000 diff pores and >160 enzymes. Using unpublished proprietary system, continue to iterate #AGBT
+54m NowgenCentre: Currently reading tweets about Oxford @Nanopore presentation at #AGBT
+54m nanopore: Nanopore movement scheme: dsDNA+enzyme engages with pore, enzyme unzips DNA so sense and antisense in 1 pass many fragments (hairpin) #AGBT
+54m NGSman: @ElementoLab #agbt it was actually 5 :)
+54m froggleston: K-mers travelling through pore blockades provide basis for base calling. Neat. #agbt
+54m djschlesinger: Brown: sequenced PhiX genome as full genome read - 5kb and 10kb reads #AGBT - wild!
+54m deannachurch: CB: Sequenced PhiX: whole 5kb genome as single fragments, 4% error rate with deletions dominating. Read length = fragment size. #AGBT
+54m nanopore: Nanopore movement scheme: after strand 1 completes, a new DNA+enzyme strand reloads, and repeat #AGBT
+54m girlscientist: Brown: "so we did a genome" = PhiX. See about 4% raw read error, mostly deletions due to base caller. #AGBT
+54m Copenhagenomics: CB, @Nanopore "4% raw read error. Mostly deletions." #AGBT
+54m nanopore: Sample prep: only requirement dsDNA with overhang. No amplification. Variety of app-specific preps available. #AGBT
+54m dgaalaas: PhiX genome as single fragments, 5kb and 10 kb dsDNA reads! #agbt
+54m illumina: Brown: ONT #AGBT Lots of enzymes and pores tried
+55m nanopore: ASIC at the heart of the technology. Low noise, high freq chip designed to measure 1,000 bases per second on '000s arrays #AGBT
+55m djschlesinger: Brown: 4% raw read error, primarily deletions #AGBT
+55m ElementoLab: #AGBT Clive Brown: seq whole phix as 1 fragment .. 5kb or 10kb reads ... 4% raw error rate mostly deletions
+55m nanopore: Sensor chip: arrayed wells each with electrode measuring single nanopore experiment. #AGBT
+55m dgaalaas: No degradation of signal over time #agbt
+55m deannachurch: CB: Not limited by fidelity of system- limited by sample fragmentation. No diff between base 1 and base 40,000. #AGBT
+55m djschlesinger: Brown: no degradation of signal over time base 10 same as base 40,000 #AGBT
+55m Copenhagenomics: CB, @Nanopore "We did a 48kb run. Quality consistent across reads - no difference between first and 40000th read!" #AGBT
+55m nanopore: Base calling: overlapping kmers cause characteristic current blocks, Viterbi path. Done in real time on node #AGBT
+55m finchtalk: #AGBT CB reading full length sequences, 10 kb for phiX. And recently the lambda genome. No signal degradation. Reads words not bases.
+56m EdgeBio: #AGBT Clive Brown: if genome is small enough it can be fully sequenced as a single fragment
+56m girlscientist: Brown: no degradation of signal over time. Principal cause of error known, engineering barrel of pores to compensate. #AGBT
+56m nanopore: 5kb genome sequenced sense and antisense (with hairpin) in single 10kb run. Further examples at tens of kbs #AGBT
+56m dgaalaas: Improvements - removal of variance needed #agbt
+56m EdgeBio: RT @dgaalaas: No degradation of signal over time #agbt
+56m froggleston: Brown: Oscillating k-mers produce majority of error. Fixable. Dips in quality with erroneous bases. #agbt
+57m Symbionticism: Oxford nanopore has sequenced largest reads ever - up to 40 kb but with 4% error. They will surpass them said clivebrown. Exciting at #AGBT.
+57m EdgeBio: RT @dgaalaas: Improvements - removal of variance needed #agbt
+57m djschlesinger: Brown: can directly read RNA, no cDNA required #AGBT
+57m ElementoLab: #AGBT Clive Brown: RNA can be DIRECTLY read using nanopores - no cDNA
+57m girlscientist: Brown: "we had a quick look at RNA" can be read directly with no need for cDNA, data look same as DNA. #AGBT
+57m deannachurch: CB: RNA can be read directly using nanopores- no need to make cDNA. #AGBT
+58m Copenhagenomics: CB, @Nanopore "RNA can be read directly. No cDNA required. This is an application we will put out at a later stage." #AGBT
+58m notSoJunkDNA: I want one! @ElementoLab: #AGBT Clive Brown: RNA can be DIRECTLY read using nanopores - no cDNA
+58m dgaalaas: Should be able to process RNA - development of base calling for RNA on hold #agbt
+58m bioinfosm: #agbt nanopore talk "the enzyme ticks after each nucleotide to overcome homopolymer issue"!! long reads, max 41kb single molecule read
+58m graveley: Wow!! @djschlesinger: Brown: can directly read RNA, no cDNA required #AGBT - looks like game changer!
+58m girlscientist: Brown: excellent shoutout to Monty Python rabbit. #AGBT
+58m Symbionticism: Wow. Oxford nanopore will sequence RNA too at same efficiency as DNA. more to come. #AGBT
+58m westr: RT @DailyScan: Sequencing Takes a Clinical Bent at #AGBT http://t.co/JLFOIksm #pm101
+59m ElementoLab: #AGBT Clive Brown: epigenetic modifications can be detected using nanopores too eg methylation
+59m neilhall_uk: Want! #agbt
+59m nanopore: Measuring direct from blood: new robust polymer membranes resistant to complex sample. #AGBT
+59m djschlesinger: Brown: sequenced rabbit DNA extracted from blood, no sample prep at all!!! #AGBT
+59m dgaalaas: Can sequence directly froml blood - no sample prep necessary... #agbt
+59m Copenhagenomics: CB, @Nanopore "DNA directly from blood. No sample prep required." #AGBT
+59m deannachurch: CB: 0 sample prep- directly sequenced rabbit blood and sewage water. #AGBT #supercool

12 - 1pm EST
+0m fluidigm: For Targeted Resequencing and Single Cell Studies swing by Suite 285 at #AGBT, let us show you what we got!>o
+0m girlscientist: Brown: "Just one more thing..." new product with single use disposable sequencer #AGBT
+0m illumina: Brown: Sequencing, RNA and epigenetic mods with ONT #AGBT
+0m Symbionticism: Nanopore will sequence directly from blood and sewage water. #blownaway #AGBT
+0m deannachurch: CB: MinION: usb sized DNA sequencer- single use disposable sequencer. #AGBT
+0m nanopore: Hardware: a single GridION node can be used alone as a desktop or lots clustered. Each node analyses data locally in real time. #AGBT
+0m cwduffy_lshtm: So going by the #AGBT tweets @nanopore may have completely changed the face of sequencing. 40kb+ reads! Can't wait to see some publications.
+0m AdamKraut: And one more thing MiniION. USB key size sequencer that plugs into your laptop. Same data as GridION #AGBT
+0m djschlesinger: Brown: one more thing: MiniION portable Nanopore sequencer, plugs right into USB port of your laptop #AGBT
+0m dgaalaas: Going to launch MinION later this year, a USB disposable sequencer. wow! Plug it directly into your laptop.... #agbt
+0m Massgenomics: Oxford MinION USB-sized disposable DNA sequencer, 150 Mbp per hour for 6 hours.. YHGTBFKM! #AGBT.
+0m liveinsymbiosis: @Symbionticism That's amazing!!! Will it be competitive cost/bp? #AGBT
+0m nanopore: And now for something completely different #AGBT
+1m girlscientist: Brown: competitive with current desktop prices at launch, Tolerates body fluids and plant extracts. #AGBT There's your headline, people.
+1m omespeak: Plug and play sequencer from Oxford Nano. #agbt
+1m nanopore: Introducing the MinION, a nanopore sequencer the size of a USB stick. Works just like GridION, but smaller #AGBT
+1m girlscientist: Brown: new sequencer called MinION, powered from USB on your laptop. #AGBT
+1m ElementoLab: #AGBT Clive Brown: MinION sequencer basically looks like a USB key
+1m djschlesinger: Brown: sequencer will be USB powered and disposable #AGBT
+1m girlscientist: Brown: MinION app-driven and open. "lets any bench scientist put their arms around process" of sequencing. #AGBT
+1m Copenhagenomics: CB, @Nanopore "We're launching a USB sized disposable sequencer later this year: 'MinION' - 150MB/hr, runtime 6 hrs." <-- Amazing! #AGBT
+2m rowan_UK: Following @nanopore tweets from #AGBT. Smokin performance reported by Clive Brown
+2m AdamKraut: You can even yank the USB sequencer out, it pauses, re-insert and it continues sequencing #AGBT
+2m finchtalk: #AGBT CB sequenced rabbit blood directly, sewage with minimal prep. MiniION, a USB sequencer. Just need a laptop and software.
+2m drgitlin: Game changer? Wow. RT @nanopore: Measuring direct from blood: new robust polymer membranes resistant to complex sample. #AGBT
+2m pathogenomenick: Too many amazing @nanopore tweets to retweet them all. Follow #AGBT or go to http://t.co/KUVmX75N to see them all.
+2m froggleston: Holy crap. Minion. A USB sized sequencer with real time informatics. This changes the game. I'm grinning. Electrochemistry issues tho #agbt
+2m djschlesinger: Brown: MiniION launched later this year, 5-25 Gb per day, chip will last ~6 hours #AGBT
+2m notSoJunkDNA: MinION sounds like "mignon" in French, which means cute! @nanopore: Introducing the MinION, a nanopore sequencer #AGBT
+2m 613SportsChick: Collective gasp at #AGBT as Brown announces the MinIon.
+2m nanopore: GridION node 2012: 2,000 nanopore experiments at a time, in 2013 to 8,000. Node designed for tens of Gb/24 hours, no fixed run time #AGBT
+3m bkmacy: Nanopore discusses new MinION USB 3.0 based personal DNA/RNA sequencer later this year, #AGBT
+3m NGSman: #agbt miniIon....outrageous!
+3m omespeak: If the machines perform as promised, The Oxford Nano announcements are indeed quite game changing. #agbt
+3m ElementoLab: #AGBT Clive Brown: MinION can seq 1-5 Gb/day
+3m djschlesinger: Brown: future improvements will extend that to over 600Gb per day #AGBT
+3m archivist84: MiniION from @nanopore - in the conference goody bag next year? #AGBT
+3m drgitlin: OMFG RT @nanopore: Introducing the MinION, a nanopore sequencer the size of a USB stick. Works just like GridION, but smaller #AGBT
+3m girlscientist: Brown: price list. MinION about $1000/Gb, will retail at $500-$1000. #AGBT
+3m rowan_UK: Buy disk stocks MT @nanopore Introducing the MinION, a nanopore sequencer the size of a USB stick. Works like GridION, but smaller #AGBT
+3m AdamKraut: MiniION will cost between $500-$1000. Lower cost per Gb with GridION #AGBT
+4m liveinsymbiosis: @djschlesinger Is the ~6hr a limitation/exhaustion of the chemistry? #AGBT
+4m nanopore: New pricing schemes: no more box/instr price.Think cellphone pricing - packages. Price per base competitive at launch with other techs #AGBT
+4m mbeisen: i'm not at #AGBT but @nanopore USB sequencer sounds totally badass
+4m Symbionticism: NANOPORE will introduce usb- drive sequencer called minion. Benchtop sequ. in laptop. 150mb per hr if i heard that right. $1000. #AGBT
+4m Massgenomics: The throw-away USB sequencer, second half of this year, will cost $500-1000 per use, supposedly. #AGBT.
+4m DailyScan: Truly! #AGBT MT @pathogenomenick Too many amazing @nanopore tweets to retweet them all.
+4m AdamKraut: Always knew @nanopore was the dark horse. Clive just killed it! #AGBT
+4m Copenhagenomics: CB, @Nanopore "Nanopore sequencing is high-throughput. MinION $1000/Gb. GridION2K $25-40/Gb. GridION8K $10/Gb" #AGBT
+4m girlscientist: Brown: future = GridION cluster. <$10/Gb by hooking up cluster together. #AGBT Eric Green "I can't imagine there are any questions."
+4m djschlesinger: MiniION - holy crap!!!!!! Amazing!!!! #AGBT
+4m AdamKraut: First question: "When can I buy one?" #AGBT
+4m djschlesinger: MiniION available second half of this year #AGBT
+5m ElementoLab: #AGBT Clive Brown: MinION to be released second half of this year
+5m CRIgenomics: gridion and MinIon coming mid 2012 #AGBT #ONT really rocks...
+5m obahcall: Will be available second half of this year... #AGBT
+5m froggleston: GridION and MinION available Q3 2012. Want. #agbt
+5m Symbionticism: Will be released in 2nd half of year. #AGBT
+5m bkmacy: Nanopore MinION expected to cost $500-1000 / experiment, #AGBT
+5m aaron_best: RT @pathogenomenick: Too many amazing @nanopore tweets to retweet them all. Follow #AGBT or go to http://t.co/9XtYwi30 to see them all.
+5m Copenhagenomics: CB, @Nanopore "MinION and GridION2K will be launched in the second half of 2012." <-- Q4 perhaps? #AGBT
+6m girlscientist: Eric Green asks if MinION will work on Mac and PC -- Brown says he is Mac user to applause from room. #AGBT
+6m BARCLABS: AGBT: Oxford Nanopore to Begin Selling Two Low-Cost DNA Strand Sequencing Instruments this Year:
read more

http://t.co/P3Y9TDFz
+6m Symbionticism: Yay! Minion will work on your macs. #AGBT
+6m pathogenomenick: The full Oxford Nanopore press release up here http://t.co/JnJHjsD4 #AGBT
+6m Personal_RX_WI: #AGBT Oxford Nanopore MinION USB sized disposable sequencer. Available sencond half of 2012.150Mb/hour
+7m genomigence: InSequence: AGBT: Oxford Nanopore to Begin Selling Two Low-Cost DNA Strand Sequencing Instruments this Year:
r... http://t.co/NbamPTje
+7m InSequence: AGBT: Oxford Nanopore to Begin Selling Two Low-Cost DNA Strand Sequencing Instruments this Year:
read more

http://t.co/RDy3CMMs
+7m archivist84: http://t.co/Pz7eFAub #OGT website is back up! #AGBT
+7m Copenhagenomics: I do think @nanopore presented a potential game changer today: The MinION brings something totally new, with disposable sequencers! #AGBT
+8m AdamKraut: Small mob forming around Clive now #AGBT
+8m pathogenomenick: Oxford Nanopore megaton announcement: Why do you need a machine? exclusive interview on my blog! http://t.co/tJxQit9T #AGBT
+9m rnomics: RT @notSoJunkDNA: I want one! @ElementoLab: #AGBT Clive Brown: #RNA can be DIRECTLY read... http://t.co/MPjnke5h #rnomics-bioscience @MyEN
+9m MoleculaBiology: Oxford Nanopore minIon announced at AGBT. Unbelievable. The revolution is here for single molecule sequencing.
+9m CrapBio: SO what i am hearing is that Oxford Nanopore have taken all the fun out of sequencing. #AGBT
+10m Symbionticism: MiniION will make the tricorder a reality:-) awesomeness at #AGBT
+10m rnomics: RT @deannachurch: CB: #RNA can be read directly using nanopores- no need to make cDNA. #AGBT http://t.co/5dNOOxYt #phylogenomics-gen @MyEN
+10m westr: RT @Personal_RX_WI: #AGBT Oxford Nanopore MinION USB sized disposable sequencer. Available sencond half of 2012.150Mb/hour #pm101
+11m ChaunceyGrattan: My head is about to explode. #RNAtoo RT: @pathogenomenick The full Oxford Nanopore press release up here http://t.co/Jp4DCgqP #AGBT
+11m liveinsymbiosis: Welcome to the new age of sequencing tec. AGBT: Oxford Nanopore to Begin Selling Low-Cost DNA Sequencing http://t.co/nsXrplry @AddThis #AGBT
+11m InSequence: Details on ONT's GridIon and disposable nanopore sequencer, MinIon: http://t.co/WwPKPXQ5 #AGBT
+12m UK_Biomek: Woah RT @nanopore: Introducing the MinION, a nanopore sequencer the size of a USB stick. Works just like GridION, but smaller #AGBT
+13m westr: RT @InSequence: Details on ONT's GridIon and disposable nanopore sequencer, MinIon: http://t.co/pcJC5Wtu #AGBT #pm101
+13m mcaccamo: CB: 48KB lambda genome in one read #agbt
+13m ezequiel_coelho: #AGBT Does anyone know the price for the grid ION from oxford nanopore?
+14m avsmith: Those Ion Torrent tweets suddenly got much less interesting. Drooling over Oxford Nanopore reveal at #agbt.
+14m liveinsymbiosis: #AGBT this will be great for bringing sequencing tech to the classroom.
+16m sumansen2011: Affordable and accessible DNA sequencing, a big step in personalized medicine http://t.co/X3I345iJ via @AddThis
+16m notSoJunkDNA: So, it's for real? DNA sequencer the size of a USB key: http://t.co/VSOyO4WD #AGBT (via @nanopore )
+17m bethasullivan: wow, so exciting! MT @girlscientist Brown (of Oxford Nanopore): new sequencer called MinION, powered from USB on your laptop. #AGBT
+18m ribozyme: Agreed! RT @bffo: GS from Illumina "under review, no tweet" is a very lame excuse that is becoming very bogus .. #badexcuse #verylame #agbt
+20m omespeak: So guess what the lunch time discussions will be at #AGBT?
+20m assemblathon: RT @pathogenomenick: Too many amazing @nanopore tweets to retweet them all. Follow #AGBT or go to http://t.co/pCPsTBaw to see them all.
+20m GenomeWeb: Big stories from this year's #AGBT? It will be hard to beat Oxford Nanopore's announcement of the disposable MinIon http://t.co/P6eVIKjz
+21m rowan_UK: True! RT @avsmith
Those Ion Torrent tweets suddenly got much less interesting. Drooling over Oxford Nanopore reveal at #agbt.
+22m assemblathon: RT @djschlesinger: Brown: sequenced rabbit DNA extracted from blood, no sample prep at all!!! #AGBT
+22m assemblathon: RT @deannachurch: CB: MinION: usb sized DNA sequencer- single use disposable sequencer. #AGBT
+22m timjph: New sequencers announced at #AGBT by Oxford Nanopore; one USB sized @pathogenomenick: full press release here http://t.co/fYNWJYEf #AGBT
+23m NextBio: Exciting news! RT @nanopore: Introducing the MinION, nanopore sequencer the size of a USB stick. Works just like GridION, but smaller #AGBT
+23m kbradnam: A disposable sequencer is the perfect successor to years of throwaway sequencing data ;-) #AGBT
+24m assemblathon: RT @Massgenomics: Oxford MinION USB-sized disposable DNA sequencer, 150 Mbp per hour for 6 hours.. YHGTBFKM! #AGBT.
+24m assemblathon: RT @djschlesinger: Brown: MiniION launched later this year, 5-25 Gb per day, chip will last ~6 hours #AGBT
+25m assemblathon: RT @girlscientist: Brown: price list. MinION about $1000/Gb, will retail at $500-$1000. #AGBT
+26m jung_gt: For real? RT: @Massgenomics: Oxford MinION USB-sized disposable DNA sequencer, 150 Mbp per hour for 6 hours.. YHGTBFKM! #AGBT.
+26m nparmalee: I assume that all the geneticists I know are already following the #AGBT hashtag. If not, you should be. #FF
+26m morinryan: Keith Robison's blog post (Omics! Omics!) on Oxford Nanopore's big #AGBT reveal is now live: http://t.co/UQ7mHm2H
+28m rowan_UK: @zerojinx @nanopore Who do I have to mug to get a MinION? #AGBT
+28m illumina: Loman and Robison on #AGBT big news, the MiniIon http://t.co/EUYEpp1d and http://t.co/iGRNR6gq
+29m bioitworld: Full story on Oxford @nanopore stunning presentation from CTO Clive Brown at #AGBT http://t.co/VNvCxLQN
+29m fluidigm: LEARN about targeted resequencing on all major next-gen sequencing systems. Stop by Suite 285. #AGBT ^S
+29m archivist84: Too much excitement! Too many NGS slides to change next week! Off to the pub! #AGBT #OGT #nanopore
+29m sargoshoe: Is it weird that I'm excited about this? RT @omespeak: Well, here it is. #nanopore #agbt
+30m iontorrent: Join Us - Ion lounge at AGBT, Friday, 9:00 p.m.--2:00 a.m.: http://t.co/OExjUIVf via @youtube
+30m Copenhagenomics: RT @larsgt: Wouldn't want to be the guy running the PacBio workshop this afternoon... #AGBT
+30m westr: Thanks to all the tweeters at #AGBT for keeping the rest of us informed about sequencing & genomic breakthroughs!
+31m Jeylen: +1 Wow @pathogenomenick: Oxford Nanopore megaton announcement: Why do you need a machine? exclusive interview http://t.co/7TXozcQo #AGBT
+32m EpicentreBio: Keith Robison on Oxford Nanopore #AGBT announcements http://t.co/wh6Vvmp4
+32m AdamKraut: How far will the PacBio, Illumina, and Life stocks drop after that? #AGBT
+32m assemblathon: RT @pathogenomenick: The full Oxford Nanopore press release up here http://t.co/RzKT3s4f #AGBT
+33m nparmalee: #FF @girlscientist Chris Gunter tweeting from #AGBT This is what twitter is for.
+33m ijivanjee: @pathogenomenick Great interview, this technology blows my mind! #AGBT #ONT
+33m pathogenomenick: jeez I need a lie-down at this point #AGBT @nanopore
+34m ribozyme: Go Mac! RT @girlscientist: Eric Green asks if MinION will work on Mac and PC -- Brown says he is Mac user to applause from room. #AGBT
+35m LucigenCorp: Need libraries for NexGen Seq? Sample prep solutions you can use for better libraries! Posters at #AGBT:http://t.co/iUh67GSb
+35m kbradnam: RT @CrapBio: SO what i am hearing is that Oxford Nanopore have taken all the fun out of sequencing. #AGBT
+37m genetics_blog: Cool. Oxford Nanopore's tiny DNA sequencing instrument - (MinION) doubles as USB drive #AGBT http://t.co/NfsIUEsD http://t.co/AMNU6m3v
+39m SEQanswers: Vaporware is in the air at Marco Island. Oxford Nanopore owes me a thorough computer monitor cleaning. #AGBT
+40m leonidkruglyak: "Hard to compete against reductions in cost, labor and input DNA reqs, esp when data is many fold more useful." http://t.co/DT2WMfJH #AGBT
+40m djschlesinger: MiniION - haven's been this excited about a piece of technology since the original iPhone. #AGBT
+40m djschlesinger: MiniION - haven's been this excited about a piece of technology since the original iPhone. #AGBT
+40m ribozyme: This year at #AGBT: a USB stick giveaway with data from trios; next year a USB stick disposable sequencer giveaway - awesome!
+41m djschlesinger: MiniION - will Life sue over the use of the name "Ion"?? #AGBT
+41m kristen_hallam: Also, it's possible to sequence a human genome in 15 min. using @nanopore's GridION system. http://t.co/MZhO16lr #agbt
+41m leonidkruglyak: "would the processivity limits be reached at BAC scale? Whole bacterial chromosomes? Whole yeast chromosomes?" http://t.co/DT2WMfJH #AGBT
+42m genome_gov: Lots of great tweets from the Marco Island meeting! Interested? Follow the #AGBT hashtag
+42m CompleteGenomic: Today at #AGBT, catch customer Carlos Bustamante of Stanford U. present on population genetics at 2:55 pm in Islands Ballroom
+43m djschlesinger: MiniION - kind of wish the made the announcement on Saturday, the rest of the meeting won't be nearly as exciting #AGBT :p
+43m AdamKraut: People are literally on the phone with their brokers right now #AGBT
+43m drgitlin: If @nanopore's 4% error rate is uniform, does that mean it goes away with high enough coverage? #AGBT
+44m MicheleClamp: So the fancy new OxNano pocket sequencers I can finally rave about!!! Sequencing has finally broken free of the lab!! #AGBT
+45m t_basi: Too right! RT @AdamKraut: People are literally on the phone with their brokers right now #AGBT
+46m mrkrly: #FF #FollowFriday @nanopore - tweeting the future from #AGBT today!
+46m akmi3: MinIon, USB sequencer for $900 with 512 nanopores, 150mb/hour. Disruptive Innovation! http://t.co/wArJWkLV #DigitalHealth #personalmed #AGBT
+47m BioInfo: AGBT: Oxford Nanopore to Begin Selling Two Low-Cost DNA Strand Sequencing Instruments this Year | In Sequence | Sequencing | GenomeWeb http:
+51m BozelosP: @nanopore DNA sequencer with USB plug for $900 - 512 nanopores, 150mb/hour - Disruptive Innovation! http://t.co/vXOqpFcj #AGBT
+51m dud3k: Bets on Roche lowering its bidding price for $ILMN after today? #agbt Also, anyone short $PACB, $ILMN and $LIFE? =)
+51m cwduffy_lshtm: Is it wrong that I want a minION just to put on my key chain? #AGBT #livinginthefuture
+52m nlbigas: A disposable USB pocket-sized nanopore sequencer. http://t.co/zqvmzkZz #AGBT
+53m Gavin_Oliver: Attempting to live-blog Clive's talk was an unmitigated disaster. Too much info. In a good way. Good work @nanopore #AGBT
+55m wboonn: Thx! RT @PopperandCo: It's #FF - @Paul_Sonnier @wboonn @Doherty_pd @kenwalz @portablegenomic @DivaBiotech @westr @illumina @agbt @Forbes
+55m markgenome: #AGBT tweet stream lit up, and no wonder. @nanopore had an amazing announcement up its sleeve. http://t.co/udJ6IvO8
+56m nparmalee: Can I make #AGBT requests? Would love to "hear" Carlos Bustamante's talk, 2:55p today, Islands Ballroom.
+56m genetics_blog: If looking through the #AGBT tag is too daunting, @pathogenomenick is doing a fine job summarizing at http://t.co/CWWf79Yi. Thank you sir
+56m lexnederbragt: Congrats to @pathogenomenick for the scoop, interview with @nanopore #AGBT
+57m Copenhagenomics: Gotta love the duality of "MinION" - even the name is cool! :) #AGBT
+58m timjph: @nanopore parodies Apple! Eyeing the future value of universal DNA sequencing? RT @girlscientist: Brown: "Just one more thing..." #AGBT

