Which technology won AGBT?

This picture tells quite a story (Wordle constructed from 3,386 tweets and retweets tagged #AGBT with mentions/@s removed).

AGBT 2012 Day 4 Tweets

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

Well, yesterday's megaton announcement from Oxford Nanopore certainly made up for what had been a slightly subdued AGBT 2012, at least in the way of new technology. I'd definitely recommend checking out this list of excellent blog posts covering the scientific sessions, which I will continue to update for the next few days. And so here are the day 4 tweets, streaming live into the blog. Refresh to see updates.

Scientific agenda

Plenary Session: Genomic Studies II (Deanna Church, NCBI, Chair)

9:00-9:35 am Keynote Speaker: Michel Georges, University of Liege
9:35-10:05 am Jesse Gray, Harvard Medical School, “An RNA-Seq Snapshot Reveals Genome-Wide, in vivo mRNA Dynamics From Unperturbed Cells at Steady-State”
10:05-10:35 am Patrick Schnable, Iowa State University, “Gene Loss During a Domestication Bottleneck: Identification, Characterization and Genetic Mapping of Teosinte Genes That are Absent From the Maize Genome”
11:10-11:40 am Emily Hodges, Howard Hughes Medical Institute & Cold Spring Harbor Laboratory, “Directional Changes and Poised DNA Methylation Characterize Epigenetic Patterns That Underlie Lineage Identity of Human Blood Cell Methylomes”
11:40 am-12:10 pm James Galagan, Boston University, “Discovering the Regulatory Network of TB: Dissecting the Regulation of the Hypoxic Response”

Plenary Session: Genomic Studies III (Elaine Mardis, Washington University School of Medicine, Chair)

2:30-3:00 pm Vivian Cheung, University of Pennsylvania, “RNA and DNA Sequence Differences in the Human Genome”
3:00-3:30 pm Lior Pachter, University of California, Berkeley, “Streaming Algorithms for Analyzing and Maintaining RNA-Seq Data”
3:30-4:00 pm Gerald Tuskan, Oak Ridge National Laboratory “Integrating Population-Scale Resequencing and Shotgun Proteomics Within the Populus Common Garden Experiment”
4:00-4:30 pm Steve Benner, Foundation for Applied Molecular Evolution, “Reagent Innovations for Sensitive, Clean, and Highly Multiplexed Analysis of DNA”


Most popular tweets
(10) pathogenomenick: I think wordles are often a bit lame, but this one from #AGBT tells a good story http://t.co/6gGV6Bbs
(10) mbeisen: b/c nobody knows about overhyped and not ready for prime time sequencing tech like jonathan rothberg http://t.co/boqzG4uv #AGBT @nanopore
(9) bioitworld: A bit harsh! Ion Torrent's Jonathan Rothberg compares @nanopore technology to cold fusion! #AGBT #nanopore Forbes http://t.co/HCcEgmIk
(8) omespeak: As expected, the New York Times picks up on the Oxford Nanopore story: http://t.co/FFOo7EdS #AGBT
(8) girlscientist: In case you have been under a rock, Cheung's lab found much larger than expected numbers of sequence diff's bn RNA/DNA of same person. #AGBT
(7) bffo: Jesse Gray: next: "after yesterday's talk, you may be disappointed, but all I have on my USB stick is my talk" #agbt
(5) SEQanswers: Spy pic of next gen @PacBio just arrived in my inbox.... #AGBT http://t.co/950CcUBg
(3) neilhall_uk: Rothberg does not believe it. http://t.co/bAPfYKXJ Who would have thunk? #agbt #nanopore
(3) bffo: JG introns have negative slope 1st principles: transcription, splicing & degraded steady state #agbt cool to go back to 1st principles!
(3) CRIgenomics: Knock knock, can we come in? There are 1000 attendees at #AGBT that want a new sequencer. http://t.co/Un5TZO3n
(3) obahcall: Schnable: yes... 1ks of expressed genes in teosinte are missing from B73 ref #AGBT
(3) WeigelWorld: Oxford Nanopore @pathogenomenick: I think wordles are often a bit lame, but this one from #AGBT tells a good story http://t.co/v4krjrI8
(3) finchtalk: #AGBT VC, question about sequencing and cell purity. Are DNA and RNA sampling different sub-populations?
(3) nanopore: Thank you all the amazing speakers at #AGBT and safe travels home! ps did you spot the clue in our Xmas card? http://t.co/csnL08oc
(3) Personal_RX_WI: #AGBT February 20-23 2013. New registration process will be in place.
(2) nanopore: RT @genomesunzipped: Making sequencing simpler with nanopores: Our take on the new Oxford @Nanopore machines #AGBT http://t.co/pqWhsQYp
(2) djschlesinger: Gray: some transcripts are longer than diameter of the nucleus, how then do splice sites find each other? #AGBT
(2) bffo: Birney also urges JG to look at encode data http://t.co/PNEDOtZI #AGBT
(2) bffo: RT @pathogenomenick: I think wordles are often a bit lame, but this one from #AGBT tells a good story http://t.co/RPfETLOG
(2) girlscientist: Hodges: no surprise, hypomethylated regions mostly at promoters. But strong subclass outside genes. Every tissue has unique set HMRs. #AGBT
(2) girlscientist: Vivian Cheung of Penn kicking off last session. RNA:DNA differences. #AGBT
(2) joe_pickrell: For background on Cheung RNA-DNA differences talk, see http://t.co/g65UAGHA http://t.co/oRzySH0q #AGBT
(2) Massgenomics: Vivian Cheung at #AGBT: found 10,210 RNA-DNA differences in 4,741 genes, of which 8,163 sites seen in >50% of samples examined.
(2) girlscientist: Original paper Cheung is describing with RNA:DNA differences: http://t.co/vWyBwCbY ($) #AGBT
(1) kevinltweets: diluting rabbit's blood in water = your sample prep I.M.P.R.E.S.S.E.D. Oxford @Nanopore machines #AGBT http://t.co/RoarVw4d
(1) pathogenomenick: Well here you go, #AGBT day 4 tweets http://t.co/gedbgq8q - I guess we're not expecting announcements today.
(