1 - 2pm EST
+0m j_perkel: Oxford Nanopore details GridION and MinION systems at AGBT: http://t.co/8keFNrKJ
+0m BozelosP: Introduction to Nanopore Technology http://t.co/dpRlpoYE 4th generation DNA sequencing is here.. Great news for personal genome era #AGBT
+1m nakedideas: We just launched the new @nanopore website in a #Apple Keynote style whirlwind for #AGBT So exciting! Congrats to them! http://t.co/EbsX3CfF
+1m liu3zhen: This video helps understand the Wow Nanopore tech: http://t.co/0tOJygpv #AGBT
+2m djschlesinger: Correct spelling is MinION, not MiniION. I was so excited to tweet about it, I forgot to spellcheck #AGBT
+2m iontorrent: Come to the Ion Lounge tonight! Beer, food and science on the beach. Meet us at the bus. #agbt #ionbus http://t.co/gpXIbNV6 via @youtube
+3m GenomicsIo: MT @nlbigas: A disposable USB pocket-sized nanopore sequencer. http://t.co/PfKkmrmg #AGBT Mind-boggling, but incredibly exciting!
+4m notSoJunkDNA: Starting today, we'll never hear @illumina or @SOLiDSequencing referred to as "Next-Gen Seq" But I think they still have a future. #AGBT
+4m nakedideas: We just launched the new @nanopore website in a #Apple Keynote style whirlwind for #AGBT So exciting! Congrats to them! http://t.co/U516x2Uo
+5m dud3k: Wow, them markets don't snooze. $ILMN $LIFE $PACB all down 5-6% in last hour. #agbt
+7m leonidkruglyak: "We wander into the realms of sci-fi at this point." @pathogenomenick interview with @nanopore http://t.co/5A6wlkfc #AGBT
+8m omespeak: Most commonly overheard snippet at #AGBT right now: 'it is amazing, but we have to see it work in practice'. No prize for guessing 'it'.
+8m kristen_hallam: Shares of $LIFE, $ILMN falling after Oxford Nanopore unveils portable DNA sequencing device, GridION scalability. #agbt
+10m notSoJunkDNA: Amen @omespeak: Most commonly overheard snippet at #AGBT right now: 'it is amazing, but we have to see it work in practice'
+12m dud3k: errr correction, on yesterday's close. RT @dudek Wow, them markets don't snooze. $ILMN $LIFE $PACB all down 5-6% in last hour. #agbt
+13m leonidkruglyak: Great problem to have: "how will 100kb+ reads change your research?" http://t.co/5A6wlkfc #AGBT
+15m yokofakun: @Fuzzyraptor oui a buzz fort la confrence #AGBT : un squenceur de la taille d'une clef USB: see also: http://t.co/lBCg8WaG
+15m SEQanswers: Waiting to see the 48.5kb lambda read. @nanopore ?? #AGBT #makemeeatmywords
+15m _a_muse: Excited about the Oxford plug and sequence announcement. And I am not at #AGBT . That place will be buzzing right now with discussions.
+17m michaelhoffman: @leonidkruglyak The first problem is I'm going to have to clean up all this drool. (sorry) #agbt
+17m caddymob: minions and gridions! Gridion (not grid-ion) will forever be the title bestowed on most productive summer intern. Thx #AGBT
+18m khedkarsupriya: Sequencing technology reads bases in triplets and detects them using electrochemistry http://t.co/dXhCVl0P http://t.co/ssFjZtpZ #AGBT
+18m omespeak: Wondering when we shall see real world data from Oxford Nanopore? #AGBT
+24m ijivanjee: I am in a state of shock. #AGBT #ONT
+25m RickyConnolly: "@nanopore: Introducing the MinION, a nanopore sequencer the size of a USB stick. Works just like GridION, but smaller #AGBT" neat tech
+26m pedrobeltrao: @mndoci just a very small selection bias :).those not at the AGBT meeting probably wished they were
+28m j_perkel: .@Erika_Check at @NatureNews on today's Oxford Nanopore announcement at AGBT: http://t.co/Cml2zV63. // A human genome in 15 minutes?
+34m kbradnam: Reactions to @nanopore news. Biologists: cheer. Bioinformaticians: groan. System admins: weep. #AGBT
+36m omespeak: Hmmm...... a 'nanopore war'!!! http://t.co/7S3iWnPG #AGBT #ONT
+37m jung_gt: Indeed! RT: @liveinsymbiosis: #AGBT this will be great for bringing sequencing tech to the classroom.
+37m GenomeBiology: Oxford nanopore had everyone talking at lunch. Is the minION going to be the next next gen? Wow. #agbt
+37m SEQanswers: Realists: spit take. @kbradnam: Reactions to @nanopore news. Biologists: cheer. Bioinformaticians: groan. System admins: weep. #AGBT
+37m druvus: Oxford Nanopore Doesn't Disappoint http://t.co/Hbf2tI6r #sequencing #AGBT
+40m schip: RT Watch ILMN rebound on purchase of Oxford @dudek Wow, them markets don't snooze. $ILMN $LIFE $PACB all down. #agbt
+45m illumina: How did we get 4 whole human genomes on 1 USB drive? Find out at our talk in the Island Ballroom at 2:15p #AGBT
+45m dfjenkins3: Only after nerding out. RT @SEQanswers: Realists: spit take. @kbradnam: Reactions to @nanopore...Bioinformaticians: groan...#AGBT
+47m kbradnam: Every picture tells a story #AGBT http://t.co/trbX0XFX
+48m Matt_Francis: Hard act2follow RT @illumina How did we get 4 whole human genomes on 1 USB drive? Find out at our talk in the Island Ballroom at 2:15p #AGBT
+49m assemblathon: RT @genetics_blog: If looking through the #AGBT tag is too daunting, @pathogenomenick is doing a fine job summarizing http://t.co/vXy0mFRw
+49m DPMelters: RT @kbradnam Every picture tells a story #AGBT http://t.co/bsh3FiJI
+50m Matt_Francis: #AGBT so the nanopore + a laptop is almost a star trek tri-corder. #futureishere #wheresmyhoverboard
+52m girlscientist: Oh yeah? Well, our new R10K project gives free reagents! And it's sexy! And you can use a USB drive for it, kind of! Find out at 7:30. #AGBT
+55m Bobmorevc: Moore's law blown away @kbradnam: Reactions to @nanopore news. Biologists: cheer. Bioinformaticians: groan. System admins: weep. #AGBT
+58m kbradnam: You will now be able to tell your kids "I remember when USB thumb drives were only used to store files" #AGBT

2 - 3pm EST
+0m fluidigm: IT'S NOT TOO LATE!! Stop by and learn about eliminating the need for paired-end read sequencing. Suite 285. #AGBT ^S
+0m EquallyBalance: RT @GenomeBiology: Oxford nanopore had everyone talking at lunch. Is the minION going to be the next next gen? Wow. #agbt
WOW!
+1m illumina: Illumina Talk: From Sample to Answer: Fast and Accurate Genome Seq for the Clinic -- starts in 10 min, Island Ballroom #AGBT
+2m assemblathon: I wonder if tourism to Oxford, UK will see a little spike in the coming months? #AGBT
+2m BioMickWatson: I'm a bioinf not groaning! RT @kbradnam Reactions to @nanopore news. Biologists: cheer. Bioinformaticians: groan. System admins: weep. #AGBT
+4m lexnederbragt: I guess 100kb reads make the bioinformatics of whole genome assembly problem go away... #ONT #AGBT
+5m emmecola: NGS: News on Genomic Studies: Flash report: two new Next Generation Sequencers presented at AGBT http://t.co/vh3Qpd9l
+5m illumina: Come pick up a "Genome on a Stick" in the Illumina Lounge after Elliott Margulies' talk. 4 genomes, 1 USB drive. #AGBT http://t.co/KNW7EMzr
+11m BiotechMarketer: Looks like @nanopore stole the show with 15 min talk. Did all other platform cos waste their marketing budgets at #AGBT ?
+12m WeigelWorld: Sequencing on a USB stick? http://t.co/aZh8Z7f5
+13m folded: Someone should go and park an #ONT branded matchbox bus next to the #ionbus at #agbt.
+14m rob_carlson: Recalling that just two months ago several prominent biologists assured me #nanopore sequencing was fairy dust. Oops. #AGBT
+15m maureen_mack: hey @Personal_RX_WI apparently @illumina is giving away genomes on a stick #agbt don't miss it!
+16m omespeak: Afternoon sessions just starting. Will anyone actually listen? #AGBT #ONT
+23m ribozyme: I want sequencers on a stick! @maureen_mack, RT: @illumina is giving away genomes on a stick #agbt don't miss it! #AGBT
+25m CompleteGenomic: Find out more about our Cancer Sequencing Service from our own Srinka Ghosh, in the #AGBT Complete Suite at 4:15pm
+26m pathogenomenick: I've embedded all the nanopore videos on the blog here http://t.co/rhBpP9XS #AGBT
+27m rob_carlson: ILMN cheers storing genomes on a USB stick while Oxford #Nanopore was showing sequencing genomes WITH a USB stick? #AGBT #futureshock
+27m Personal_RX_WI: #AGBT @illumina HiSeq2500 DNA in to gene annotation in 60hr 40 min. Perfect for clinical whole genome sequencing.
+27m ribozyme: 4% error still needs deep cov; also mixtures (i.e. cancer), het calls also. RT @drgitlin: goes away with high enough coverage? #AGBT
+28m GarimaKushwaha: "Miniaturized, disposable USB DNA-sequencer" OH MY GOD!!! #amazing #AGBT
+32m omespeak: Market reacts to #ONT announcement at #AGBT RT @matthewherper: The Next DNA Disruptor? - Forbes http://t.co/ZCLKzhXi
+35m illumina: Marguiles: Data integration from multiple databases including medical risk data w/ variant calls using ISAAC to detect causal muts #AGBT
+36m illumina: Marguiles: Accelerated analysis, 7 hrs for total analysis workflow w/ iSAAC + GATK, one command operation #AGBT
+37m illumina: Marguiles: 120 Gb BAM reduced to just 6 Gb as CRAM file #AGBT
+37m westr: RT @pathogenomenick: I've embedded all the nanopore videos on the blog here http://t.co/6uD2uSzc #AGBT #pm101
+38m lykkebak: eller Video from #AGBT with Anja about #CPHx 2012 June 14-15 http://t.co/w5Vnp0kL
+42m leonidkruglyak: RT @pathogenomenick: I've embedded all the nanopore videos on the blog here http://t.co/C7CrCTMO #AGBT
+42m finchtalk: #AGBT Kevin Hrusovsky on where PerkinElmer is going, mentions that 4th leading cause of death: drug side effects.
+44m kbradnam: The @nanopore press release also reveals that the MinION syncs with iTunes, acts as a 3G modem, and has a fresh lemon scent #AGBT
+44m nanopore: of course! RT @kbradnam: @nanopore release also reveals that MinION syncs with iTunes, acts as a 3G modem, and has a fresh lemon scent #AGBT
+47m ING_SYS: Check out our poster: Biological Interpretation of NGS Re-sequencing Data- today 4:30pm to 6:00pm # 293 #AGBT
+53m howitts_done: Very cool technology! @pathogenomenick: Oxford Nanopore megaton announcement: Why do you need a machine? http://t.co/HydaHnmL #AGBT
+55m genetics_blog: Hmm. What will Oxford @nanopore's 4% error rate mean #bioinformatics? #AGBT
+55m Copenhagenomics: Anja introducing #CPHx 2012 from #AGBT - we hope to see you in Copenhagen, June 14-15 :) http://t.co/F1ExdRRx
+59m deannachurch: OK @nparmalee Carlos Bustamante is up now talking about Complete Genomics and population genetics inference in the personal era. #AGBT
+59m kbradnam: Things to tell your grandchildren: "and we used to work in large buildings called sequencing centers" #AGBT

3 - 4pm EST
+0m iontorrent: Yoga flash mob, informal 45 min, with Garrick @ 3:30 pm, Palms Lawn - Northern most lawn of the Marriott. Mats provided #namaste #AGBT
+1m deannachurch: CB: trying to address how many mutations do genomes from different populations carry + looking at ancient genomes and modern genomes. #AGBT
+1m deannachurch: CB: Comp. Genomics: average 55X coverage. Reference guided assembly + de novo assembly in variant regions. #AGBT
+2m deannachurch: CB: What can you find out from high coverage genomes that you miss with low coverage genomes? #AGBT
+2m ChaunceyGrattan: Can the pores sequence more than one fragment per run? @nanopores #AGBT
+3m mrfoyle: RT @rob_carlson Recalling that just two months ago several prominent biologists assured me #nanopore sequencing was fairy dust. Oops. #AGBT
+5m Awesomics: On the @Nanopore splash at #AGBT RT @matthewherper: The Next DNA Disruptor? - Forbes http://t.co/6ondWpl0
+5m illumina: Bustamante: CGI released 69 genomes avail as a reference and plans to do 500 more genomes #AGBT
+6m deannachurch: CB: Populations can vary in nucleotide diversity by two fold. #AGBT
+6m Copenhagenomics: Did the AV guy fall asleep? Bustamante is LOUD... #AGBT
+7m acdarby: I am a bit worried that my computer does not have enough USB ports to turn it into a sequencing lab #AGBT @nanopore!
+8m ldtimmerman: RT @Awesomics: On the @Nanopore splash at #AGBT RT @matthewherper: The Next DNA Disruptor? - Forbes http://t.co/vHisjesO
+9m deannachurch: CB: pop load of damaging homozygous mutations does not track w/ diversity. e.g. CHB low div. but higher rate of damaging mutations. #AGBT
+10m illumina: Bustamante: Genetic diversity among Chinese, Eurpoean, African pops. Excess diversity damaging? #AGBT
+11m bioinfosm: with so much #agbt buzz after the #oxford #nanopore talk, it might actually have become a trending topic on #twitter!!!
+11m deannachurch: CB: bottleneck followed by expansion allows for retention of deleterious mutations. Admixture is protective for hom. deleterious mut. #AGBT
+12m deannachurch: CB: Rest of talk not tweetable. #AGBT
+14m bkmacy: Nanopore genome sequencer makes its debut http://t.co/P7k0G5E0 @naturenews #AGBT
+14m omespeak: Somewhat lost in the hype of the MINIon is that the nanopore can potentially sequence RNA directly. Big news for RNA researchers. #AGBT
+14m illumina: Bustamante: Excess deleterious homoz muts characterized by >1 severe dramatic bottlenecks followed by population expansion #AGBT
+18m bkmacy: Can MinION by nanopore sequence RNA for gene expression investigations? #AGBT
+19m stveep: It's that time of year when I realise how "small potatoes" my sequencing projects are...but then why do they cause so much grief?! #AGBT
+20m Copenhagenomics: Bustamante: "Finns are special." <-- A return trip to Helsinki easily confirms that... ;) #scandinavianlove #AGBT
+21m saxscience: #AB471 MT @pathogenomenick: I've embedded all the #nanopore videos on the blog here http://t.co/wdAbG98h #AGBT
+22m leonidkruglyak: +1, and I'm not even at #AGBT No one is talking about much else right now. http://t.co/u2fQZhIM
+23m JasonDeKoning: Crazy stuff being announced at #AGBT! http://t.co/iDJ3V9E2
+24m bslatko: @agbt
+25m ayrrisbio: Why do you need a machine to do next-generation sequencing?http://t.co/wZIuV4Dk Lots more 'omics data coming!! #AGBT HT @Nanopore
+26m drgitlin: +2 RT @leonidkruglyak: +1, and I'm not even at #AGBT No one is talking about much else right now. http://t.co/7Kd3YPRG
+27m illumina: Watson: 1B reactions per day based on droplet streams #AGBT
+29m illumina: Watson: V. large number of singleplex PCR primers merged with gDNA in a droplet, then PCRd #AGBT
+30m froggleston: Rothberg: "Nanopores are an 'elegant' technology [..] but Ion Torrent already has a foot in the door" (NewSci). Palpable desperation? #agbt
+30m SarahSalbu: wow RT @finchtalk: #AGBT Kevin Hrusovsky on where PerkinElmer is going, mentions that 4th leading cause of death: drug side effects.
+39m GenomeBiology: Raindance discusses Olivier Harismendy's recent Genome Biology paper that used their technology #agbt
+40m illumina: #AGBT poster 191: Deep seq ribosome protected mRNA frags from poly- & monosomes isol by size excl chrom
+44m joe_pickrell: +1 RT @leonidkruglyak +1, and I'm not even at #AGBT No one is talking about much else right now. http://t.co/MZxSS5n4
+45m illumina: #AGBT poster 126: High accuracy and high speed sequencing on Illumina platforms
+45m parijata: RT @kbradnam: Reactions to @nanopore news. Biologists: cheer. Bioinformaticians: groan. System admins: weep. #AGBT
+45m EpicentreBio: RT @illumina: #AGBT poster 191: Deep seq ribosome protected mRNA frags from poly- & monosomes isol by size excl chrom
+46m NextBio: Visit us at #AGBT poster 370: Mining TCGA glioblastoma data for potential #biomarker! #PM101
+46m bioontology: RT @bioitworld: Full story on Oxford @nanopore stunning presentation from CTO Clive Brown at #AGBT http://t.co/5esocobA
+46m TrishWhetzel: RT @bioitworld: Full story on Oxford @nanopore stunning presentation from CTO Clive Brown at #AGBT http://t.co/0lpJgvWi
+46m bioontology: RT @bioitworld: Full story on Oxford @nanopore stunning presentation from CTO Clive Brown at #AGBT http://t.co/eE67nP5n
+50m illumina: #AGBT poster 234: #Nextera amplicon lib prep for Illuminas #MiSeq personal sequencing system
+54m drchriscole: @davidmam I'm not sure that'll happen. 100x coverage genomes will be unnecessary #ngs #nanopore #AGBT
+54m djschlesinger: Elaine Mardis talking about NuGen's microfluidics technology #AGBT
+55m illumina: #AGBT poster 149 Using #HiSeq2000 to detect de novo germline and somatic muts in clinical WGS
+56m rbuels: Huge, accurate, fast, super-cheap DNA reads? :-O Oxford #nanopore #ngs at #AGBT shot has definitely been heard round the world.
+58m EdgeBio: #AGBT @EdgeBio SAB chair Elaine Mardis up next to talk about NuGen microfluidics technology
+58m eonsim: I want some MinIon minions! Cheapish and disposable just as they should be! #agbt
+59m Massgenomics: Elaine Mardis on making libraries w/ 10-20 ng of DNA: "You gotta have Sean. But the bad news for you is, you can't have Sean." #AGBT.

4 - 5pm EST
+0m fluidigm: Only 60 minutes left! Stop by Suite 285 and learn how you can obtain reads from both ends with single-read sequencing. #AGBT ^S
+1m kbradnam: My #AGBT tweets have gained me several new followers today. Wonder how quick I'll lose them when I revert to tweeting about angry penguins?
+1m illumina: #AGBT poster 353: Single-day, highly multiplexed amplicon sequencing with #MiSeq
+1m illumina: Have a cocktail and meet our experts at Happy Hour in the Illumina Lounge (Capri Ballroom 2/3) now thru 7:00pm. #AGBT
+1m djschlesinger: If you haven't seen the NuGen system in person, it's pretty neat. Droplets move across the circuit board look like cartoon animation. #AGBT
+1m KamounLab: Oxford #Nanopores MinIon "run-until" option is cool. Great for sloppy labs. If wrong sample is loaded then stop the run #ngs #AGBT
+7m Massgenomics: Mardis: Low-input libraries @WashU: PCR cycle optimization helps control the duplication rate ==> better sequencing efficiency. #AGBT.
+9m suganthibala: AGBT 2012 Day 1: Clinical Annotation and Fierce Competition http://t.co/e9MMaa72
+9m razoralign: AGBTOxford Nanopore minIONw
+12m NEBiolabs: Meet NEB scientists at the #AGBT poster session at 4:30. We're at booth 256 talking about strand-specific RNA.
+13m Copenhagenomics: Here's a spy photo from a projected sequencing center, planned to open in early 2013: http://t.co/BjaSNe1P #AGBT
+15m lexnederbragt: Our competitors are like a pregnant woman" #ONT #AGBT http://t.co/hQHJY0at
+15m kbradnam: Heh! RT @Copenhagenomics: Here's a spy photo from a projected sequencing center, planned to open in early 2013: http://t.co/KcOFGxcZ #AGBT
+15m NEBiolabs: Meet NEB scientists at the #AGBT poster session at 4:30. We're poster 256 and talking about strand-specific RNA.
+17m schnablep: #AGBT #NGS game changer? press release from @nanopore: http://t.co/HC51JxFo more: http://t.co/FZoyImTP (do check these out)
+20m illumina: #AGBT Workshop: Illumina Targeted Reseq and Sample Prep Solutions -- starts in 10 min, Illumina Lounge (Capri Ballroom 2/3)
+20m daweonline: I'm not at #AGBT but I heard a couple of bombs falling!
+21m NEBiolabs: #AGBT poster session - visit us at poster 214 to learn about our library prep developments in adaptors!
+21m Matt_Francis: #AGBT obi-wan:I felt a great disturbance in the force, as if a million #illumina investors cried out in pain #oxford #Nanopore
+21m NeonAardvark: RT @bioinfosm with so much #agbt buzz after the #oxford #nanopore talk, it might actually have become a trending topic on #twitter!!!
+26m NEBiolabs: Come to Collier Hall and learn about #automation at poster 153 at the #AGBT poster session starting in 5 minutes!
+26m NeonAardvark: RT ILMN cheers storing genomes on a USB stick while Oxford #Nanopore was showing sequencing genomes WITH a USB stick? #AGBT #futureshock
+29m Calo_BM: #AGBT
+29m eperlste: @nparmalee +1! I've been on both sides of conference tweeting. Maybe it's the subject matter, but following #AGBT has been a blast.
+30m NEBiolabs: Chat with NEB scientists and learn about microbiome enrichment at poster 82 at the #AGBT poster session starting now in Collier Hall.
+33m EpicentreBio: Thursday afternoon at #AGBT: roundup from @Illumina http://t.co/NOYpw7qX
+36m kbradnam: Warning to all employees of @Nanopore. If you carry any 'regular' USB flash drives on you, prepare to be mugged by rabid genomicists #AGBT
+41m xprize: #AGBT RT @agxp: Head to poster 170 to meet Grant Campany Sr. Dir Archon Genomics X PRIZE presented by Medco. learn abt the $10M Competition
+42m emergentnexus: @MiriamGoldste There's also #AGBT where Oxford Nanopore announced USB stick sized ultra-long read $900 nanopore DNA sequencer #aaasmtg
+44m t_basi: I'm so relieved that's OVER. I don't understand any of it yet I've been on the edge of my seat all week. Well done Zoe @nanopore . #agbt
+46m eperlste: @sargoshoe #AGBT has generated the most scientific buzz I've seen on Twitter, and it has nothing to do with PLoS, arsenate or retractions!
+47m liu3zhen: Crazy world. I guess many PIs will re-write their proposals based on the unbelievable Nanopore new system #AGBT
+51m Jeylen: I plan to start up a sequencing center. :) MT @Copenhagenomics: a projected sequencing center in early 2013: http://t.co/9wvLMS1H #AGBT
+51m KazanLaw: I liked a @YouTube video from @iontorrent http://t.co/qFqVyIVX Follow the Ion Bus to AGBT 2012...Get On
+55m NEBiolabs: Visit NEB scientists at posters 82, 153, 214, and 256 at the #AGBT poster session going on now! http://t.co/z2Ex5VuN
+58m aindap: Twitter feed is exploding with @nanopore related #AGBT tweets!

5 - 6pm EST
+4m rkirkbride: Today, everyone was watching the race for the $1000 genome got blindsided by the $1000 genome sequenceER. #AGBT #nanopore
+5m illumina: Come on by for happy hour in the Illumina Lounge! #AGBT
+6m rkirkbride: Today Evonne who was watching the race for the $1000 genome got blindsided by the $1000 genome sequencER. #AGBT #minION
+13m bkmacy: RT @ING_SYS: Check out our poster NOW: Biological Interpretation of NGS Re-sequencing Data- today 4:30pm to 6:00pm #293 #AGBT
+17m nygenome: Lots of energy and interest in #nygenome at the #AGBT poster session. Stop by Collier #173 if you haven't visited us yet.
+17m nanopore: RT @kbradnam: Warning to all employees of @Nanopore. If u carry 'regular' USB drives on you, prepare to be mugged by rabid genomicists #AGBT
+18m sujaik: Keith Robinson adds a dash of realism to the #nanopore #agbt gushiness :-) http://t.co/AKwoNpbo
+19m bkmacy: At heart of the sequencing debate, researchers face the difficult task of relating data to affected biology http://t.co/ObGCOIR8 #AGBT
+21m genomesunzipped: Making sequencing simpler with nanopores: Our take on the new Oxford @Nanopore machines #AGBT http://t.co/cjrQX1db
+24m Clarksearch: U R Funny RT @kbradnam: Things to tell your grandchildren: "and we used to work in large buildings called sequencing centers" #AGBT
+24m GenomeInstitute: Details of Oxford Nanopore's Next Gen sequencing technology http://t.co/NkWv97NW (@bioitworld) #AGBT
+28m CompleteGenomic: Another exciting day at the #AGBT Complete Suite with our customers and partners. Hope everyone had a great time!
+31m JTBiotech: Crazy announcement at the #AGBT conference: #MiniION, a disposable USB pocket-sized nanopore sequencer: http://t.co/cg2JO6Xa
+34m rkirkbride: Everyone looking for $1000 genomes surprised today by $1000 genome sequencER. #AGBT #nanopore
+42m belvario: Entering the age of the $1K genome - http://t.co/RPVGsmMj and http://t.co/nXxdoeuf @nanopore @iontorrent #AGBT
+49m belvario: So, what is the exact use case for the @nanopore MinION? #AGBT
+52m coding_doc: @belvario Have look at the @GenomesUnzipped blog http://t.co/gkPdIm14 #AGBT
+52m mjcgenetics: Oxford @Nanopore's MiniON. A DNA sequencer the size of a memory stick! Put away that tricorder, Bones. http://t.co/ZTbMe5Od #AGBT #genomics
+53m Copenhagenomics: We sure are minions of the MinION... Thanks for all the retweets :) #AGBT
+54m neilhall_uk: "Its like youve been in a band. doing gigs in grotty little venues,then you wake up and youre number one" http://t.co/GQr4acRW #ONT #AGBT

6 - 7pm EST
+3m belvario: Anyone else thinking GATTACA? RT @coding_doc: @belvario Have look at the @GenomesUnzipped blog http://t.co/E35JYGeK #AGBT
+5m kbradnam: If you're going to get a MinION then you may as well buy one of these as well (http:/worldssmallestpc.com/ultrasmall.htm) #AGBT #smallworld
+6m DonRosenthal: MT @westr @genomesunzipped: Making sequencing simpler w/ nanopores: Our take on the new Oxford @Nanopore machines #AGBT http://t.co/IPrsp8Zt
+19m Personal_RX_WI: #AGBT Not a bad place to spend 4 days. Thanks AGBT! http://t.co/Z2eKHkT8
+28m genomematt: New announcement from oxford @nanopore are the talk of the sequencing world after #agbt announcements http://t.co/8kDyKQOd
+29m 8iterations: Rack-mounted USB nanopore DNA sequencers RT @Copenhagenomics: spy photo : http://t.co/Eyz3RMxf #AGBT
+31m HRSearchPros: Are you a good fit for this job? Recruiting Manager in Houston, TX http://t.co/KyymMXgs #job
+32m assemblathon: RT @genomesunzipped: Making sequencing simpler with nanopores: Our take on the new Oxford @Nanopore machines #AGBT http://t.co/SZmpwcbz
+32m GenomeWeb: Impact of @nanopore's #minIon announcement on rest of sequencing market is pretty telling: http://t.co/GCB4Up9l #AGBT
+33m assemblathon: How long before a MinION is featured on CSI? Though it would of course need a blue light and be able to sequence a genome in seconds. #AGBT
+35m kbradnam: Of course @nanopore are having the last laugh as they haven't told people that the MinION syncs data over USB 1.0 #AGBT
+43m TrishWhetzel: RT @genomeweb: Impact of @nanopore's #minIon announcement on rest of sequencing market is pretty telling: http://t.co/wlg0kWvY #AGBT
+47m kb_macrolee: $1000 genomes in 2013 ? RT @genomesunzipped: simpler with nanopores: on the new Oxford @Nanopore machines #AGBT http://t.co/XFXn9Pln

7 - 8pm EST
+2m becky_furlong: looks like I should have gone to #agbt just for the @nanopore talk ...
+8m humanlifee: AGBT 2012 Tweets Day 3: 9:00-9:35 am, Keynote Speaker: Rick Myers, HudsonAlpha Institute for Biotechnology, Gen... http://t.co/6F3Aclqd
+8m aninditaarci: AGBT for ...
+9m IanGoodhead: I feel sorry for anyone else giving a talk today at #AGBT.
+12m belvario: Everyone's focusing on the price/speed - my money's on the real story being long reads... @nanopore #AGBT
+18m Symbionticism: Oxford nanopore usb-sequencer is like bringing social media to genomicists. We will all be empowered instead of waiting for cores. #AGBT
+29m deannachurch: Getting ready for @girlscientist to talk in the Genome Biology session tonight: measuring T cell repertoire diversity. #AGBT
+31m chloe46037: Chris gunter is up #AGBT "measurement of TCell repertoire diversity
+31m genomeresearch: The fabulous Chris Gunter from HudsonAlpha talking about T cell repertoire diversity at #AGBT
+32m deannachurch: CG: focusing on the beta receptor- looking to measure genetic and environment interaction #AGBT
+33m 613SportsChick: I need to tweet as @girlscientist is presenting at #AGBT right now! #tweetfriendlytalk
+34m deannachurch: CG: Looking at the diversity using RNA rather than DNA. mostly sequencing on 454 but also some Illumina. #AGBT
+34m iontorrent: Great AGBT talk by Dr. Tim Triche about long-read RNA Seq on the Ion PGM...: http://t.co/eCJbdXV9 via @youtube #agbt #ionbus
+35m deannachurch: CG: looking at repeatability (looks good) and quantitation (semi-quantitative). #AGBT
+36m ElementoLab: #AGBT Scott Grimmond: genomic analysis of pancreatic adenocarcinoma
+36m chloe46037: CG:multiplexing PCR primers in the TCRB genes #AGBT.
+37m genomeresearch: related http://t.co/vQRlXuBF RT @deannachurch: CG: focusing on the beta receptor-looking to measure genetic & environment interaction #AGBT
+38m bffo: CG cool visualization tools .#agbt
+38m deannachurch: CG: Able to see difference in TCRB between normal samples and both Lupus and colon cancer samples. #AGBT
+38m bffo: Chris Gunter (.@girlscientist) talks about cool stuff.! #agbt
+41m GenomicsIo: MT @belvario: [] - my money's on the real story being long reads... @nanopore #AGBT & RNA & protein & small molecue-seq on same hardware
+41m deannachurch: CG: advertising the "R10K" project- want to sequence the immune repertoire of 10,000 individuals, 100 each and 100 diseases. #agbt
+41m salisburymw: Full house for the @girlscientist talk on immune response. Very cool work. #agbt
+41m coding_doc: RT @genomeresearch: The fabulous @girlscientist from HudsonAlpha talking about T cell repertoire diversity at #AGBT
+41m deannachurch: CG: go to http://t.co/rekf2Gkd for more information on joining the project! #AGBT
+43m ElementoLab: #AGBT Scott Grimmond: DNA damage repair genes often mutated in PDAC .. also includes p300
+43m GenomicsIo: MT @iontorrent: AGBT talk by Dr. Tim Triche about long-read RNA Seq on the Ion PGM.: http://t.co/AjQLr5Vd via @youtube #agbt #ionbus thx!
+44m obahcall: @girlscientist speaking on http://t.co/GWcVJCOQ , sequence immune repertoire in 10k, 100 each in 100 diseases #AGBT
+44m JChrisPires: FREEDOM! fancy new OxNano pocket sequencers #sequencing has finally broken free of the lab! #genome #bioinformatics #AGBT
+45m JChrisPires: RT @bffo: CG cool #visualization tools #bioinformatics #agbt
+46m ElementoLab: #AGBT Scott Grimmond: axon guidance genes eg Robo2, Slt2, Sema3A often mutated in pancreatic adenocarcinoma
+47m jewmanchue: @bmooreUT @foryvonne @genotyper: Congrats! Major #VAAST twitter activity from #AGBT including: @illumina @iontorrent #YandellLab #FTW
+48m jewmanchue: @illumina FYI its Lynn Jorde; not Lynne :-) #VAAST #AGBT
+48m obahcall: Joanna Kelley on multi platform de novo assembly of self fertilizing hermaphroditic fish #AGBT
+48m ElementoLab: #AGBT Scott Grimmond: ROBO2 and ROBO3 expression correlate significantly with survival in pancreatic adenocarcinoma
+50m CaitieL: "game changer" new sequencer revealed at #AGBT - thoughts? http://t.co/IeEyjnc6
+51m deannachurch: Joanna Kelley talking about sequencing and de novo a self-fertilizing hermaphroditic fish. #AGBT
+51m froggleston: No tweets about surname leakage. A tad ironic one could say. #agbt
+53m jewmanchue: @GholsonLyon Dr. Jorde shared the NAA10 story at #AGBT
+53m obahcall: Kelley: multi-platform approach de novo genome sequence of self fertilizing hermaphroditic fish ... We are literally swimming in data #AGBT
+54m ElementoLab: #AGBT David Smith: Exome, Transcriptome and Methylome Analysis of Oropharygneal Cancers
+54m mgberlin: @nanopore Why not set up with a minION and a laptop in the corner of #AGBT and sequence genomes? All promises, no proof.
+56m rnomics: RT @GenomicsIo: MT @iontorrent: AGBT talk by Dr. Tim Triche about long-read #RNA Seq on... http://t.co/2OHsXK34 #rnomics-bioscience @MyEN
+57m bioinfosm: multiple Informatics Specialist job openings at Mayo Clinic http://t.co/kkuFWskx
#agbt #jobs #ngs
+58m jgreid: AGBT Agilent Party http://t.co/n5M4nkqp
+59m girlscientist: Thanks all for the tweets of the talk! Main message: we welcome you to participate in the R10K project, http://t.co/Cj2Qcz0s #AGBT
+59m Massgenomics: David Smith (Mayo) on oral pharynx carcinoma: Some exomes, some RNA-seq, some methylome. Talking so fast I can't write anything down. #AGBT

8 - 9pm EST
+2m genome_gov: Kelley: will use RNASeq to improve assembly in future work #AGBT
+2m obahcall: Kelley: discussing challenges to taking mixed approach, mainly bioinformatics, some assemblers not handle ion torrent data. #AGBT
+3m genome_gov: Kelley: population genomic analysis shows highly homozygous populations #AGBT
+3m girlscientist: Like being attacked by dementors, eating chocolate helps after giving an #AGBT talk.
+5m girlscientist: Joanna Kelley did a great job talking about fish genome sequencing and problems with trying to combine data from multiple platforms. #AGBT
+5m Massgenomics: David Smith: No differences in somatic mutation count between current smokers (HPV-) and never-smokers (HPV+). Doesn't make sense. #AGBT
+5m lykkebak: #AGBT Interesting talk on smokers/non smokers/former smokers by David Smith. Still hope for the smokers - if they stop smoking.
+6m genome_gov: Martin Hirst: Epigenetic contributions to cell identity in human breast #AGBT
+10m ElementoLab: #AGBT John McPherson: Evaluating Targeted Resequencing as a Diagnostic Tool: a Prospective Clinical Trial
+11m obahcall: John McPherson on targeted resequencing as a cancer diagnostic tool #AGBT
+12m girlscientist: Martin Hirst: "I would argue one of seminal findings of RNA seq-ing in cancer are the recurrent findings of epigenetic modifiers." #AGBT
+13m chloe46037: John McPherson "evaluating targeted resequencing as a diagnostic tool" #AGBT
+16m jewmanchue: hey #AGBT folks: do you have a link to @nanopore summary statistics? #depth #coverage #quality?
+16m girlscientist: Hirst has asked us not to tweet the details of his breast cancer epigenetic data, sorry. #AGBT
+16m Massgenomics: Hirst on breast cancer epigenetics. Epigenetic modifiers recurrently mutated: MLL2, ARID1A examples. Ever heard of DNMT3A, guy? #AGBT.
+17m Massgenomics: Well I guess I asked for it - Hirst just asked for "no tweeting" at #AGBT. Rarely a good sign for a talk, ironically.
+20m chloe46037: JMP reports to clinician composed of mutation, frequency and clinical studies relevant to reported mutations #AGBT
+27m illumina: Hirst: Many cancers associated with genome hypomethylation and paradoxically CpG island hypermethylation #AGBT
+28m genome_gov: Alan Harris on Evolutionary genetics of small body size and dizygotic twinning in Callitrichine Primates #AGBT
+28m girlscientist: Awwww...Alan Harris of Baylor showing cute monkeys. #AGBT
+29m girlscientist: [except that one of the small monkeys in Harris's slide looks like he has wicked teeth and he is gouging a tree to get the bark off. #AGBT]
+30m girlscientist: Weird. Harris: these callitrichine primates have dichorionic, dizygotic twins 80% of wild births. Twins all the time: dream genetics! #AGBT
+30m ElementoLab: #AGBT John McPherson: reported cancer diagnostic testing results of 19 actionable genes, using PacBio and Sequenom on 30 patients
+31m obahcall: Samuel Levy: somatic detection in tumor genomes using Illumina and Ion Torrent seq data #AGBT
+33m ElementoLab: #AGBT John McPherson: on 19 gene panel, PacBio found a few more actionable mutations than Sequenom, because entire genes were sequenced
+33m Massgenomics: Levy: Assembly-to-assembly comparison can reveal complex DNA variation, i.e. as found in Craig Venter's genome. Ah, name-dropping. #AGBT.
+33m neandrothal: @dgmacarthur We haven't seen the real product yet. PacBio gave similar predictions at AGBT before
+37m Massgenomics: Levy: De novo Assembly Assembly Mapping (DAAM). Wins the acronym award, at least. #AGBT.
+38m girlscientist: You're at #AGBT? And you're reading twitter? You should meet the other tweeps in person. Hotel lobby bar, when sessions end.
+38m ElementoLab: #AGBT Samuel Levy: using an assembly approach to look for indels (instead of simply aligning reads using short read aligners)
+39m ElementoLab: #AGBT Samuel Levy: assembly approach is called DA-AM, detects 2-10 fold longer indels than GATK
+41m BiotechMarketer: I absolutely love being able to attend #AGBT vicariously via twitter. Thanks to all the tweeps at Marco Island!
+41m Massgenomics: The DAAM approach calls them somatic. The DAAM approach ends up producing stuff that's more accurate. I'll be DAAMed. #AGBT.
+43m ElementoLab: #AGBT Samuel Levy: showed a nice 15bp somatic insertion missed by GATK (functionality unclear since it is in 5'UTR of a LOC gene)
+44m Massgenomics: Levy: 96-97% mapping rate for IonTorrent 200-bp reads. DK: But let's be honest: 2x coverage is a far cry from validation. #AGBT.
+44m bigfeet5grl: 10Kbp > 40bp reads @belvario: Everyone's focusing on the price/speed - my money's on the real story being long reads... @nanopore #AGBT
+46m spbccar: #Agbt push button perfect bacterial assemblies from david jaffe using allpaths-lg
+48m ElementoLab: #AGBT Rebecca Kusko: comprehensive profiling of lung transcriptome in COPD and IPF patients using RNA-seq
+53m girlscientist: Michael Talkowski: importance of balanced chromosomal rearrangements in autism. Sorry but I didn't catch whether talk tweetable. #AGBT
+53m genome_gov: Michael Talkowski on Balanced chromosomal rearrangements in Autism and other neurodevelopmental disorders #AGBT
+54m thinkCara: I so want to go to a scientific conference with a hashtag. But alas, I'm a first year grad student so I must wait. #AGBT
+56m froggleston: Flagging. Need beverages. #agbt
+57m benoitbruneau: Transcripts, assembly RT@belvario: Everyone's focusing on the price/speed - my money's on the real story being long reads... @nanopore #AGBT
+57m genomeresearch: Original Allpaths http://t.co/AzC6Plgf RT @spbccar: #Agbt push button perfect bacterial assemblies from david jaffe using allpaths-lg
+58m NJL_Broad: David Jaffe of @broadinstitute : near perfect assemblies of microbes by combining illumina fragments, jumps and pacbio long reads. #AGBT

9 - 10pm EST
+0m spiremk: Just absorbing the #AGBT @nanopore talk from earlier today. Screw the #iPhone introduction, this is truly mind-blowing http://t.co/J2vupPcE
+1m ElementoLab: #AGBT Rebecca Kusko: most interesting finding is wound healing cytokine alternatively spliced in IPF and emphysema
+2m genome_gov: Talkowski: chromothrpsis = chromosomal shattering and rearrangement #AGBT
+5m froggleston: Potential use of @nanopore for gut microbiomes? Glad those USB sticks are throw away. @CrapBio takeover imminent? #agbt
+7m girlscientist: Talkowski's work is pretty cool, on chromothripsis in autism. More on him at http://t.co/h5sltduP #AGBT
+7m djschlesinger: Anyone going to the Ion Bus party? #AGBT
+10m deannachurch: Getting ready for @NCBI 's Eugene Yaschenko's talk on compression strategies for NGS data. #AGBT
+11m girlscientist: Crowd filing back into room and standing in back for Eric Schadt talk next. Modestly titled on slide, "Reveal the true biology." #AGBT
+12m ElementoLab: #AGBT Maria Mendez-Lago: Genomic analysis of DLBCL
+12m genome_gov: Eric Shcadt on Kinetic Variation events, SMRT sequencing and novel regulatory mechanisms #AGBT
+13m obahcall: Eric Schadt on novel regulatory mechanisms from more complete characterization DNA methyl #AGBT
+14m deannachurch: EY: Going over decision circle needed for defining compression: what to store, remove redundancy, lossy vs. lossless, tuning. #AGBT
+14m girlscientist: Strap in people: Schadt starting on real-time pathogen outbreak studies with @pacbio. First: summer 2011 E. coli outbreak in Germany. #AGBT
+14m genome_gov: Schadt: E.coli outbreak in Germany; why was it so virulent? #AGBT
+16m girlscientist: Schadt: got 8 E. coli genomes of strain to compare, and can see outbreak strain only has shiga toxin gene addition. Explains pathology #AGBT
+16m genome_gov: Schadt: phagelike element encoding shiga toxin found in outbreak strain #AGBT
+16m obahcall: Schadt reviews their studies on pathogen sequencing during epidemic outbreaks, first on Ecoli outbreak in Germany July 2011 #AGBT
+17m genome_gov: Schadt: horizontal gene transfer indicated in the increased virulence in outbreak strain #AGBT
+18m girlscientist: Schadt: sequence data led them to hypothesize that some antibiotics would make symptoms much worse; held up with data. #AGBT
+19m deannachurch: EY: need to update SRA compression to accommodate BAM and other formats containing both raw reads and alignments. #AGBT
+20m pyknosis: RT @kbradnam: Reactions to @nanopore sequencer news. Biologists: cheer. Bioinformaticians: groan. System admins: weep. #AGBT
+20m deannachurch: EY: describing update of cSRA toolkit- you can get this software here: http://t.co/9KWUl5G3 #AGBT
+20m girlscientist: Schadt: now to add methylation data. Going through methods of 5meC detection on @pacbio. #AGBT
+20m genome_gov: Schadt: using PacBio to detect base modifications #AGBT
+22m girlscientist: Schadt: see massive signature of methylation on outbreak genome compared to reference E. coli strain. What are modfications doing?? #AGBT
+22m djschlesinger: Do you have all your Ion tiles?? #AGBT http://t.co/EUX8EcTR
+22m deannachurch: EY: testing new compression method on 1000G data- over 3114 files taking 27 Tb of data after compression. #AGBT
+23m obahcall: Schadt: now reanalyzing this Ecoli outbreak seq data using @PacBio to ID kinetic variation events #AGBT
+25m girlscientist: Schadt: found completely novel sequence contexts for adenine methylation in this outbreak strain. #AGBT
+28m girlscientist: Schadt: then use RNA-seq to look for enrichment of pathways in outbreak strain. Genes upregulated likely to have new motif, modified. #AGBT
+29m girlscientist: Schadt: now giving us an animated summary of his entire talk, with videos. #AGBT Guess I shouldn't have worried about Prezi being too fancy.
+29m deannachurch: EY: Updates to SRA Run browser to add additional information and to make it easier to show alignment. #AGBT
+29m myopomme: Sequencing Takes a Clinical Bent at AGBT http://t.co/Z8VPpukx We can follow the NGS meeting. tech, application, and clinical use. #AGBT
+30m deannachurch: EY: New tool to make access to 1000 Genomes data (BAMs and genotypes)- including downloading BAM slices: http://t.co/9KWUl5G3 #AGBT
+31m girlscientist: Whew. The tweetup should begin shortly. #AGBT
+34m omespeak: Already here... RT @girlscientist Whew. The tweetup should begin shortly. #AGBT
+36m 454Sequencing: Don't miss the Roche Applied Science Workshop tomorrow at noon in the Palms Ballroom! #AGBT
+43m ramoyw2: AGBT
+45m 454Sequencing: "A draft assembly of Cannabis saliva and Cannabis indica" Presented by Kevin McKernan, Medicinal Genomics - Don't miss it! #AGBT
+54m Massgenomics: Day 2 summary of #AGBT and cool photo posted on Massgenomics: http://t.co/APPtxVay
+56m jgreid: @AGBT IonLounge http://t.co/gJTVd6lB
+57m ElementoLab: #AGBT Maria Mendez-Lago: found novel fusions including w FOXP1, also novel targets of aberrant somatic hypermutation in DLBCL, many overexp

10 - 11pm EST
+6m liu3zhen: A great AGBT notes; get information without attending the conference http://t.co/ueTd1A72 #AGBT
+15m kbradnam: A crazy day of #AGBT-related tweets. Hello to my new followers...I'm sure you will be unfollowing me within a week!
+24m bffo: at bar, waiting for tweet up ... middle table ... #agbt
+34m dgmacarthur: Great coverage of #AGBT by @Massgenomics: http://t.co/Hv3aZdSz
+35m girlscientist: Massive turnout for tweetup! Feeling the love. #AGBT
+44m Dr_Bik: @kbradnam are you at #AGBT IRL or just following online? Sounds cool either way!
+51m liu3zhen: MinIon can be used to QC your DNA libraries. Whatever libraries. That is great. #AGBT

11 - 12pm EST
+1m sciolato: So cool! RT @pathogenomenick: I've embedded all the nanopore videos on the blog here http://t.co/mD6XZINx #AGBT
+32m SEQanswers: Thanks to @nanopore for driving a subset of dummies out of $ILMN!! #AGBT
+43m caddymob: Is this still a thing #AGBT? "Illumina and Oxford Nanopore Enter into Broad Commercialization Agreement" http://t.co/IPWdRYv6
+45m hiro_h: AGBT tweets 2012 (2) http://t.co/8YWvx4S9
+46m TogetterJP: :

@hiro_h
AGBT tweets 2012 (2)

fav:0 view:0
http://t.co/WtUd5zah
+10m ribozyme: Also this: "Illumina Joins $41M Bet on Oxford Nanopore" http://t.co/V84gR201 RT @caddymob: Is this still a thing?. #AGBT
+17m fionabrinkman: Wow MT @pathogenomenick Oxford Nanopore megaton announcement: Why do you need a machine? interview http://t.co/8br4kwtb #AGBT
+29m EvgenyGlazov: Video: Dr. Tim Triche talks about long-read ncRNA Seq on the @iontorrent PGM and transcriptional complexity at #AGBT http://t.co/4ubDsVPo
+31m terryvrijenhoek: RT@nanopore: Introducing the MinION, a nanopore sequencer the size of a USB stick. Works just like GridION, but smaller #AGBT
+29m drsteventucker: "We wander into the realms of sci-fi at this point." @pathogenomenick interview with @nanopore #AGBT http://t.co/uIoDGvNa
+34m gantengp2: AGBT
+47m Arabgenes: Rt @nanopore Introducing the MinION, a nanopore sequencer the size of a USB stick. Works just like GridION, but smaller #AGBT
+49m KamounLab: @AnneOsterrieder @ThePlantJournal @MPPjournal @PetraKiviniemi @PlantBizarre Easy: Ask them to check hashtags #AGBT #LGD2012 #FRA2012 etc.
+50m Arabgenes: Rt @genetics_blog If looking through the AGBT tag is too daunting,@pathogenomenick is doing a fine job summarizing at http://t.co/Py4R8uA8.
+1m jessfl4: AGBT
+6m flyembtn9: HiSeq 1500 is same as 2500 with single lane flow cell. AGBT - what's the point?
+37m Hyoobaloinz: RT @genomesunzipped: Making sequencing simpler w nanopores: Our take on the new Oxford @Nanopore machines #AGBT http://t.co/6WMW7GfV
+43m mrrizkallah: Iit's been 2 hours and I am half way #AGBT tweets. This is a 500X coverage :-)

AGBT 2012 Blog Post Round-up

17 Feb 2012

A round-up of blog posts covering AGBT ... will add to this when something catches my eye.

This blog

• Oxford Nanopore megaton announcement: “Why do you need a machine?” – exclusive interview for this blog!
• All the Oxford Nanopore videos
• Which technology won AGBT?
• AGBT 2012 day 1 tweets
• AGBT 2012 day 2 tweets
• AGBT 2013 day 3 tweets
• AGBT 2012 day 4 tweets </ul>

  Massgenomics (Dan Koboldt)

  • AGBT 2012 Day 1: Clinical Annotation and Fierce Competition
  • AGBT 2012 Day 2: Cancer, Technology, and Oxford Nanopore
  • AGBT 2012 Last Day: Elephants in the Room </ul>

    Omicsomics (Keith Robison)

    • Oxford Nanopore Doesn't Disappoint </ul>

      CoreGenomics (James Hadfield)

      • Oxford Nanopore did not disappoint
      • Day 1 round-up
      • Day 2 round-up </ul>

        GenomesUnzipped (Luke Jostins and gang)

        • Making sequencing simpler with nanopores </ul>

          EdgeBio

          • AGBT Update #2 "Jonathan Rothberg did not disappoint and delivered some pretty bold statements about where they are heading with the Proton" </ul>

            Seqanswers.com

            • Discussion of GnuBIO and Lasergen announcements </ul>

              Illumina

              • Perspectives from the Illumina user group meeting discusses the MiSeq: "at 250 cycles, the raw error rate is only 0.69%"
              • Thursday Morning at AGBT
              • Illumina AGBT coverage page </ul>

                #notAGBT

                • A new sequencing technology enters the ring: SHTseq(TM)
                • Breaking News: CAKSeq announce legal challenge against CrapBio </ul>

#NotAGBT Breaking News: CAKSeq announce legal challenge against CrapBio

16 Feb 2012

Woah, the news is hotting up at AGBT's parallel conference #notAGBT (the anti-conference for those too impoverished, disillusioned or lazy to make it to AGBT this year). This press release just in from Chad Bower at CAKSeq suggesting CrapBio's machine - announced yesterday - might have hit serious problems before it's even released! Release follows:

Today the CEO of the UK public-private partnership company CAKSeq announced a legal challenge against UK startup CrapBio claiming the core technology infringes a number of their patents.

Chad Bower, CEO of CAKSeq, said “we have been doing this for years, the core principals behind the randomized base calling technology that is central to SHT sequencing was patented by CAKSeq years ago …. CrapBio has simply repackaged it” he continued .. “although out technology could only read 2 bases (G and A) , its average accuracy was the same”

However Neil Hall, CEO of CrapBio, who are talk of the town at the current #notAGBT conference in Birmingham, UK. Said “their so called “di-base encryption” technology is far inferior to ours. They use CAKspace base calling that does not read the base itself but simply probability of any base being a G or a C. This is computationally expensive and totally useless.”

Chad Bower responded that their technology “had some advantages once it was mapped to a high quality reference and had a niche for certain applications” he continued if customers buy our CAK-Scope software suite the di-base encryption will be dealt with “under the hood”.

Mack Witson, the brains behind the CrapBio system and SHT-head scientist said “I have never heard of CAKSeq and if I had I would have forgotten about them already, this di-base encryption is a joke.”

AGBT 2012 Day 2 Tweets

16 Feb 2012

(Day 1, Day 2, Day 3, Day 4)

Well not much in the way of huge announcements yesterday at AGBT. The biggest announcement was probably the information that Illumina are testing 400bp single-end reads in R&D on the MiSeq, with the longest achieved overlapping paired-read of 678bp. Pretty impressive stuff.

The other news was of course the announcement of the incredible sounding SHTseq(TM) from CrapBio which can produce 100Mb reads at 25% accuracy. This was announced at the parallel #notAGBT conference being held on Toll Island near Winson Green prison in Birmingham. But rumour has it a patent suit may be winging it's way to CrapBio already!!

Oh I should say, if you are at AGBT go and have a word with James Hadfield about our sequencer map in the afternoon poster session!

Right, so .. on with the show. Tweets will update automatically every couple of minutes but you'll have to refresh the page to see them.

Scientific agenda:

Plenary Session: Clinical Translation of Genomics, (Chad Nusbaum, Broad Institute of MIT and Harvard, Chair)
9:00-9:10 Opening Remarks
9:10-9:45 Keynote Speaker: Lynn Jorde, University of Utah School of Medicine, “Whole-genome Sequencing, Mutation Rates, and Disease-gene Detection.”
9:45-10:15 Heidi Rehm, Partners Healthcare Center for Personalized Genetic Medicine, “Supporting Large Scale Sequencing in a Clinical Environment”
10:15-10:45 Lisa Shaffer, Perkin Elmer, Inc., “A Genotype First Approach to the Identification of New Chromosomal Syndromes”
11:10-11:40 * Darrell Dinwiddie, Children's Mercy Hospital, “Initial Clinical Experience with Molecular Testing for >600 Severe Childhood Diseases by Target Enrichment and Next-Generation Sequencing”
11:40 am-12:10 * Rong Chen, Personalis Inc., “Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation Among Human Populations, Compared to Other Diseases”
1:10-2:40 Poster Session with Coffee & Dessert - Collier Hall

Plenary Session: Genomic Studies I (Len Pennacchio, Joint Genome Institute, Chair)
2:40-3:10 Goncalo Abecasis, University of Michigan “Sequencing Thousands of Human Genomes”
3:10-3:40 Ewan Birney, European Bioinformatics Institute, “ENCODE: Understanding Our Genome”
4:05-4:35 Charles Perou, The University of North Carolina at Chapel Hill, “Molecular Classification of Breast Tumors Using Gene Expression Profiling and Its Translation Into Clinical Practices”
4:35-5:05 * Arend Sidow, Stanford University, “Breast Cancer Progression From Earliest Lesions to Clinically Relevant Carcinoma Revealed by Deep Whole Genome Sequencing”
5:05-7:00 Pacific Biosciences Roundtable Discussion/Dinner

Most popular tweets
(35) girlscientist: Jorde: Male mutation rate is about 5X the female mutation rate. We males are responsible for most of the havoc in the human genome. #AGBT
(7) bffo: LJ: VAAST is a lot better than SIFT and ANNOVAR re: table 1 in VAAST paper: http://t.co/fkD51HzS #AGBT
(6) girlscientist: Lynn Jorde on to mutation rate estimation by sequencing and mass-spec. Each gamete contributes about 35 new variants. #AGBT
(6) girlscientist: Jorde: As a longtime human geneticist, I am especially happy to see that we are going back to families. Word. #AGBT
(5) iontorrent: Ion's first Human AmpliSeq Paired End (bi-directional) run on Ion Community. Corrected raw mean accuracy of 99.4% http://t.co/QA8CRt9u #agbt
(5) djschlesinger: Dinwiddie: 7043 mendialian diseases, 3328 with known molecular basis #AGBT
(5) Massgenomics: Summary of first day at #AGBT: http://t.co/IDALVCxP
(4) girlscientist: Rehm: shes's been told Myriad still detects 10-20 new missense variants in BRCA1/2 each week, even after testing 100's of 1000's ppl. #AGBT
(4) illumina: Real data from HiSeq 2500. Read the newest application note #AGBT #keepingitreal http://t.co/Dd5cvpU1
(4) nanopore: Curious about how to use nanopores to analyse proteins or miRNA? Go to our poster, Dr Dan Turner will tell all - poster 360 #AGBT
(3) CompleteGenomic: Today at #AGBT we announced our Biological Discovery Software Partners Program . Read more: http://t.co/nhsNsiDa
(3) schnablep: #AGBT Heidi Rehm,Supporting Large Scale Sequencing in a Clinical Environment genetic tests now available for ~2,500 diseases;
(3) MishaAngrist: MT @girlscientist: Rehm: Myriad still detects 10-20 new missense variants in BRCA each week, even after testing 100's of 1000's ppl. #AGBT
(3) genomeresearch: H Rehm: integrate vast amt of genetic info into patient care by storing millions of variants in electronic health records #AGBT
(3) illumina: Shaffer, Perkin Elmer. Many syndromes caused by chromosomal abnormalities cannot be IDd by NGS, instead need arrays. #AGBT
(3) djschlesinger: Dinwiddie: Sanger sequencing costs ~$10k testing for 1-10 diseases, ~$1k for 600 diseases using NGS #AGBT
(3) illumina: Dinwiddie: ~7k known mendelian diseases, 3k with known molecular basis. Together affect about 3-4% of children. #AGBT
(3) finchtalk: #AGBT Rong Chen, genetic risk map of the world http://t.co/XDad805M
(3) deannachurch: AG: Making the important point that the entire genome is not accessible to current sequencing technology. #AGBT
(3) gabecasis: Let's tweet about the design of Birney slides. Some look crowded. #AGBT #NoScience #TopSecret
(3) ElementoLab: #AGBT Ewan Birney: scoop: promoters exist and they are important
(3) EdgeBio: #AGBT Update #1 via @dgaalaas http://t.co/JdhzqtiF
(3) girlscientist: Shameless plug FTW! RT @genomeresearch: Breast cancer genomics now at #AGBT. For more, see special issue http://t.co/VRX3QPn0
(2) Personal_RX_WI: #AGBT. Look into the future of @Illumina. They have sequenced to 678 bp in house on MiSeq. Very interesting....
(2) illumina: New blog post from Abizar Lakdawalla with exclusive highlights of yesterday's Illumina User Group Meeting at #AGBT http://t.co/isP5PzDn
(2) girlscientist: Jorde found X-linked mutation http://t.co/VV034xOE while mother pregnant again, but couldn't comm. result since in non-CLIA lab. Sad. #AGBT
(2) bffo: Li "Males mostly responsible for mutation havoc" in human genome #agbt
(2) deannachurch: Heidi Rehm from Harvard Partners up next to talk about the sequencing in the clinical environment. #AGBT
(2) iontorrent: Average time to assess a novel variant - 21.5 to 119.6 min depending on other data/publications available for gene. Heidi Rehm #AGBT
(2) schnablep: #AGBT Heidi Rehm, 60-80% of clinically significant variants are found in only one family.

7 - 8am EST
+41m Personal_RX_WI: Day 2 of #agbt about to get started. First up @illumina talks followed by clinical genomics.
+58m stuka: I slept to the relaxing sounds of the ocean. No I didn't go to #AGBT, my people bought me a sound machine to helps w/ my not sleeping

8 - 9am EST
+3m CompleteGenomic: Today at #AGBT we announced our Biological Discovery Software Partners Program . Read more: http://t.co/nhsNsiDa
+15m djschlesinger: Up first, more on the upgrades to the HiSeq and MiSeq from Illumina #AGBT
+17m westr: RT @CompleteGenomic: Today at #AGBT we announced our Biological Discovery Software Partners Program . Read more: http://t.co/XWAsGO9J #pm101
+19m ING_SYS: Ingenuity will be part of IGN for new Illumina Cancer Analysis Service http://t.co/ZZxzu8wb learn more #AGBT Lanai 179
+22m ING_SYS: Ingenuity to work with Complete Genomics for new Genomics Discovery Program http://t.co/UTb7mfHc learn more #AGBT Lanai 179
+23m ezequiel_coelho: Thanks guys at #AGBT, for all your postings. For all of us who cannot be there, this is really helpfull
+23m djschlesinger: HiSeq 1500 is same as 2500 with single lane flow cell. #AGBT - what's the point?
+25m Massgenomics: Breakfast at AGBT. First session will be "Clinical Translation of Genomics" chaired by Chad Nusbaum of the Broad Institute.
+25m maureen_mack: @Personal_RX_WI tweeting latest and greatest from world of #agbt have fun Jaime and Mike!
+25m djschlesinger: HiSeq 1500 will be fully upgradeable to 2500 #AGBT
+29m jacquimiller: @pathogenomenick super useful wrap up of #AGBT tweets. thanks! http://t.co/8L9ZzJtm
+30m iontorrent: Ion's first Human AmpliSeq Paired End (bi-directional) run on Ion Community. Corrected raw mean accuracy of 99.4% http://t.co/QA8CRt9u #agbt
+37m iontorrent: Be the first to see the Ion Proton Sequencer at AGBT. Drop Life Genetic Analysis Showcase, Lanai Suite 185 at AGBT http://t.co/7l6VxwDZ
+45m djschlesinger: MiSeq improvements will require hardware upgrades for dual surface imaging and faster PC, no cost to existing MiSeq owners #AGBT
+45m ING_SYS: Accurate biological interpretation is critical to efficiently identify causal variants http://t.co/UTb7mfHc learn more #AGBT Lanai 179
+51m ING_SYS: #AGBT the place to be: Complete Suite in the Everglades Room from 5-7 p.m. tonight! http://t.co/UTb7mfHc
+54m salisburymw: Whatever happened to easing in to #agbt? Late parties 1st night, hangovers start early!
+54m girlscientist: Awaiting the start of #AGBT 2012. Don't forget the tweetup Fri night at the hotel bar!
+58m Single_Molecule: I will be at my AGBT poster (#352) today, 1-240 PM. "Detection of Structural Variations Using Nanodetector Positional Sequencing" @nabsys
+59m EdgeBio: RT @agxp: Are you at AGBT#? Learn about our partnership with @EdgeBio during today poster session!

9 - 10am EST
+2m Personal_RX_WI: #AGBT. Look into the future of @Illumina. They have sequenced to 678 bp in house on MiSeq. Very interesting....
+4m bioinfophd: Excited to be at #AGBT
+5m deannachurch: Getting ready for Lynn Jorde opening up the first #AGBT session on whole genome sequencing and finding disease causing mutations.
+5m bioinfophd: Be sure to check out #AGBT poster 38 to learn more about using RNA-seq to identify alternative splicing associated with chronic lung disease
+7m ElementoLab: #AGBT Lynn Jorde: WGS and disease causing mutations
+8m genomeresearch: #genomeresearch at #AGBT 2012 Lynn Jorde using whole genome sequence data to estimate mutation rate
+9m ElementoLab: #AGBT LJ: what is the human mutation rate ?
+9m bffo: good tweet policy at #AGBT http://t.co/m0T5YsLp (default == tweetable, just say "no tweet" if you don't want your talk tweeted #openess
+11m finchtalk: #AGBT Lynn Jorde estimating human mutation rate. JBS Haldane, first recognized the importance of de novo mutation rates
+11m dgaalaas: Welcome to #AGBT . Conference starting now with Lynn Jorde of Univ Utah Sch of Med
+11m ElementoLab: #AGBT LJ: studies Miller syndrome, 1 family of 4
+11m ElementoLab: #AGBT LJ: craniofacial deformation, missing digits, short arms etc
+12m richardbadge: Enjoying the anticipation of #AGBT meeting start, but must remember to go to BEER (Bioinformatics Expertise Enabling Research) meeting soon!
+12m ElementoLab: #AGBT LJ: only 2 reccurrent Miller families in the world
+13m ElementoLab: #AGBT LJ: 7 individuals = 25% of affected patients
+13m bioinfosm: @neilhall_uk of course, I was talking about sour grapes for the #agbt folks ;)
+14m ElementoLab: #AGBT LJ: Miller family also had lung disease, gene not clear
+15m ElementoLab: #AGBT LJ: Miller syndrome exome seq => mutations in DHODH
+15m pathogenomenick: OK you guys, #AGBT tweets from day 2 being streamed to the blog http://t.co/SGK6XrBj including exciting "popular tweets" feature!
+16m ElementoLab: #AGBT LJ: also mutation in DNAH5 which explain lung disease
+16m NorthernAutumn: Lynne Jorde Miller Syn 2recurrent families in world. 1 family w recurrence had cousin w/CF, clue to gt cause? But mat CFTR normal #AGBT
+16m ElementoLab: #AGBT LJ: both chidren inhnerited 5 disease mutations !
+18m NorthernAutumn: Lynne Jorde Miller Syn so did WGS on recurrent family & found at least 5 novel muts in each. #AGBT
+18m ElementoLab: #AGBT LJ: also estimated mutation rate from data ... needed to reseq all 34K Mendelian inheritance errors
+18m ElementoLab: #AGBT LJ: only 28 were true by capture + reseq
+19m girlscientist: Lynn Jorde on to mutation rate estimation by sequencing and mass-spec. Each gamete contributes about 35 new variants. #AGBT
+19m illumina: Good morning #AGBT! Kicking off the day with a session about HiSeq 2500 and MiSeq in our Illumina Lounge. http://t.co/uzdfUm54
+20m ElementoLab: #AGBT LJ: 1.1 e-8 mutation rate
+20m NorthernAutumn: Lynne Jorde Mutation Rate estimation estimated 35 new variants/gamete in his calculations. 1K genome Proj had similar estimates. #AGBT
+20m ElementoLab: #AGBT LJ: estimate agrees with 1000 genome estimates on trios
+21m ElementoLab: #AGBT LJ: all in 1 tool to analyze variants: VAAST
+21m deannachurch: LJ: Discussing using the VAAST software for variant analysis: http://t.co/shKTT16X #AGBT
+22m ElementoLab: #AGBT LJ: VAAST compares variants to dbSNP, 1KG
+22m ElementoLab: #AGBT LJ: gene by gene analysis, fewer tests
+22m ElementoLab: #AGBT LJ: can incorporate pedigree data in latest version
+22m bioinfosm: #agbt Lynn Jorde talks about vaast that identifies disease-causing variants on a gene-by-gene basis; and could use pedigree info #ngs
+23m ElementoLab: #AGBT LJ: uses composite likelihood ratio test, null= variant does not cause disease
+23m NorthernAutumn: Lynne Jorde developed VAAST Variant Anotation Analysis & Selection Tool. Compare patient seq w/variant seq & freq in multiple db. #AGBT
+23m ElementoLab: #AGBT LJ: exome published in Ng et al 2010 (DHODH)
+24m bffo: #AGBT VAAST http://t.co/kyql87hi from the Yandell lab : Variant Annotation, Analysis and Search Tool #bioinformatics
+24m bioinfosm: #agbt tweeps; there is an #ngs twibe = http://t.co/kLjN2XXG for next-gen seq discussions;
+24m ElementoLab: #AGBT LJ: VAAST identified ONLY 2 causal variants from WGS
+24m schnablep: #AGBT Lynn Jorde: Mutation detection via WGS using #VAAST (Yandell et al., Genome Res 2011); exploits pedigree data thereby improving calls
+24m finchtalk: #AGBT LJ on VAAST, shows statistical model, but says too early in the morning to be tortured with math
+24m NorthernAutumn: Lynne Jorde VAAST simplified results fr Millet Syn WGS to 2 candidate genes #AGBT
+25m ElementoLab: #AGBT LJ: used VAAST on unknown lethal X linked condition, 1 family
+25m ElementoLab: #AGBT LJ: progeria like features
+25m ElementoLab: #AGBT LJ: VAAST identified disease causing locus in 20 mins, on X chrom
+26m ElementoLab: #AGBT LJ: brand new genetic disease, named Ogden syndrome
+26m ElementoLab: #AGBT LJ: mutation in NAA10 N-acetyltransferase
+26m illumina: New blog post from Abizar Lakdawalla with exclusive highlights of yesterday's Illumina User Group Meeting at #AGBT http://t.co/isP5PzDn
+27m NorthernAutumn: Lynne Jorde VAAST analysis of novel x-linked. Exome-Seq & VAAST in 20 min identified mut in NAA10 cause of new gt disease Ogden Syn #AGBT
+27m ElementoLab: #AGBT LJ: mother was 5 mo pregnant when diagnostic came up
+27m iontorrent: Mutation in NAA10 causes a new genetic disease: "Ogden syndrome". Lynn Jorde #VAAST #AGBT
+27m ElementoLab: #AGBT LJ: could not tell her because not CLIA and child died
+28m genomeresearch: L Jorde discusses VAAST, which identifies disease-causing variants #AGBT http://t.co/ee8MrtR4
+28m NorthernAutumn: Lynne Jordan Discovered mother was pregnant with Ogden-affected fetus but couldn't inform her of result b/c test not done in CLIA lab #AGBT
+28m ElementoLab: #AGBT LJ: NAA10 in second family
+28m ElementoLab: #AGBT LJ: independent mutations, families unrelated
+29m ElementoLab: #AGBT LJ: VAAST increases power to detect NOD2 mutation in Crohn cohort
+30m ElementoLab: #AGBT LJ: increased power due to additional information used (BLOSUM etc)
+30m fluidigm: For Targeted Resequencing and Single Cell Studies stop by Suite 285 at #AGBT, let us show you what we got!
+30m NorthernAutumn: Lynne Jorde Used VAAST to detect NOD2 mut in Crohns disease cohort of 300 cases & ctrls. Example of VAAST in common complex disease #AGBT
+30m girlscientist: Jorde found X-linked mutation http://t.co/VV034xOE while mother pregnant again, but couldn't comm. result since in non-CLIA lab. Sad. #AGBT
+30m ElementoLab: #AGBT LJ: another condition with cardiac septal defects, identified GATA4 using VAAST
+31m MishaAngrist: MT @girlscientist: Jorde found X-linked mutation http://t.co/O0MDstRR but couldn't comm. result since in non-CLIA lab. Sad. #AGBT
+31m ElementoLab: #AGBT LJ: VAAST adds pedigree term to LOD
+32m NorthernAutumn: Lynne Jorde VAAST in single muti-generational family w dilated cardiomyopathy by adding LOD scores in new 'pedigree VAAST' #AGBT
+32m bioinfosm: #agbt LJ: power of vaast increases by more than an order of magnitude on using more control genomes #ngs #bioinformatics
+32m ElementoLab: #AGBT LJ: esimated male specific mutation rate
+33m ElementoLab: #AGBT LJ: 2.0e-8 per base pr generation
+33m NorthernAutumn: Lynne Jorde Power of pedigree #VAAST increases as more control genome assembled. #AGBT
+33m ElementoLab: #AGBT LJ: twice as high as average mutation rate, 5 times female
+34m ElementoLab: #AGBT LJ: males are responsible for most havoc in human genome (joke)
+34m girlscientist: Jorde: Male mutation rate is about 5X the female mutation rate. We males are responsible for most of the havoc in the human genome. #AGBT
+34m NorthernAutumn: Lynne Jorde 'Males responsible for most of havoc in human genome' b/c mut rate 5x that of female rate #AGBT
+35m ElementoLab: #AGBT LJ: Haldane was pretty close with not seq tools, two-fold difference only
+35m ElementoLab: #AGBT LJ: Haldane also found male rate 10 times higher than female
+35m girlscientist: Jorde goes old-skool and points out Haldane in 1947 suggested male mut rate was up to 10X higher; now supported by data. #AGBT
+36m ElementoLab: #AGBT LJ: how do you explain variation in mutation rates is question that can be addressed
+36m NorthernAutumn: Lynn Jorde new q? Direct effect of paternal age on male mutation rate #AGBT
+36m bffo: Li "Males mostly responsible for mutation havoc" in human genome #agbt
+37m bioinfosm: is the hashtag case sensitive!! #agbt is not same as #AGBT ?
+37m girlscientist: Jorde: As a longtime human geneticist, I am especially happy to see that we are going back to families. Word. #AGBT
+38m ElementoLab: #AGBT LJ: question: structural variation rate ?
+38m ElementoLab: #AGBT LJ: deletions might be more common in female transmission
+39m GenomeBiology: Lynn Jorde discusses VAAST. A powerful tool for detecting mutations #agbt
+39m djschlesinger: Lynn Jorde gave very inspiring talk on identification of causative variants in WGS data. Very cool. #AGBT #VAAST
+39m geniachip: Lynne Jorde, Univ of Utah: WGS providing consistent estimates of the human mutation rate. WGS / VAAST id's disease causing mutations; #AGBT
+40m djschlesinger: Heidi Rehm from Partners Healthcare up next to talk about large scale sequencing in a clinical lab #agbt
+40m MishaAngrist: kinda wish i were at #agbt
+41m ElementoLab: #AGBT LJ: male gametes have undergone more meioses which explains higher mutation rate
+41m eperlste: Kudos to all tweeting from #AGBT! This is what good conference tweeting looks like. Non-genetics biologists please watch and learn.
+42m deannachurch: Heidi Rehm from Harvard Partners up next to talk about the sequencing in the clinical environment. #AGBT
+42m ElementoLab: #AGBT Heidi Rehm: CLIA lab prospective for using seq in clinical applications
+43m girlscientist: well here you go, Heidi Rehm starts off with "I was asked to give the CLIA lab perspective on testing." #AGBT
+43m NorthernAutumn: Lynn Jorde males have higher mut rate b/c spermatogonia contly undergoing spermatogensis, so 50 year old male has had 800 divisions #AGBT
+43m illumina: Lynne Jorde: #VAAST for funct impact of amino acid changes, disease causing variants, pedigree info. Uses comp likelihood ratio test #AGBT
+43m ElementoLab: #AGBT HR: her lab offers > 150 tests, testing in large multigene panels
+44m bffo: LJ: VAAST is a lot better than SIFT and ANNOVAR re: table 1 in VAAST paper: http://t.co/fkD51HzS #AGBT
+44m omespeak: Quick look at nanopore abstracts from Oxford Nano & Gundlach confirms my suspicion that polymerase will be used to ratchet DNA. #AGBT
+44m djschlesinger: Heidi Rehm shows graph from GeneTests showing how fast clinical sequencing tests are being developed over the past decade #agbt
+45m finchtalk: #AGBT Heidi Rehm, NGS in a CLIA lab. 2500 diseases being testes. Striking feature is the increase in content / test
+45m schnablep: #AGBT Heidi Rehm,Supporting Large Scale Sequencing in a Clinical Environment genetic tests now available for ~2,500 diseases;
+46m ElementoLab: #AGBT HR: 5 years ago launched HCM cardiochip panel
+46m omespeak: RT @finchtalk: #AGBT Heidi Rehm, NGS in a CLIA lab. 2500 diseases being testes. Striking feature is the increase in content / test
+47m ElementoLab: #AGBT HR: GLA variant is actionable (Fabri disease? did not get the name)
+48m NorthernAutumn: @Affymetrix Heidi Rehm discussing gene tests on Affy arrays @ #AGBT
+48m ElementoLab: #AGBT HR: 1 chip multiple genes, test for many genes, diagnose unexpected conditions
+48m ElementoLab: #AGBT HR: example with Hearing Loss and Usher syndrome; would not have tested both together without chip
+49m djschlesinger: Heidi Rehm says very few families opt for prenatal genetic testing for hearing loss #AGBT - I'm surprised that it's even offered
+49m deannachurch: HR: Clinical labs still have to confirm variants identified by NGS- by Sanger. #AGBT
+50m ElementoLab: #AGBT HR: they need 95% coverage of gene regions
+50m NorthernAutumn: Heidi Rehm accepted standard for clinical labs is to confirm NGS b/c of possibility of mixed samples & to fully cover missing info #AGBT
+50m ElementoLab: #AGBT HR: 80% not enough
+50m bioinfosm: #agbt Rehm talks about sample mixup possibilities with ngs (many manual steps) so sanger validation for all cases
+51m ElementoLab: #AGBT HR: 20X coverage is their cutoff
+51m finchtalk: #AGBT HR still Sanger sequence to confirm results from NGS. Variant DB integrated into the workflow in real time.
+51m ElementoLab: #AGBT HR: converted OtoChip to OtoGenome
+52m schnablep: #AGBT Heidi Rehm, Multi-gene tests now widely available (e.g., OtoChip for hearing loss); they Sanger confirm positive NGS results
+52m NorthernAutumn: Heidi Rehm mostly use Sanger Seq for confirmation of novel variants #AGBT
+52m ElementoLab: #AGBT HR: confirmatory Sanger seq assays bottleneck
+52m girlscientist: Rehm: moved their OtoChip array test to OtoGenome test. Bottleneck = Sanger confirmation for 1000+ potential muts ID'd by test. #AGBT
+53m ElementoLab: #AGBT HR: 99.5% sensitivity for OtoGenome w SNVs, indels not as good
+53m bioinfosm: @Massgenomics Dan good to see you on twitter.. will try to catch you at #agbt
+54m girlscientist: Rehm: other bottleneck is novel variant assessment. When they launched pan-cariomyopathy NGS test, they started drowning in this. #AGBT
+54m ElementoLab: #AGBT HR: continuously need to add novel variants in database
+54m iontorrent: Average time to assess a novel variant - 21.5 to 119.6 min depending on other data/publications available for gene. Heidi Rehm #AGBT
+55m schnablep: #AGBT Challenge of novel variant assessment in targeted clinical assays (lots of manual searches, 21-120 min/variant)
+55m bioinfosm: #agbt HR: Novel Variant Assessment is 21 to 120mins given a single post-doc or phd person looking at that variant!!
+55m obahcall: Opening talk at #AGBT: Lynn Jorde speaks on direct estimates human mutation rate using whole genome seq data
+56m finchtalk: #AGBT HR board certification requires measure the time it takes to assess novel variants, about 2-3 hrs.
+56m djschlesinger: Heidi Rehm - 17% of variants they detect are novel #AGBT
+56m ElementoLab: #AGBT HR: 10-20 BRCA1 new variants each week ... keeping up w novel variants is a challenge
+56m bioinfosm: #agbt HR: HCM mutations from 2000 cases tested, >60% are unique to a family
+57m girlscientist: Rehm: shes's been told Myriad still detects 10-20 new missense variants in BRCA1/2 each week, even after testing 100's of 1000's ppl. #AGBT
+57m finchtalk: #AGBT HR now showing the huge number of novel variants that are unique to families.
+57m ElementoLab: #AGBT HR: dbSNP is mostly unannotated; problem is small control pop which leads to biased frequencies
+58m NorthernAutumn: Heidi Rehm 66 to 88% of clinically significant variants seen only in 1 family, depending on disease (88% of hearing loss for example) #AGBT
+58m genomeresearch: "game's not over yet for most genes" still so many unique muts MT @girlscientist: Rehm: other bottleneck is novel variant assessment. #AGBT
+58m ElementoLab: #AGBT HR: wants to create a universal human genomic mutation database
+58m omespeak: Most annotated genomic data in public domain is mostly wrong! Heidi Rehm. #AGBT
+58m schnablep: #AGBT Heidi Rehm, 60-80% of clinically significant variants are found in only one family.
+58m deannachurch: HR: Need to get more clinical annotation on variation in the public domain- not much data is there and some of what is there is wrong. #AGBT
+59m obahcall: Heidi Rehm speaks on sequencing in clinical environment at #AGBT
+59m ElementoLab: #AGBT HR: can be hard to discriminate clinical grade variants from non clinical grade

10 - 11am EST
+0m djschlesinger: Heidi Rehm proposing one variant database with varying levels of annotation #AGBT - great idea
+0m NorthernAutumn: Heidi Rehm has grant to create universal human mutation db so can lower mistake in public db that lead to overestimates of effects #AGBT
+0m bongopondit: This will be a huge undertaking, but very useful. RT @ElementoLab: #AGBT HR: wants to create a universal human genomic mutation database
+0m fluidigm: PREPARE amplicons for sequencing on all major next-generation sequencing systems. Learn more in Suite 285. #AGBT
+0m girlscientist: Rehm: debate on creating databases for clinical genetic data. She favors putting all into one database and marking w/curation level. #AGBT
+0m ElementoLab: #AGBT HR: many labs have agreed to share their curated variant data
+1m omespeak: Initially 9 different disease areas will be the focus of the curated variant data being developed by Rehm. #AGBT
+1m ElementoLab: #AGBT HR: GeneInsight Suite to provide genetic reports, published in Human Mutation
+1m geniachip: Heidi Rehm: dbSNP contains lots of data, but most unannotated. Need curated data in public domain! #AGBT
+2m MishaAngrist: MT @girlscientist: Rehm: Myriad still detects 10-20 new missense variants in BRCA each week, even after testing 100's of 1000's ppl. #AGBT
+2m spurim: Don't miss! Agilent's Luncheon session today as 12:10pm @ Palms Ballroom. Amazing speakers from OICR, Hubrecht, Erasmus MC! #AGBT
+2m omespeak: Variant classification changes - ~300 category changes overs the last few years. #AGBT
+2m ElementoLab: #AGBT HR: has a paper acceped about changse in variant clinical annotation in Genetics in Medicine
+3m obahcall: Rehm: discusses creating single database for clinical data, with tiered levels of curation #AGBT
+3m ElementoLab: #AGBT HR: shows a GeneInsight report screenshot
+3m NorthernAutumn: Heidi Rehm new universal human mutation db entries have levels of curation from expert 2 uncurated 2 reflect confidence in each entry #AGBT
+3m geniachip: Heidi Rehm: Solution is one variant database with various levels of annotation. Has already signed up various labs to share data. #AGBT
+4m omespeak: Heidi Rehm - database interface (GeneInsight) will inform physicians about changes in variant classification. #AGBT
+4m illumina: Heidi Rehm, Seq from CLIA perspective U41 Grant for clinical data, not easily accessible, into public domain as clin grade variant db #AGBT
+4m ElementoLab: #AGBT HR: software FDA registered
+5m NorthernAutumn: Heidi Rehm future:patient genome variants stored & proactive warnings generated as new clinically actionable info is learned #AGBT
+5m genomeresearch: H Rehm: integrate vast amt of genetic info into patient care by storing millions of variants in electronic health records #AGBT
+6m ElementoLab: #AGBT HR: GeneInsight would be hub in network between labs, databases, etc
+6m omespeak: Best way to leverage WGS to patient care will be by integrating into electronic database. Heidi Rehm. #AGBT
+7m omespeak: Also, there needs to be networking between sequence providers, academic labs, hospitals all integrated into a central hub. Heidi Rehm. #AGBT
+7m illumina: Rehm: dbSNP data mostly un-annot'd for clinical sig, most annots wrong due to small ctrl pops. Clinical lab data not in public domain #AGBT
+7m ElementoLab: #AGBT HR: GeneInsight allows sharing data, including deidentified case history
+7m djschlesinger: Partners Healthcare is doing some incredible work bringing NGS to the clinic #AGBT
+8m GenomeBiology: Labs need to share clinical data more. Rehm's new infrastructure will allow this in real time #agbt
+8m illumina: Rehm: Avg time to asses a novel variant from NGS is approx 21-119 min (dbSNP, publications, etc., plus in silico assessments #AGBT
+8m mgollery: I wish I was at #AGBT to check out the latest in sequencing technology- http://t.co/V5kBRegM
+9m omespeak: Amazing presentation by Heidi Rehm. Glimpse into the future of genome-sequencing applications in clinics and patient healthcare #AGBT
+11m omespeak: Last two talks by Heidi Rehm & Lynn Jorde shows using WGS information to treat/prevent disease is challenging but bound to happen. #AGBT
+12m ElementoLab: #AGBT Lisa Shaffer: genotype first approach to id of new chromosomal syndromes
+12m djschlesinger: Lisa Shaffer from Perkin Elmer talking about using genotyping to identify new chromosomal syndromes #AGBT
+12m MishaAngrist: RT @omespeak: Last two talks show using WGS information to treat/prevent disease is challenging but bound to happen. #AGBT
+13m EdgeBio: #AGBT next up Lisa Shaffer from Perkin Elmer. New chromosomal syndrome IDs by genotype approach
+13m girlscientist: Lisa Shaffer: Im probably giving the only non-sequencing talk at the meeting" but chromosomes still relevant! Word again. #AGBT
+13m _Gugaa_pimentel: Hoje foi engra dmaais agbt conversando na aula de mat e a prof "quietos, se nao chamo o Davyd" UAHSAHSHHAHS
+13m ElementoLab: #AGBT Lisa Shaffer: took 100 years to link Down syndrome to chr21
+13m NorthernAutumn: Lisa Shaffer 1866 Down's first described as a syndrome but genetic etiology not described until 1950s #AGBT
+14m ElementoLab: #AGBT Lisa Shaffer: several syndromes due to 10Mb+ deletions
+15m westr: Second that! RT @geniachip: Heidi Rehm: dbSNP contains lots of data, but most unannotated. Need curated data in public domain! #AGBT
+16m ElementoLab: #AGBT Lisa Shaffer: talking about Potocki-Shaffer syndrome
+16m eperlste: Clinical application of WGS to human disease is awesome but let's not forget to bring model organism genetics into 21 century, too. #AGBT
+16m ElementoLab: #AGBT Lisa Shaffer: 27 individuals from 17 families reported, visible 11p deletions
+17m NorthernAutumn: Lisa Shaffer in 80 & 90s syndromes began to be recognized as caused contigous gene deletions. #AGBT
+19m ElementoLab: #AGBT Lisa Shaffer: was using genetic mapping, now uses microarray to characterize microdeletions
+19m NorthernAutumn: Lisa Shaffer 'back in the 90s we had to build our own maps'. Taking us back to the pre-genome era....ahh memories :) #AGBT
+20m ElementoLab: #AGBT Lisa Shaffer: has database of abnormal cases and deletions (Genoglyphix)
+20m GMiadydiz: @_CaiioSilva kkkkkkk qualque dia agbt tira amr *-*
+21m illumina: Shaffer, Perkin Elmer. Many syndromes caused by chromosomal abnormalities cannot be IDd by NGS, instead need arrays. #AGBT
+21m ElementoLab: #AGBT Lisa Shaffer: can query by deletion region, will show you cases and syndroms in which it was previously found
+22m EdgeBio: #AGBT LS: Genoglyphix is a searchable database of abnormal cases
+23m ElementoLab: #AGBT Lisa Shaffer: example: 50 cases of del(1)q43q44, overlapping clinical features
+23m illumina: Shaffer: microarray analysis to id deletions. Database with 16k cases run on arrays, avail to researchers (Genoglyphix) #AGBT
+24m ElementoLab: #AGBT Lisa Shaffer: sometimes phenotypic features not obviously similar, but share same deletion
+25m schnablep: #AGBT Software (ERSA) mentioned by Lynn Jorde for estimating recent shared ancestry from sequence data: http://t.co/UqVtM76t
+25m Gavin_Oliver: Wondering how much tweaking VAAST would require to be useful for drug-response association and if this is planned future functionality #AGBT
+26m ElementoLab: #AGBT Lisa Shaffer: was not clear whether AKT3 involved in microcephaly
+26m ElementoLab: #AGBT Lisa Shaffer: her analysis of deletions in 22 microcephaly cases shows that AKT3 is the common gene
+27m westr: RT @GenomeBiology: Labs need to share clinical data more. Rehm's new infrastructure will allow this in real time #agbt #pm101
+27m NorthernAutumn: Lisa Shaffer has built db of 'gene deletion syndromes'. New patient presents - search db 2 find others w/similar phenotypes. #AGBT
+29m ElementoLab: #AGBT Lisa Shaffer: for agegenesis of corpus callosum phenotype, she found ZNF238 in minimal region of the del q43q44
+29m NorthernAutumn: Lisa Shaffer after identifying overlapping deletions b/w different patients can narrow candidate genes 4 follow up & confirmation #AGBT
+29m ElementoLab: #AGBT Lisa Shaffer: 3 genes in minimal region q43q44 for seizure phenotype
+30m ElementoLab: #AGBT Lisa Shaffer: 1 in 3 genes in critical region is HNRPU, predicted to be haploinsufficient
+32m EdgeBio: #AGBT LS: phenotypic characteristics may be subtle and variable so genotype might be only way to group and identify syndrome
+33m ElementoLab: #AGBT Lisa Shaffer: array based genotyping faster than NGS
+36m illumina: Shaffer, Whole genome arrays, small deletions can be ID'd in many patients, and overlap to find critical regions for phenotype #AGBT
+36m ElementoLab: #AGBT Lisa Shaffer: can go down to <1kb resolution by packing oligos
+39m SpunkyScientist: RT @illumina Shaffer, Perkin Elmer. Many syndromes caused by chromosomal abnormalities cannot be IDd by NGS, instead need arrays. #AGBT
+42m assemblathon: RT @djschlesinger: HiSeq 1500 will be fully upgradeable to 2500 #AGBT
+42m SpunkyScientist: RT @ElementoLab #AGBT Lisa Shaffer: array based genotyping faster than NGS
+58m zerojinx: All this talk of genotyping for new syndromes takes me back to DECIPHER https://t.co/r9FTY3T3 . Take that and add NGS. (See also DDD) #agbt

11 - 12pm EST
+0m AgilentLife: Edwin Cuppen- Hubrecht Institute and Willem van IJcken- Erasmus MC will speak at our Featured Luncheon today at 12:10 Palms Ballroom. #AGBT
+2m bkmacy: @illumina + @ING_SYS working together to deliver the most accurate data, analysis and interpretation for cancer studies, #AGBT
+11m bkmacy: Dr. van der Spek's work with @CompleteGenomic and @ING_SYS resulted in the ID of a novel causal variant for craniosynostosis, #AGBT
+16m EdgeBio: #AGBT Darrell Dinwiddie, Children's Mercy talks about clinical testing of severe childhood diseases with target enrichment and NGS
+17m djschlesinger: Darrell Dinwiddie discussing a 600 gene panel at Children's Mercy Hospital #AGBT
+17m deannachurch: Darren Dinwiddie talking about clinical seq for >600 childhood diseases. #AGBT
+19m girlscientist: Children's Mercy Hospital, Pediatric Genomic Medicine, in Kansas City is hiring. See/contact Darrell Dinwiddie. #AGBT
+19m ElementoLab: #AGBT Darrell Dinwiddie: there are 7K Mendelian diseases
+20m djschlesinger: Dinwiddie: 7043 mendialian diseases, 3328 with known molecular basis #AGBT
+22m ElementoLab: #AGBT Darrell Dinwiddie: testing >600 disease at a time, $1000 per patient, 30K patients annually, turnaround 4 wks, 90% get diagnosis
+22m finchtalk: #AGBT Darrell Dinwiddie on pediatric medical sequencing. Diseases related to rare mutations are a reason many kids visit children's hosps.
+22m djschlesinger: Dinwiddie: Sanger sequencing costs ~$10k testing for 1-10 diseases, ~$1k for 600 diseases using NGS #AGBT
+23m ElementoLab: #AGBT Darrell Dinwiddie: semi automated 96 samples testing platform
+24m bongopondit: Dinwiddie - expecting that genomic medicine will reduce cost by 10x, look at 60x more diseases, 10x increase in patients tested. #AGBT
+24m NorthernAutumn: Dinwiddie advocating testing for all recessive diseases (in kids) to save $, time and help get right treatment @ right time. #AGBT
+24m ElementoLab: #AGBT Darrell Dinwiddie: testing 8K genomic regions, 526 genes
+24m cheyennexo3: AGBT
+24m ElementoLab: #AGBT Darrell Dinwiddie: 97.5% of targets have >16X coverage
+24m omespeak: Dinwiddie - expecting that genomic medicine will reduce cost by 10x, look at 60x more diseases, 10x increase in patients tested. #AGBT
+25m finchtalk: #AGBT DD current approaches cost $10k, sample few genes, have 50% success. Genome potential: sample 600 genes, $1000 cost, 90% success
+25m omespeak: Also, shorter turnaround time and almost 2-fold increase in diagnosis using genomic medicine vs traditional testing. Darrell Dinwiddie #AGBT
+25m genomeresearch: Estimation of recent shared ancestry (ERSA) also from L Jorde http://t.co/AzC6Plgf #AGBT
+25m ElementoLab: #AGBT Darrell Dinwiddie: for ethical reasons, they need to limit what they discover and report
+26m bongopondit: RT @ElementoLab: #AGBT Darrell Dinwiddie: for ethical reasons, they need to limit what they discover and report
+26m djschlesinger: Dinwiddie: need to limit what we look at in the genomes of children, don't look at carrier status #AGBT
+26m girlscientist: Dinwiddie going over ethics of genetic testing for children. They have created "orderly interface" to manage. Hmmm. #AGBT
+26m EdgeBio: #AGBT DD: test >600 diseases at once with a turnaround of 4 weeks and a diagnosis rate of 90%
+26m omespeak: RT @ElementoLab: #AGBT Darrell Dinwiddie: for ethical reasons, they need to limit what they discover and report
+26m NorthernAutumn: Dinwiddie test for over 600 diseases but do not report on adult onset carrier status as no benefit to child #AGBT
+27m ElementoLab: #AGBT Darrell Dinwiddie: showing screenshot of interface for ordering test
+27m girlscientist: whoops sorry that should have been "ordering interface" from Dinwiddie, based on phenotype /clinical findings. My typo! #AGBT
+27m ElementoLab: #AGBT Darrell Dinwiddie: need to enter clinical symptoms
+27m ElementoLab: #AGBT Darrell Dinwiddie: systems comes up with genes to test based on clinical features
+28m ElementoLab: #AGBT Darrell Dinwiddie: gene-feature matching based on SNOMED terms
+28m EdgeBio: #AGBT DD: target 526 genes + mt genome with Illumina TruSeq enrichment. Generate 4Gb of data per sample
+29m ElementoLab: #AGBT Darrell Dinwiddie: correct gene nominated in 286/290 test cases
+30m fluidigm: MULTIPLEX 96 different samples in a single sequencing run. Learn more in Suite 285. #AGBT
+30m ElementoLab: #AGBT Darrell Dinwiddie: align reads with GSNAP, can detect up to 10kb deletions, 60pb insertions
+30m CompleteGenomic: Catch our own Jason Laramie presenting on family-based studies, today in the #AGBT Complete Suite at 12:45 pm
+31m ElementoLab: #AGBT Darrell Dinwiddie: there are 6 ACMG categories of variants
+31m NorthernAutumn: Dinwiddie looked @ 290 patients who were referred to gene testing based on SNOMED and 286 got correct gene test based on symptoms #AGBT
+31m ElementoLab: #AGBT Darrell Dinwiddie: cat 1-4 presented in prioritized manner according to number of symptoms matched
+32m ElementoLab: #AGBT Darrell Dinwiddie: insertions and CNV account for 5-20% of disease causing variants
+33m ElementoLab: #AGBT Darrell Dinwiddie: looks for deletions by looking at local reduction in normalized aligned reads
+33m ElementoLab: #AGBT Darrell Dinwiddie: found a 966bp hets deletion in CLN3 this way
+33m illumina: Now #AGBT Darren Dinwiddie, Childrens Mercy Hospital, non-profit, 15k in-patient admiss, 335k outpatient visits, 144k urgent care visits
+33m NorthernAutumn: Dinwiddie 5-20% of disease caused by CNV but analysis pipelines have difficulty detecting #AGBT
+34m spurim: #AGBT Don't miss! Agilent's Luncheon session today as 12:10pm @ Palms Ballroom. Amazing speakers from OICR, Hubrecht, Erasmus MC!
+34m kimwhit: Advances in #Genome Biology and Technology(AGBT) day 1 tweets at http://t.co/bR8rDybi Thx @pathogenomenick @lexnederbragt
#genomics #in
+35m ElementoLab: #AGBT Darrell Dinwiddie: validation of 700 samples nearly complete
+35m omespeak: Darrell Dinwiddie: validating 700 samples, including ethnic diversity (very important IMO). #AGBT
+36m ElementoLab: #AGBT Darrell Dinwiddie: his first 2 patients, 5 years no molecular diagnosis, >$23K
+36m NorthernAutumn: Dinwiddie in midst of 3 phase clinical validation of their testing pipeline w/ 700 samples of varying ethnicities & disease status #AGBT
+36m ElementoLab: #AGBT Darrell Dinwiddie: found causal gene in APTX
+37m ElementoLab: #AGBT Darrell Dinwiddie: APTX is actionable, treatment with CoQ10 started
+37m bioinfosm: #agbt Dinwiddie from CMH: a patient for 5yr and >$23k tests with no diagnostic .. sanger confirmed APTX mutation found using #NGS
+39m NorthernAutumn: Dinwiddie Ex of where diagnosis has changed treatment (APTX caused coQ10 deficiency) & lead to child regaining mobility. Yay! #AGBT
+39m ElementoLab: #AGBT Darrell Dinwiddie: good question, how do you deal with genes with IP issues ?
+39m ElementoLab: #AGBT Darrell Dinwiddie: did not deal with that type of situation yet
+39m girlscientist: Chad Nusbaum asks Dinwiddie how they deal with gene testing in genes that have IP. Unfortunately, no clear answer. #AGBT
+40m EdgeBio: #AGBT DD on power of genomic medicine: first 2 patients that came to them had gone through $23K in testing over 5 yrs with no Dx...
+40m omespeak: They haven't dealt with it yet. RT @ElementoLab: #AGBT Darrell Dinwiddie: did not deal with that type of situation yet
+40m ElementoLab: #AGBT Rong Chen: published clinical assessment of Steve Quake's genome a few years ago
+40m bongopondit: They haven't dealt with it yet. RT @ElementoLab: #AGBT Darrell Dinwiddie: good question, how do you deal with genes with IP issues ?
+40m EdgeBio: #AGBT DD: Genomic Med was able to provide Dx and were able to start treatment
+41m MishaAngrist: RT @girlscientist: Chad Nusbaum asks Dinwiddie how they deal with gene testing in genes that have IP. Unfortunately, no clear answer. #AGBT
+41m illumina: Dinwiddie: Example, 2 patients, hospital for 5 yr spent $20K+ on neg genetic tests. NGS found a mut in APTX, conf w/ sanger. #AGBT
+42m omespeak: #AGBT Rong Chen: how to calculate genetic risk of a particular disease across populations through the world.
+42m ElementoLab: #AGBT Rong Chen: now working in type 2 diabetes
+42m NorthernAutumn: Rong Chen T2D genetic risk decreased as people migrated out of Africa till lowest risk in SE Asia and America #AGBT
+42m girlscientist: Rong Chen: showed graph from Eric Corona at Stanford with claim that T2D genetic risk decreased as human migrated over time. #AGBT
+43m ElementoLab: #AGBT Rong Chen: used Hapmap3, HGDP, Complete Genomics to find T2D risks
+44m ElementoLab: #AGBT Rong Chen: manually curated all disease associated SNPs from literature
+45m EdgeBio: Were excited to be at #AGBT w/ our partner @AGXP. Learn about this #genomics competition at todays poster session.
+45m ElementoLab: #AGBT Rong Chen: each SNP was annotated along 100+ features
+45m illumina: Dinwiddie: ~7k known mendelian diseases, 3k with known molecular basis. Together affect about 3-4% of children. #AGBT
+45m ElementoLab: #AGBT Rong Chen: >100,00 SNPs for 2400 diseases
+45m illumina: Dinwiddie: Why test for all recessive diseases? Timely Dx rules out diseases & avoid unnecessary treatments #AGBT
+45m ElementoLab: #AGBT Rong Chen: published in PLoS ONE 2 years ago
+46m ElementoLab: #AGBT Rong Chen: 12 replicated and haplotype independent SNPs for T2D
+46m NorthernAutumn: RongChen 2 interpret gt disease risk need 2 know risk alleles, pops studied, gt freq case:control & strand dir where risk alleles rep #AGBT
+46m omespeak: 12 independent SNPs for T2D replicated over five ethnic groups #Rong Chen #AGBT
+46m surt_lab: Thanks mom and dad :) MT @girlscientist Lynn Jorde : Each (human) gamete contributes about 35 new variants. #AGBT
+47m ElementoLab: #AGBT Rong Chen: several SNPs causal across several ethnic groups
+47m iontorrent: Check out the Ion Proton Sequencer at AGBT: http://t.co/wjGqu6cy via @youtube
+47m girlscientist: Rong Chen describing Personalis and their work on manual curation of SNPs as in this paper http://t.co/hjXtfkib #AGBT
+47m omespeak: T2D risk allele - highest frequency in African (inlc African-Amercans), lowest in Asian. Rong Chen #AGBT
+48m DNAsizing: Sweets in the suite. Covaris Candy Shop Now Open! Sage Science lanai 286 until 5 pm #AGBT
+49m ElementoLab: #AGBT Rong Chen: T2D risk allele frequencies decrease with igration
+49m ElementoLab: #AGBT Rong Chen: finding coming in plos genetics
+50m ElementoLab: #AGBT Rong Chen: T2D risk alleles show higher freq in SubSaharan Africa
+51m surt_lab: So JBS Haldane almost got it right #standingontheshouldersofgiants RT @ElementoLab: #AGBT LJ: 2.0e-8 per base pr generation
+51m ElementoLab: #AGBT Rong Chen: in prev tweet, igration -> migration
+52m ElementoLab: #AGBT Rong Chen: why would T2D risk freq decrease when humans migrate ?
+52m illumina: Rong Chen, Personalis, Manual curation of disease assoc SNPs from 800 pubs- Varimed (VARiants Informing Medicine) database #AGBT
+53m ElementoLab: #AGBT Rong Chen: mismatch bet genetic and environment upon migration ?
+53m ElementoLab: #AGBT Rong Chen: energy storage needs change ?
+53m ElementoLab: #AGBT Rong Chen: just hypotheses
+54m ElementoLab: #AGBT Rong Chen: calc a likelihood ratio of disease for personal genome from multiple allele risks
+55m NorthernAutumn: RongChen why T2D risk allele freq change w/human mig? Thrifty gene hypo:diff energy req when migrating OR mismatch b/w gene&enviro #AGBT
+57m CRIgenomics: James is now at #AGBT. The next four days should be fun.
+57m ElementoLab: #AGBT Rong Chen: genetic risk prediction consistent with known ethnic group different risks
+57m ElementoLab: #AGBT Rong Chen: have a Genetic Risk World Map web application
+58m omespeak: Mapping genetic risk of disease across the world: http://t.co/CSa06ZrX Rong Chen. #AGBT
+59m girlscientist: The map from Rong Chen et al. was covered as news in Science magazine here: http://t.co/WuhWZpsE #AGBT
+59m GenomeBiology: Genetic risk of T2D decreased as humans migrated from africa #agbt
+59m illumina: Rong Chen: T2D risk SNP, rs1196205_C-TCF7L2 highest in African pop. Why do daibetes risk alleles decrease when humans migrate? #AGBT
+59m NorthernAutumn: RongChen 'More GWAS in Africans and Indian Asians urgently needed.' #AGBT
+59m CRIgenomics: #AGBT Clinical Translation of Genomics session: Panels for targeted sequencing, pipelines for analysis of mutations, Sanger validation.
+59m finchtalk: #AGBT Rong Chen, genetic risk map of the world http://t.co/XDad805M
+59m omespeak: "More GWAS in diverse populations especially African and Indian Asian are *uregently* needed". Rong Chen (emphasis mine). #AGBT

12 - 1pm EST
+0m iontorrent: "More GWAS in diverse populations, especially African & Indian Asian are urgently needed" to accurately predict genetic risk Rong Chen #AGBT
+0m illumina: Rong Chen: More GWAS urgently needed in African and Indian asian populations. #AGBT
+1m Symbionticism: #AGBT pic. Ion Torrent has a well crafted presence. Not only a beach bus but coffee holders too. Well done. http://t.co/uB2ml7ua
+3m bffo: Rong Chen is .@rongchenbioinfo #agbt
+10m intrepidbio: "Non- and Synonymous Coding SNPs" http://t.co/ljEltFH1 by @RongChenBioinfo. We take both SNP & NGS data, @PersonalisInc. @ElementoLab #AGBT
+10m intrepidbio: "Non- and Synonymous Coding SNPs" http://t.co/ikdhHhei by @RongChenBioinfo. We take both SNP & NGS data, @PersonalisInc. @ElementoLab #AGBT
+12m westr: RT @illumina: Dinwiddie: ~7k known mendelian diseases, 3k with known molecular basis. Together affect about 3-4% of children. #AGBT #pm101
+13m westr: MT @ElementoLab: #AGBT Rong Chen: >100,000 SNPs for 2400 diseases #pm101
+14m westr: RT @illumina: Dinwiddie: Why test for all recessive diseases? Timely Dx rules out diseases & avoid unnecessary treatments #AGBT #pm101
+16m westr: RT @girlscientist Rong Chen describing Personalis & their work on manual curation of SNPs as in this paper http://t.co/7c83OUx0 #AGBT #pm101
+25m illumina: #AGBT poster 48 Enhanced RiboZero tech: Removal of rRNA & Improved RNA-Seq lib quality
+28m westr: RT @ElementoLab: #AGBT Rong Chen: calc a likelihood ratio of disease for personal genome from multiple allele risks #pm101 causal/protective
+30m illumina: #AGBT poster 119 PvuRts1I, MspI, & T4-betaGT: Tools for bisulfite-free ID of epigenetic cytosine modifications
+30m fluidigm: RT @EdgeBio Check out Views From Edge Blog: #AGBT Marco Island Never Gets Old @dgaalaas http://t.co/HgcXgIT2 >Nice synopsis of conference
+30m AgilentLife: Stop by to see Posters: 70, 108, 161 and 266 at the 1pm #AGBT Poster Session. Learn about #HaloPlex #Methyl-Seq & more http://t.co/ec5AzqGt
+35m westr: RT @omespeak: Mapping genetic risk of disease across the world: http://t.co/B2qiCGeE Rong Chen. #AGBT #pm101
+37m westr: RT @girlscientist: The map from Rong Chen et al. was covered as news in Science magazine here: http://t.co/FpknbiUw #AGBT #pm101
+41m agxp: Dont forget to learn more about our #genomics competition during todays poster session at #AGBT! 1:10 pm EST; poster 170.
+46m Medco: Are you attending #AGBT? Stop by the poster session today and tomorrow to learn more about Medco's sponsorship of the @AGXP!
+46m nygenome: For those at #AGBT, our first #nygenome poster session is about to begin. Find us in Collier Hall #173. http://t.co/95pn6py8
+49m nygenome: Gearing up for our #AGBT Feinstein Institute announcement & reception with @Ilumina at 5pm -- read more about it at http://t.co/0RWEkWlg
+50m LucigenCorp: Low bias, reduce chimera activity with NxSeq Technology. See Lucigen poster http://t.co/6l6KINCM @ #AGBT.
+53m intrepidbio: The map from @RongChenBioinfo etal. was covered as news in @sciencemagazine magazine here: http://t.co/cXjgv4KA #AGBT via @girlscientist.
+54m rtginvestigator: Emerging case evidence of clinical sequencing and genomic medicine #AGBT @Erika_Check @NatureNews http://t.co/4YDYgpvC
+58m ING_SYS: Don't be left out, see what everyone at #AGBT is talking about. Lanai Suite 179 Variant Analysis Demo. http://t.co/uF9DtjHI

1 - 2pm EST
+0m agxp: RT @completegenomic: Safe travels to everyone heading to #AGBT, we'll see you there!
+5m RainDanceTech: At #AGBT? Come by Lanai Suite #287 to see our new ThunderStorm System; the new standard in targeted sequencing. http://t.co/ObAtbF8l
+11m illumina: Real data from HiSeq 2500. Read the newest application note #AGBT #keepingitreal http://t.co/Dd5cvpU1
+16m NEBiolabs: Come check out a few posters by NEB scientists at the #AGBT poster sessions starting now in Collier Hall! http://t.co/sEdSZFDF
+17m GoldenHelixInc: #AGBT Hope to see you @CompleteGenomic reception with Dr. Christensen from Golden Helix at 5 pm tonight!
+20m EpicentreBio: Perspectives from the @Illumina User Group Meeting #AGBT http://t.co/4v1Gjzvv
+20m SEQanswers: Wow. Only 2 lanes/FC...and 39h for 2x151 run MT @illumina: Real data from HiSeq 2500. Read the newest app note #AGBT http://t.co/faj1P7Gq
+22m dnanexus: Come and join DNAnexus in the Complete Genomics Suite tonight 5-7 p.m. at #AGBT in the Everglades suite http://t.co/US5fPsFu
+24m EpicentreBio: MT @illumina: Real data from HiSeq 2500. Read the newest application note #AGBT http://t.co/umXEbRS9
+46m agxp: At AGBT conf.? Meet @XPRIZE Sr. Dir. Grant Campany @ poster location #170 now! #AGBT more at: http://t.co/UV2rUBaq http://t.co/iDcpE1TI
+46m nanopore: Curious about how to use nanopores to analyse proteins or miRNA? Go to our poster, Dr Dan Turner will tell all - poster 360 #AGBT
+54m pathogenomenick: @massgenomics Hey Dan, welcome to Twitter. Don't forget to use the AGBT hashtag in your tweets so people can find them easily!

2 - 3pm EST
+0m fluidigm: OBTAIN reads from both ends with single-read sequencing. Learn more in Suite 285. #AGBT
+2m CompleteGenomic: Dont miss Srinka Ghosh presenting on our Cancer Sequencing Service today in the #AGBT Complete Suite at 3:45 pm
+4m deannachurch: If you want to see software we are developing for exploring variant data, see me at #AGBT (in lower lobby near posters now).
+5m notSoJunkDNA: @girlscientist @nparmalee Check this out: http://t.co/b5uBCa0d #nygenome #AGBT
+18m lipscombe1: Seems to be quite a bit of platform sparring coming out #AGBT #DNA #Sequencing
+42m EdgeBio: #AGBT afternoon session about to kick off with Goncalo Abecasis from U of Mich talking about sequencing 1000s of human genomes.
+43m ElementoLab: #AGBT Goncalo Abecasis: sequencing to study complex traits
+43m ElementoLab: #AGBT Goncalo Abecasis: will use LDL genetics to illustrate quantitative trait genetics
+43m deannachurch: Annnnnnndddddd we're back: Goncalo Abecasis talking about sequencing 1000s of people. #AGBT
+44m Personal_RX_WI: #AGBT We just had lunch with the fine people at @Roche_com. Afternoon session of Genomic studies. Right now " Sequencing 1000s of Genomes"
+44m ElementoLab: #AGBT Goncalo Abecasis: several variants linked to low or high LDL levels
+46m ElementoLab: #AGBT Goncalo Abecasis: found GALNT2 in GWAS, not clear what link to HDL was initially
+47m ElementoLab: #AGBT Goncalo Abecasis: mouse studies show strong effect on HDL
+47m bioinfosm: #agbt Abecasis from UMich: found an older set of slides on sequencing 1000s of genomes = http://t.co/1AmtCB55 #ngs
+48m schnablep: #AGBT Goncalo Abecasis: Sequencing to decipher complex traits. Rare variants have on average larger effects than common variants.
+49m ElementoLab: #AGBT Goncalo Abecasis: talks about the amount of rare variation in human genome
+49m ElementoLab: #AGBT Goncalo Abecasis: 400K nonynonymous variants in NHLBI seq project, 57% found in 1 individual only
+50m westr: Gr8 choice! RT @ElementoLab: #AGBT Goncalo Abecasis: will use LDL genetics to illustrate quantitative trait genetics #pm101
+50m girlscientist: Goncalo Abecasis: early results from large exome seq project = 57% of variants seen are singletons. #AGBT
+52m ElementoLab: #AGBT Goncalo Abecasis: because there are so many rare variants, could explain a very large fraction of phenotypic variation
+53m ElementoLab: #AGBT Goncalo Abecasis: early results from NHLBI exome study
+53m ElementoLab: #AGBT Goncalo Abecasis: selected 400 individuals with extreme LDL levels
+55m ElementoLab: #AGBT Goncalo Abecasis: tally up all variants with max MAF in a given gene ... basically one test per gene
+56m ElementoLab: #AGBT Goncalo Abecasis: found a few potential associations this way
+56m illumina: Abecasis. Why study rare variants? From exome seq 12K individs, many rare functional vars.discovered. Non-syn muts at higher freq. #AGBT
+56m ElementoLab: #AGBT Goncalo Abecasis: SardiNIA WGS study
+56m obahcall: Goncalo Abecasis on sequencing from ESP and Sardinia at #AGBT
+57m ElementoLab: #AGBT Goncalo Abecasis: seq 1700+ individuals at >3.7X coverage
+58m ElementoLab: #AGBT Goncalo Abecasis: key is to select the individuals to sequence, e.g grandparents in families
+58m froggleston: Like cameraphones at gigs, I keep finding myself reading tweets about the talk I'm actually in. Sardinian rare variants! #agbt

3 - 4pm EST
+0m ElementoLab: #AGBT Goncalo Abecasis: draft genome of key individuals, genotype relatives, then association study
+1m illumina: Join us for a cocktail now through 7pm in the Illumina Lounge (Capri Ballroom 2/3), and chat with our experts. #AGBT
+1m ElementoLab: #AGBT Goncalo Abecasis: 1 locus was only found by sequencing Q39X in HBB
+2m ElementoLab: #AGBT Goncalo Abecasis: Q39X HBB protects from malaria in Sardinia
+2m lykkebak: Goncalo Abecasis talks about Sardinia sequence studies, whole genome sequencing #AGBT http://t.co/g5XJ5kFQ
+2m ElementoLab: #AGBT Goncalo Abecasis: other genes like APOE, APOB, SIRT1 etc previously found
+3m ElementoLab: #AGBT Goncalo Abecasis: HBB was missed on GWAS because in a region hard to impute, end of chromosome and very population specific
+4m lykkebak: Abecasis: How is sequencing progressing... #AGBT http://t.co/ZzYGAHuc
+4m nygenome: Thanks to all who attended our #AGBT poster session. We'll be back at Collier #173 Fri 4:30-6:00. http://t.co/95pn6py8 http://t.co/i6YhvRCv
+4m CompleteGenomic: Food, drink, demos and cheer -- tonight at the #AGBT Complete Suite from 5-7!
+4m pathogenomenick: Who are we expecting announcements from at #AGBT this year apart from @nanopore ?
+5m ElementoLab: #AGBT Goncalo Abecasis: benchmarked methods to call SNPs
+5m ElementoLab: #AGBT Goncalo Abecasis: each SNP calling method good at something, all methods good on average
+6m ElementoLab: #AGBT Goncalo Abecasis: consensus of 3 SNP calling methods worked bes, errors decreased by 40%
+6m deannachurch: GA: three calls sets on data, hard to say which was best (depends on metric) but taking the consensus set was the best. #AGBT
+7m ElementoLab: #AGBT Goncalo Abecasis: designed SVM-based classifiers to filter variants
+8m IanGoodhead: @pathogenomenick: What ever came of that ABI 3rd gen company? Was it Visigen? #AGBT
+8m deannachurch: AG: Making the important point that the entire genome is not accessible to current sequencing technology. #AGBT
+9m omespeak: RT @deannachurch: AG: Making the important point that the entire genome is not accessible to current sequencing technology. #AGBT
+9m obahcall: Abecasis: how much of the genome are we reaching with whole genome sequencing? #AGBT
+9m ElementoLab: #AGBT Goncalo Abecasis: now talking about 1000 Genomes, build integrated maps with SNPs, indels, dels
+9m ElementoLab: #AGBT Goncalo Abecasis: 98.5% SNPs validate, indels not as good
+9m deannachurch: AG: 1000genomes data, can validate 98.5% of SNPs but only 70% of indels. #AGBT
+10m ElementoLab: #AGBT Goncalo Abecasis: 10 samples account for 200K indel errors
+10m obahcall: Abecasis: estimate accessible 80-85%, in 2011 94-95% of reference #AGBT
+11m froggleston: Mediterranean low cholesterol down to genetics. Flora spread share price plummets. #agbt
+12m Massgenomics: Abecasis: Variant calling accuracy improves with more samples and when consensus of multiple callers is taken. #AGBT
+12m obahcall: Abecasis: the challenge of indels in 1KG.. .10 samples account for 5% of indels, very high indel error rate #AGBT
+13m deannachurch: Up next @ewanbirney to talk about the ENCODE project. #AGBT
+13m ElementoLab: #AGBT Ewan Birney: ENCODE project to annotate functional elements in human genome
+14m ElementoLab: #AGBT Ewan Birney: tweets not allowed
+14m deannachurch: @ewanbirney paper under review so can't tweet about science. #AGBT
+15m illumina: Abecasis, low pass sequencing of Sardinian population.By selecting 3 out of a family, can inform more thanks to inheritance. #AGBT
+15m nygenome: Thanks to all who attended our #AGBT poster session. We'll be back at Collier #173 Fri 4:30-6:00.... http://t.co/FUQJ2YIB
+15m girlscientist: Poor @ewanbirney has just told us that we can tweet his talk except not any science as paper is under review. #AGBT
+15m finchtalk: #AGBT Ewan Birney on super secrete encode project, no tweeting on the science.
+18m lykkebak: Nice to see a #DTU poster at #AGBT: The future of epidemiology is genomic... http://t.co/bwuqoD6M
+18m lykkebak: Ewan Birney: you can tweet, but please don't tweet any of the science... ;) ENCODE: Understanding Our Genome #AGBT http://t.co/r8w7h2eg
+18m PacBio: At #AGBT ? Come to Palms Ballroom at 5 PM for Tasty Dinner & Provocative Panel Chat led by Eric Schadt on Infectious Disease in 2030
+19m girlscientist: Can tweet that Flo Pauli of @hudsonalpha was one of the six data wizards given a shout out by Ewan for making ENCODE happen. #AGBT
+20m illumina: #AGBT Workshop: Introducing the HiSeq 2500 & Latest MiSeq Improvements -- starts in 10 min, Illumina Lounge (Capri Ballroom 2/3)
+20m gabecasis: Let's tweet about the design of Birney slides. Some look crowded. #AGBT #NoScience #TopSecret
+21m schnablep: #AGBT Speaker has no science spoiler tweet policy. Perhaps spkrs shouldn't present topics @ lg conferences they don't want people 2 discuss?
+21m EpicentreBio: RT @deannachurch: AG: 1000genomes data, can validate 98.5% of SNPs but only 70% of indels. #AGBT
+21m gabecasis: Encode is "bloody"! Details top secret. #AGBT #TopSecret
+23m GenomeBiology: Can't tweet about science of ENCODE. EB: genome is a big place #agbt
+25m malachigriffith: MindMap for: "large scale sequencing in a clinical environment" http://t.co/lJMx2kQ7 #AGBT
+25m girlscientist: Look like broccoli to me. With some dessert. RT @gabecasis: Let's tweet about the design of Birney slides. Some look crowded. #AGBT
+26m ljthomps4214: Ewan Birney says sequencing technology cost to analyze 1% of ENCODE regions in 2007 dropped enough to cover 100% of genome about 4X. #AGBT
+28m malachigriffith: If you don't use MindMaps yet, check out FreeMind. http://t.co/zRxm1Dpq #AGBT
+30m fluidigm: ELIMINATE the need for paired-end read sequencing. Learn more in Suite 285. #AGBT
+32m froggleston: No tweets eh? Well I can confirm for those in the blackout that EBs talk on ENCODE is chock full of stuff about some bits and bobs. #agbt
+33m girlscientist: And now @michaelhoffman getting a shoutout from @ewanbirney! But I can't tell you why. #AGBT
+34m ElementoLab: #AGBT Ewan Birney: scoop: promoters exist and they are important
+35m CrapBio: are we alowed to skypechat about Ewan Birney #agbt ? are we alowed to talk about it in the bar later?
+36m assemblathon: RT @SEQanswers: Wow. Only 2 lanes/FC...and 39h for 2x151 run MT @illumina: Real data from HiSeq 2500. #AGBT http://t.co/nTjv1ADN
+40m girlscientist: If you're interested in #AGBT and not following @CrapBio: do. But I sure wish they hadn't given me visual image of group skinny-dipping.
+43m girlscientist: All you UCSC users of ENCODE data, @ewanbirney encourages you to "fly European" every so often and use Ensembl too! #AGBT
+46m maureen_mack: @medicalcollege team from @Personal_RX_WI hanging with top genomics experts at #agbt
+50m NextBio: At #AGBT? Stop by our poster #370 on identifying potential tumor biomarker in TCGA glioblastoma data!
+59m CRGenomica: @CompleteGenomic: Today at #AGBT we announced our Biological Discovery Software Partners Program . Read more: http://t.co/jiKHkxkN

4 - 5pm EST
+0m EdgeBio: #AGBT Update #1 via @dgaalaas http://t.co/JdhzqtiF
+2m CompleteGenomic: Great interactive presentations today in the #AGBT Complete Suite! http://t.co/KkCD3gs7
+9m deannachurch: Chuck Perou up to discuss gene expression profiling and molecular classification of breast cancer. #AGBT
+12m carolzanholo: @thaynaismael como protesto cansa agbt passa no mc depois pra come um lanchinho eioheioheioheih
+13m ElementoLab: #AGBT Charles Perou: works on breast cancer
+14m ElementoLab: #AGBT Charles Perou: FFPE has short degraded mRNA fragments (<150nt), not compatible with Agilent array
+17m ElementoLab: #AGBT Charles Perou: developed a qPCR assay based on 50 genes to predict breast cancer subtype
+17m illumina: Charles Perou, Univ North Carolina Chapel Hill. Molec classification of breast tumors using gene expression profiling. #AGBT
+19m illumina: Perou: Started with homemade cDNA arrays ~10 y ago to develop prognostic markers for breast ca, moved to Agilent arrays #AGBT
+19m ElementoLab: #AGBT Charles Perou: prognostic tests use both old biomarkers (eg tumor size) and genomic ones (qPCR profile distance)
+21m ElementoLab: #AGBT Charles Perou: low predicted risk patient do not necessarily need chemo
+22m iontorrent: Ion Torrent Sequencing seminar at 5:20, Hilton Grand Ballroom: Jonathan Rothberg, Sean Grimmond, Marilyn Li, Tim Triche, Niall Lennon #agbt
+22m ElementoLab: #AGBT Charles Perou: use the c-index to select models that best predict patient outcome
+23m girlscientist: Chuck Perou says that genomics is adding to ability to predict prognosis in breast cancer, but no surprise: more data = better models. #AGBT
+24m irondiet: OpGen | Whole Genome Chromosome Mapping, AGBT: Gaithersburg, Md.February 14, 2012 OpGen, Inc., a whole-genome ... http://t.co/dfEFXe7W
+24m ElementoLab: #AGBT Charles Perou: FFPE great because do not need to wait for outcome of clinical trial - 10 years follow up for patients with diag FFPE
+25m ElementoLab: #AGBT Charles Perou: found set of patients with extremely good survival when given tamoxifen alone
+26m ElementoLab: #AGBT Charles Perou: qPCR great but laborious
+26m ElementoLab: #AGBT Charles Perou: used Nanostring nCounter
+28m ElementoLab: #AGBT Charles Perou: nCounter counting individual RNA molecules, no ampification, 1 tube hyb, up to 100 genes, 100-200ng total RNA
+29m ElementoLab: #AGBT Charles Perou: used qPCR, Nanostring, microarray on 28 samples; concordant in 24/28 cases
+29m morinryan: Don't forget #AGBT attendees: @apfejes will post your talk summaries on his blog (fejes.ca) if you provide them to him
+30m froggleston: I am both heartened and strangely disappointed that I haven't found the usual conference singleton poster comprising 100% Comic Sans #agbt
+30m ElementoLab: #AGBT Charles Perou: PAM50 panel (50 genes) tested by independent group, worked well
+31m ElementoLab: #AGBT Charles Perou: 850 breast tumors assayed by RNAseq for TCGA
+32m Massgenomics: Chuck Perou: qPCR, of FFPE, Nanostring of FFPE, and Agilent array of fresh frozen all concordant for 50-gene expression profile. #AGBT
+33m ElementoLab: #AGBT Charles Perou: conventional rDNA depletion does not work on FFPE
+34m illumina: Perou: Moved to RNA-Seq on #HiSeq. 850 breast tumors, 2 x 50 bp part of TCGA #AGBT
+34m ElementoLab: #AGBT Charles Perou: DSN normalization depletes highly abundant species, works on 150nt size FFPE RNA
+34m lykkebak: Charles Perou: Molecular classif of breast tumors using gene expression profiling.. into clinical practices #AGBT http://t.co/4T9tAcSi
+35m iontorrent: "Every tumor is an individual" -Chuck Perou's excellent breast cancer gene expression profiling talk #AGBT
+36m ElementoLab: #AGBT Charles Perou: mRNA-seq fresh vs DSN RNA-seq FFPE, r=0.89
+36m genomeresearch: Breast cancer genomics now at #AGBT. For more, see special issue @genomeresearch http://t.co/xLW14lWc
+37m girlscientist: Shameless plug FTW! RT @genomeresearch: Breast cancer genomics now at #AGBT. For more, see special issue http://t.co/VRX3QPn0
+37m ElementoLab: #AGBT Charles Perou: did mRNA-seq on >2000 tumors for TCGA ! not only breast cancer
+39m Massgenomics: Chuck Perou: UNC has RNA-seq data for 2000+ TCGA tumors. Come and get it! #AGBT
+39m iontorrent: Gene expression data together with standard pathology parameters is best. Will need to combine various mol assay types -Chuck Perou #AGBT
+39m girlscientist: Perou: the development of distributed clinical assays requires commitment from researcher and their technology provider. #AGBT
+40m girlscientist: RT @morinryan: Don't forget #AGBT attendees: @apfejes will post your talk summaries on his blog (fejes.ca) if you provide them to him
+40m illumina: Perou, rRNA in FFPE samples degraded so ribo capture may not work- but you do get to skip fragmentation... #AGBT
+42m deannachurch: Don't forget the tweetup tomorrow night in the lobby bar after the last evening session! @girlscientist will be there! and @bffo too! #AGBT
+44m deannachurch: Arend Sidow is up next to talk about breast cancer progression but no tweeting. #AGBT
+44m lykkebak: Arend SIdow: No tweeting... #AGBT
+49m girlscientist: RT @deannachurch: Don't forget the tweetup tomorrow night in the lobby bar after the last evening session! #AGBT
+50m girlscientist: Skipping parties tonight #AGBT to finish my talk. Y'all have fun without me and keep an eye on the crazy journal editors who are here.
+54m nygenome: Want to hear the latest from #nygenome & @Illumina at #AGBT? Join us in Capri Ballroom 2/3 at 5pm! Signature cocktails await! :-)
+56m schip: Given multiple somatic changes in a tumor should be "Every tumor is multiple individuals" @iontorrent: "Every tumor is an individual" #AGBT
+59m omespeak: Ion Torrent or PacBio - which dinner are you attending? (wishing I could do both, but headed for the Ion Proton sighting) #AGBT

5 - 6pm EST
+2m girlscientist: Young scientists at #AGBT: getting to know journal eds is one of the best ways to learn publishing tips. At least seven are here. Say hi!
+8m NBlow: Missing AGBT this year - but wonderful the volume of Tweets coming out of the conference!
+9m CompleteGenomic: Another interesting presentation today in the #AGBT Complete Suite, if you missed out see you on Friday! http://t.co/ORyecHeW
+11m obahcall: @girlscientist young (in any sense) scientists please do say hi :) at #AGBT
+15m malachigriffith: Classification of Breast Tumors Using Gene Expression Profiling And its Translation Into Clinical Practice http://t.co/Eqq1EUIk #AGBT
+23m omespeak: Sighting people with Twitter open on their browsers at the Ion Torrent seminar. #AGBT
+27m agxp: Can @IonTorrent's sequencer win the Archon Genomics X PRIZE presented by Medco #agbt? http://t.co/RWIbpZxD
+28m CompleteGenomic: See our Partners DNAnexus, Golden Helix & Ingenuity perform demos @ #AGBT Complete Suite tonight at happy hour from 5-7 http://t.co/0v0nJXr4
+35m fluidigm: Wine, Cheese & Targeted Resequencing in suite 285 at #AGBT , stop by!
+37m djschlesinger: PacBio just showed us the trailer for the movie Contagion #AGBT - why?
+38m girlscientist: PacBio panel on managing infectious diseases starts with trailer for movie Contagion, while all are eating. #hooboy #AGBT
+45m mike_schatz: Adam Phillippy articulates the need for mobile distributed genome sequencing to monitor and respond to infectious disease outbreaks. #AGBT
+47m omespeak: Breakthrough technology AmpliSeq to be announced at Ion Torrent seminar. Also, they are going into clinical swequencing (big surprise) #AGBT
+48m djschlesinger: How can we predict what will happen in 15-20 years, did we predict today's advances 15-20 years ago? #AGBT
+50m omespeak: With Proton Sequencer you are supposed to get 6 genomes in a week. Maneesh Jain, Ion Torrent. #AGBT
+52m omespeak: HiSeq and SOLiD owners get a $50K discount on the Ion Proton sequencer. #cheeky #AGBT
+52m lauribe: @agxp: Can @IonTorrent's sequencer win the Archon Genomics X PRIZE presented by Medco #agbt? http://t.co/3Per98mY/ sounds like THE winner
+54m omespeak: Maneesh Jain: 'two-decades leap frogging of Moore's Law' with Ion Proton. #AGBT
+56m djschlesinger: PacBio discussing real time surveillance sequencing networks for infectious disease epidemiology. #AGBT - Practical discussion?

6 - 7pm EST
+0m EdgeBio: We have 2 more winners for our scratch off cards! Congrats to James Schiemer and Petri Auvinen for winning Gift Cards! #WhereisAB #AGBT
+4m djschlesinger: Is PacBio's vision of a "disease weather map" feasible? attainable? practical? Is that where epidemiology is headed? #AGBT
+7m djschlesinger: Even if the "disease weather map" is attainable, how will governments use this info? Will bureaucracies prohibit such advancements? #AGBT
+8m bgilbertABR: How accurate is ion torrent? Really most used in world? #agbt
+10m EvgenyGlazov: RT @mike_schatz: A Phillippy articulates the need for mobile genome sequencing to monitor & respond to disease outbreaks #AGBT @iontorrent
+11m Gavin_Oliver: Rothberg: More experiments run on Ion than any other platform and Ion also more accurate on homopolymers than 'older tech'. Eh? #AGBT
+13m omespeak: Ion AmpliSeq - '3000 amplicons at a time in single tube' . Better than hybridization....hmm. #AGBT
+20m illumina: Explore real HiSeq 2500 data on BaseSpace - info in our latest #AGBT blog post: http://t.co/icjWUTyd
+23m omespeak: Rothberg takes a dig at a company that is currently trying to take over the company he's mainly trying to compete against. #AGBT
+25m iontorrent: We can sequence in your parking lot. Is your idea good enough for a NY Times piece? Email me! -Jonathan Rothberg #AGBT #ionbus
+25m girlscientist: Good q at PacBio event: who's going to pay for the storage of all of these data we all want to generate? #AGBT
+26m Copenhagenomics: J. Rothberg @ ion torrent workshop: The Proton offers the most gigabases per day at lowest cost #claim #AGBT
+33m omespeak: Australian IRB insists that if any useful comes from cancer genome studies, data has to be sent back to clinic. #AGBT
+35m djschlesinger: Extrapolating from PacBio discussion: we'll have sequenced every single DNA strand on the planet within the next 20 years. #AGBT
+37m fluidigm: Suite 285 is THE place to be! Wine & cheese mixer at #AGBT. Stop by for a drink & chance to win $100 Amazon gift card
+40m girlscientist: Marc Allard asks you to please wash your hands after visiting beach bc flocks of birds are out there and "birds are out to get us." #AGBT
+44m djschlesinger: PacBio?? No cool swag after the round table discussion?? #AGBT
+48m djschlesinger: @PacBio, what?? No cool swag after the roundtable discussion?? I'm totally going to buy an Ion Proton instead #AGBT - lol :p
+51m likesky3: Good but HOW? RT @genomeresearch: H Rehm: integrate vast amt of genetic info into patient care by storing millions of variants in EHR #AGBT

7 - 8pm EST
+4m iontorrent: If you really want to study cancer you have to look at functionality, and looking at RNA is a great start. -Tim Triche #AGBT
+15m iontorrent: Looking at transcriptional complexity provides challenges to most sequence alignment software -Tim Triche #AGBT
+19m djschlesinger: Heading to "Genome Technology" concurrent session. Michael Ross from Broad will tell us about sequence bias across platforms #AGBT
+19m BiotechMarketer: @Copenhagenomics Really?! HiSeq produces 55Gb/day today (unattended). What exactly did Rothberg promise the Proton could do? #AGBT
+19m iontorrent: Saw chimeric long range RNA splicing covering >1 Mb of genome. Simple view of nice protein-coding gene is out the window -Tim Triche #AGBT
+22m RongChenBioinfo: Thank you for all the tweets on my talk at @agbt. I am eager to hear talks in the medical sequencing session organized by Elaine Mardis.
+32m CompleteGenomic: We had a great time tonight with our partners and customers at the #AGBT Complete Suite, see you tomorrow! http://t.co/0JYukNxx
+32m deannachurch: In the medical sequencing and variation session- starting with Scott Devine talking about longevity. #AGBT
+33m ElementoLab: #AGBT Scott Devine: identify genetic variants associated with longevity and good health
+34m iontorrent: More than 1200 PGM runs so far at Broad! Niall Lennon #AGBT
+34m ElementoLab: #AGBT Scott Devine: seq 10 full centenarian genomes 30-50X cov and 50 low pass centenarian genomes 4X
+36m deannachurch: SD: Sequencing 10 full (30-50X) and 50 low coveraage (4x) centarians. More females than males b/c those are the samples they have. #AGBT
+36m Massgenomics: Caliper/PerkinElmer dinner, sunset terrace of pres. suite. They just acquired Geospiza and want to help with "reporting to doctors." #AGBT
+36m salisburymw: Yay! Time for the cool tech session at #agbt. Lots of great talks coming our way.
+36m djschlesinger: Ross: bias has always existed, hides biologically important regions, breaks assemblies and increases costs #AGBT
+37m bioinfosm: #agbt It is not too many drinks, but the projector screens are vibrating slightly :P
+38m ElementoLab: #AGBT Scott Devine: looked at DNA repair genes, no clear differences overall with 1000 genomes
+39m deannachurch: SD: Looking at DNA repair genes-variant profile is not significantly different. #AGBT
+39m djschlesinger: Ross: GC content is a good indicator of bias. #AGBT
+40m deannachurch: SD: 279 rare SNPs shared by 8/8 centarians- not seen in dbSNP or phase 1 1000G. #AGBT
+40m djschlesinger: Ross: compared MiSeq, Ion, and PacBio using E. coli, all performed very well #AGBT
+40m ElementoLab: #AGBT Scott Devine: looked for rare variants in centenarians, found 279 rare SNPs shared by 8/8 high cov centenarians, not seen in 1KG/dbSNP
+41m djschlesinger: Ross: comparing a more extreme genome (P. falciparum 19% GC), PacBio provided better coverage below 20% GC #AGBT
+41m ElementoLab: #AGBT Scott Devine: 279 SNPs -> 69 genes, enriched for cell proliferation genes, hematopoiesis, T cell receptors
+41m deannachurch: SD: Using Ingenuity to analyze the 69 genes tagged by the SNPs- top category: Cell growth and proliferation and hematological genes. #AGBT
+42m djschlesinger: Ross: opposite end (R. sphaeroides 69% GC), PacBio coverage was clearly better #AGBT
+43m deannachurch: SD: Testing the idea that centenarians have a better genome to start out with- and also starting to look at Structural Variation. #AGBT
+43m djschlesinger: Ross: now looking at error bias at high GC, where PacBio's quality begins to slip. 10% I sections at higher GC #AGBT
+44m schnablep: #AGBT Scott Devine: "Natural Genetic Variation for Human Longevity" IDed rare SNPs found only in 1/10,000 who make it to >=100.
+44m djschlesinger: Ross: homopolymer bias, MiSeq and Ion show increased error rates with longer homopolymer, however the increase is relative #AGBT
+46m djschlesinger: Ross: coverage bias, HiSeq performs better at high GC ranges, but Complete Genomics does better with homopolymer regions #AGBT
+47m djschlesinger: Ross: Bias changes with changes to library prep #AGBT
+48m djschlesinger: Ross asks how much uncategorized extreme bias remains? #AGBT
+49m agbt: Abstracts are available online for registered attendees. Log in to post a comment or question for presenters. http://t.co/KPEvElhM #AGBT
+50m deannachurch: Anthony Griswold talking about sequencing variants in an autism case/control study. #AGBT
+50m ElementoLab: #AGBT Anthony Griswold: targeting next gen seq in autism cohort of 1K cases and 1K controls
+51m notSoJunkDNA: What??? @iontorrent: More than 1200 PGM runs so far at Broad! Niall Lennon #AGBT
+51m ElementoLab: #AGBT Anthony Griswold: heritability of autism is up to 90%
+52m djschlesinger: Jerod Schwartz, Univ. of Washington talking about optical sequencing #AGBT
+53m obahcall: Anthony Griswold: Targeted sequencing in autism cohort of 1k cases, 1k controls #AGBT
+53m ElementoLab: #AGBT Anthony Griswold: did GWAS, found many weak associations
+54m djschlesinger: Schwartz: De novo assembly capabilities has not kept pace with increasing volumes of sequencing data #AGBT
+55m ElementoLab: #AGBT Anthony Griswold: used Agilent SureSelect to capture exons of 689 genes nominated by GWAS + conserved regions in these genes
+55m illumina: Jerrod Schwartz, Univ Washington. Capturing natively long DNA directly in Illumina flow cells #AGBT
+56m iontorrent: Greg Buck, VCU indicated they are able to get to species level by sequencing V1-V3 of vaginal samples #AGBT
+56m ElementoLab: #AGBT Anthony Griswold: so far seq-ed 806 cases and 745 controls
+57m BiotechMarketer: @Copenhagenomics Yeah, I forget they're promising two generations out. Proton 2 might hit 200Gb/day (2 runs) #AGBT
+57m ElementoLab: #AGBT Anthony Griswold: many self-reported controls were incorrect about ethnicity
+57m Copenhagenomics: If you didn't get tix for #AGBT consider beautiful Copenhagen, June 14-15, for #CPHx 2012 instead. Exciting sessions and great speakers :)
+58m djschlesinger: Schwartz: there's a need to capture sequence and contiguity. Their solution is Infinipair #AGBT
+58m Massgenomics: Griswold on Autism: a lot of self-reported ethnicities were wrong and confounded the initial analysis. #AGBT

8 - 9pm EST
+0m djschlesinger: Schwartz: method starts with long molecular bridge (like bridge PCR) on Illumina flowcell and cleaving the molecule with tranposase #AGBT
+1m djschlesinger: Schwartz: this creates two clusters close to each other, distance related to original insert size #AGBT
+1m ElementoLab: #AGBT Anthony Griswold: single variant association yielded a few hits, but do not pass cutoff after multiple hypothesis testing
+2m schnablep: #AGBT Griswold. Autism affects 1/110; >100 genes implicated, none explains >2% of cases; seeking rare variants. Targeted sequencing 1k cases
+2m ElementoLab: #AGBT Anthony Griswold: same story for genes and damaging variants
+2m djschlesinger: Schwartz: this allows you to map adjacent clusters. Essentially like a mate pair. #AGBT
+2m fluidigm: Thirsty? Stop by Suite 285 at #AGBT and we will help you quench your thirst.. we are waiting!>o
+3m djschlesinger: Schwartz's method is pretty cool, but difficult to describe 144 characters at a time #AGBT
+4m Massgenomics: Griswold targeted sequencing in Autism: 689 gene regions on a 17 Mbp Agilent array. Caliper automation, 11 samples per HiSeq lane. #AGBT.
+5m illumina: Infinipair details MT @djschlesinger Schwartz: long molecular bridge (like bridge PCR) on flowcell & cleaving molecule with tranposase #AGBT
+6m ElementoLab: #AGBT Anthony Griswold: overall no clear association unfortunately
+7m assemblathon: RT @girlscientist: Good q at PacBio event: who's going to pay for the storage of all of these data we all want to generate? #AGBT
+8m illumina: Schwartz: Electrophoretic stretching enables 5-8 kb libraries binding directly to flow cell! #AGBT
+9m djschlesinger: Schwartz showed cool pick of clusters on a flow cell. Adjacent linear clusters (4-6) generated from same molecule. Very neat! #AGBT
+10m illumina: Schwartz: image of lambda DNA stretched on flow cell, followed by in situ transposition. Impressive! #AGBT
+10m chloe46037: Greg Buck talked on the vaginal microbiome but no right to twit. Very nice update on the vaginal microbiome #AGBT .
+11m djschlesinger: John Healy from GnuBio up next #AGBT - will talk live up to hype?
+11m beckforde9: AGBT
+12m deannachurch: Mait Metspalu on human and population structure and genome-wide signals of positive selection in South Asia. #AGBT
+12m djschlesinger: Healy: shows a picture of GnuBio instrument with beta release mid-2012 and full commercial release at end of year #AGBT
+12m djschlesinger: Healy: system has very small profile, weighs ~30 lbs #AGBT
+13m obahcall: Mait Metspalu on population structure and selection signals in South Asia #AGBT
+13m bffo: Note 2 all authors: Long titles 4 papers and 4 talks are hard/impossible to tweet! Think <140 characters when thinking of a title #agbt
+13m chloe46037: Rob edwards did not make it to agbt, but Bas Dunthil will give the talk on identification of gene repertoires #AGBT
+14m djschlesinger: Healy: machines can be stacked in a rack. Instrument itself is a dry machine, cartridge contains fluidics. #AGBT
+14m GoyaRodrigo: GnuBio... Gnu's not Unix Bio? #agbt
+15m Symbionticism: Bas Dutilh from Rob Edwards lab (SDSU) sais Vibrio cholerae has caused seven pandemics in human history. Using genomes to study evol. #AGBT
+15m djschlesinger: Healy: two libraries (PCR primer and sequencing probe) come preloaded on cartridge #AGBT
+16m Gavin_Oliver: GnuBio to release cartridge based desktop sequencer in 2012. Read length up to 1000bp. Real time variant calling. #AGBT
+17m robincoope: For reference a human hair is about 100 microns so call the gnubio channel 25. #agbt
+17m Symbionticism: Dutilh showes that new Ion Torrest chemistry is outstanding. Big improvement. High quality all the way through the 100bp reads. #AGBT
+19m froggleston: Gnubio clinical sequencer. Interesting tech. Looks like a SNES. Cartridges! Playing Duck Hunt in downtime is a great selling point #agbt
+20m illumina: Illumina Talk: WG Analysis of Monozygotic Twins & Their Parents: Accurate Detection of Variants - starts in 10 min, Island Ballroom #AGBT
+20m djschlesinger: Healy talking too fast, having trouble following #AGBT
+21m Massgenomics: Edwards: Sequenced 210 cholera isolates collected since 1910 on IonTorrent system. 314 chip had big quality dropoff; 318 way better. #AGBT
+22m djschlesinger: Healy: each base is interrogated 6 times #AGBT
+23m illumina: Healy: Confusion over "dry machine" and talk of microfluidic & tiny droplets... #AGBT
+24m Gavin_Oliver: GnuBio all runs to date Q50+ per base #AGBT
+24m djschlesinger: Healy: all runs to date have been Q50+ per base. All targets covered to 10,000 x coverage. #AGBT
+24m djschlesinger: Healy: accuracy Phred 70+, less than 1 minute prep time, cost per sample = $200 #AGBT
+25m Massgenomics: Healy lost me to microbial track w/ "Keep this picture of a car in your mind as I talk" Cholera kills 80% of Oregon Trail players. #AGBT.
+26m Gavin_Oliver: GnuBio <1 minute sample prep time and 3.5 hr run time #AGBT
+26m lykkebak: Healy: comparison vs leading desktop platform #AGBT http://t.co/JPKbR7L2
+26m NJL_Broad: If that's clear? ....... um. #AGBT
+27m Symbionticism: Dutilh: once again phages responsible for global variation in bacteria, in this case in V. cholerae genomes across time and geography. #AGBT
+27m djschlesinger: Healy: talking over my head, but the jist is that the system, as is, has tremendous room for growth in read length and data output #AGBT
+27m lykkebak: Healy #gnubio on the future #AGBT http://t.co/5KSzCcVS
+28m deannachurch: Remember- photos are prohibited without the express consent of the presenter. True for talks and posters. #AGBT
+29m djschlesinger: Healy: GnuBio interface: log into system, identify targets, oligos produced by 3rd party, validation at GnuBio, ships to customer #AGBT
+30m djschlesinger: Healy: 20ng starting input, no shearing of DNA required #AGBT - amazing!
+30m froggleston: Did I miss the car analogy? I feel like I've just been in a car accident if that helps. #agbt
+32m omespeak: So I missed first part of the talk, but is the GnuBio technology for whole genome sequencing or just certain loci? #AGBT
+33m deannachurch: Elliott Margulies: WGA of monozygotic twins and their parents for accurate detection of rare disease causing variants. #AGBT
+33m ElementoLab: #AGBT Elliott Margulies: studied family of 4, 2 parents and 2 twins concordant for a neurological disease
+34m Personal_RX_WI: Fascinating technology jump by @gnubio at #AGBT. Possibility of 64kb read length and whole genome per couple hour run. Quite simple tech too
+34m ElementoLab: #AGBT Elliott Margulies: also wanted to assess germline mutation rate, genetic differences between identical twins
+34m djschlesinger: LaserGen, Inc up next #AGBT
+35m Massgenomics: Margulies: WGS of a family quartet: monozygotic twins with an undiagnosed neurological phenotype. Illumina v3 chemistry HISeq #AGBT.
+35m ElementoLab: #AGBT Elliott Margulies: all 4 family members seq-ed at cov >35X
+37m girlscientist: Elliott Margulies of Illumina now, but talking about work from his lab at NIH. Sequencing quartet of parents and identical twins. #AGBT
+37m ElementoLab: #AGBT Elliott Margulies: medium size indels sre hard to call
+38m omespeak: Wrt to GnuBio...#agbt RT @djschlesinger @omespeak resequencing to start, but has a lot of room for growth to whole genome
+39m ElementoLab: #AGBT Elliott Margulies: used pindel to realign reads .. picked up things like 500b deletions
+40m djschlesinger: LaserGen's lightening terminators incorporate extremely fast and bind tighter than natural nucleotide #AGBT
+42m Massgenomics: Margulies' filters: 93% of genome callable in family quartet, 1025 candidate de novo mutations; 58 with NO Q>20 reads in parents. #AGBT.
+43m djschlesinger: LaserGen seems to have done a lot of engineering to these terminators, why not just sell them to Illumina?? #AGBT
+44m ElementoLab: #AGBT Elliott Margulies: several de novo mutations but no clear difference between twins
+45m deannachurch: EM: false negative calls a bigger problem in their process than false positives. #AGBT
+46m djschlesinger: LaserGen's tech is cool, but will they be able to develop a physical machine that can compete with Illumina? #AGBT
+46m ElementoLab: #AGBT Elliott Margulies: de novo indels and CNVs can be picked up manually
+47m Massgenomics: Margulies: Important to filter your data, and small-indel calling still very difficult to do with accuracy. #AGBT.
+47m deannachurch: EM: Important to know the proportion of the reference genome that you can call- this # as important as FP/FN rates. #AGBT
+47m ElementoLab: #AGBT Elliott Margulies: disease causing mutation not found
+48m djschlesinger: LaserGen, raw base call accuracy is 99.8% #AGBT
+50m deannachurch: Wigaard Kloosterman: Mate-pair sequencing to look at mechanisms driving complex genomic rearrangements. #AGBT
+51m djschlesinger: Andre Marziali from Boreal Genomics up next to discuss Multiplexed Enrichment of Rare Alleles #AGBT
+51m ElementoLab: #AGBT Elliott Margulies: Mardis believes that BreakDancer can find these medium size indels
+54m bgilbertABR: Lasergen and gnubio launch by end 2012, thoughts? # agbt
+55m omespeak: So LaserGen wants to target 100bp reads with their higher accuracy 99.8%! Cost ~$99K for instrument & $1K per run. #AGBT
+55m ElementoLab: #AGBT Wigard Kloosterman: sequencing a patient with very complex rearrangements, with parents as control
+58m djschlesinger: Andre Marziali, Boreal Genomics discussing enrichment of rare alleles #AGBT
+58m ElementoLab: #AGBT Wigard Kloosterman: found 12 de novo breakpoints
+58m ElementoLab: #AGBT Wigard Kloosterman: very complex rearrangement indeed

9 - 10pm EST
+0m ElementoLab: #AGBT Wigard Kloosterman: could be explained by chromothripsis as in Stephens et al, Cell, 2011
+1m bkmacy: RT @djschlesinger: Schwartz: De novo assembly capabilities has not kept pace with increasing volumes of sequencing data #AGBT
+2m bkmacy: RT @illumina: Geoff Smith, Illumina UK: Longest perfect overlapping read so far on #MiSeq 678 bp! #AGBT
+3m ElementoLab: #AGBT Wigard Kloosterman: larger cohorts of patients with complex rearrangements, found 130 breakpoints
+4m ElementoLab: #AGBT Wigard Kloosterman: found patterns of microhomology at breakpoints
+5m ElementoLab: #AGBT Wigard Kloosterman: what triggers chrom shattering ?
+6m djschlesinger: Marziali showing some wild videos of fluorescently labeled alleles being separated w/ microfluidics, you can see the strands separate #AGBT
+6m ElementoLab: #AGBT Wigard Kloosterman: patternal chromosome more frequently involved
+6m illumina: Andre Marziali: Enrichment of low conc of specific seq by capture onto oligos attached to electro gel & a circular electrical field #AGBT
+8m chloe46037: Come an celebrate AGBT with Roche at lanai #290. #AGBT
+8m ElementoLab: #AGBT Wigard Kloosterman: some of the rearrangements create fusion genes, eg DPYD-ETV1
+11m deannachurch: Shane McCarthy last speaker of the session- Family based WGS of schizophrenia. #AGBT
+13m ElementoLab: #AGBT: Shane McCarthy: family based WGS of schizophrenia
+15m omespeak: Technical problems galore at the Genomics Technology session. #AGBT
+17m ElementoLab: #AGBT Shane McCarthy: increased rate of de novo CNVs in schizophrenia
+18m swarmIQ: Celebrate HaloPlex tonight at a Swedish themed party. Come by the Caxambas Suite & learn about the tech. #AGBT #Agilent http://t.co/h6nD4nft
+19m deannachurch: SM: Many of the CNVs associated with schizophrenia are also associated with Dev. Delay, ASD and other neurocognitive defects. #AGBT
+19m juselenas2: gente eu fui no testaurante q almocei com a @Catch_Selena ai eu fui na mesa q agbt tinha ficado e abracei a cadera q ela sentou anw!
+19m bkmacy: New tech does take time RT @omespeak: Technical problems galore at the Genomics Technology session #AGBT
+21m iBAST: RT @bkmacy New tech does take time RT @omespeak: Technical problems galore at the Genomics Technology session #AGBT http://t.co/SgFgHpCM
+21m omespeak: Final question of the evening at #AGBT: which party?
+22m ElementoLab: #AGBT Shane McCarthy: case control studies might not work if number of causal variants very large, uses pedigrees instead
+22m iBAST: RT @bkmacy New tech does take time RT @omespeak: Technical problems galore at the Genomics Technology session #AGBT http://t.co/xVLETLEu
+23m girlscientist: After extensive technical delays, Sunney Xie presenting, with dramatic pauses, what he says is true single molecule sequencing. #AGBT
+25m ElementoLab: #AGBT Shane McCarthy: seq-ed 2 pedigrees
+26m ElementoLab: #AGBT Shane McCarthy: Looked for variants in linked regions
+30m ElementoLab: #AGBT Shane McCarthy: 3 missense variants in linked region in 1 pedigree, gene function not clear
+30m dwmohr: Good scotch at the Caliper suite, but none for you KNH #not agbt
+33m ElementoLab: #AGBT Shane McCarthy: no clear gene candidate overall
+35m ElementoLab: #AGBT Shane McCarthy: they have a mystery chrom 6 candidate, not in MHC
+36m ElementoLab: #AGBT Shane McCarthy: mystery region on chrom 6 conserved in zebrafish
+45m iontorrent: 300 people at Ion Sequencing Seminar!!! #agbt #ionbus http://t.co/jnGUwpKI
+58m EdgeBio: RT @iontorrent: 300 people at Ion Sequencing Seminar!!! #agbt #ionbus http://t.co/RZFVpNWB

10 - 11pm EST
+5m Massgenomics: Summary of first day at #AGBT: http://t.co/IDALVCxP
+36m DrugsandWhiskey: AGBT = PAUSE
+39m illumina: Missed a session? Abizar Lakdawalla blogging #AGBT. New posts for all Day 2 sessions up soon. http://t.co/isP5PzDn
+53m BlueSEQ: Good summary of #AGBT day 1 from @Massgenomics http://t.co/V4MADtAy
+56m BiotechMarketer: @omespeak What kind of output per run was LaserGen promising? #AGBT
+7m ribozyme: Thanks all for the tweets on #AGBT - it's a for those who couldnt make it this year. Keep them coming!
+10m wjgoode: RT @Massgenomics: Summary of first day at #AGBT: http://t.co/RH5kVAXo #genomics
+11m ribozyme: Thanks all for the tweets on #AGBT - its at least some solace for those who couldn't be there this year - Keep'em coming!
+34m corbishleyz5: AGBT
+53m jenningswv3: AGBT
+55m herrerak4: AGBT
+8m pittmanfh6: AGBT
+56m pathogenomenick: All of the #AGBT day 2 tweets are available at http://t.co/SGK6XrBj
+2m crs4research: Genome Biology and Technology (#AGBT) meeting: from February 15-18, 2012 http://t.co/1QlW9T1c http://t.co/1QlW9T1c

A new sequencing technology enters the ring: SHTseq(TM)

15 Feb 2012

Just received this press release from Neil Hall, CEO of a new sequencing company called CrapBio who's launching at this year's #notAGBT.. sounds very interesting!

CrapBio
CrapBio is excited to announce the release of its new SHTseq™ whole genome sequencing platform which is going to revolutionize the genomics industry and soon the healthcare industry.

SHTseq
SHTseq or Super High-throughput Template sequencing is a totally new paradigm for DNA analysis. In the era of second and third generation sequencing, scientists would take days to extract DNA and prepare it for analysis on slow cumbersome analysis machines. CrapBio is able to get around this using AngstromRealtimeSensors™ that can accurately read the DNA while still inside cells. Better than that, you don’t even need to take the DNA to the analysis machine you can simply take an image of the organism you wish to sequence and upload it to the SHTcloud and have the DNA information extracted directly by out highly trained SHTtechnicians.

With SHTseq you can simply send the sample from you iphone and have the sequencing data returned to your email address in a matter of minutes. THATS RIGHT!, you can have a SHT experiment run in minutes! Not hours or days. Download your iSHT app now and start sequencing.

Longer Reads-Better Data – noSHT (What would you do with 100Mb reads?).
We are able to generate super-long reads with our ARSesnsors. Using CrapBio-SHTseq technology we regularly get 10Mb reads and we have even seen reads of 100Mb which completely sequenced E. coli 20 times in a single read. Our base calling accuracy is 25%, but with genomes with extreme AT/GC bias it reaches 40%. Although this is lower than other platforms the longer reads allow you to extract much more information from our reads than old-fashioned 2nd generation sequencers. Also this error is totally randomly distributed (unlike homopolymer errors in other technologies!) and there is no decline in base calling accuracy toward the ends of reads. The last base in a read is just as good as the first base.

Cleaning up SHT™ with Illumina data
If, for whatever reason, you need accurate sequence data we have developed hybrid assembler that can incorporate Illumina error correcting reads. With our HybridAssemblyReadDenoisingSHT data you can simply upload you 100x illumina data with your sample and get reads returned to you will 99.999% accuracy*

CompleteSHT™ our human genome analysis service
Finally we are pleased to announce our CompleteSHT human genome sequencing service. We have optimized our laboratory and informatics pipelines for human DNA sequencing and are able generate a DNA sequence de novo, without HARDSHT, with 99.9% accuracy**. Simply send the name, ethnicity and starsign of the subject and we can return a SNP file to your email address INSTENTAINIOUSLY!***.

How much does SHT cost?
Due to the way our technology works we have very low reagent costs, therefore SHTseq is the cheapest technology on the market. Speak to a CrapBio representative to find out more.

More SHT
If you would like to speak to one of our product specialists to find out how SHT will change the way you do science please email SHT@CRP.COM

*there may be a high chimera rate with this product.
** this works best with samples of European decent
*** for research use only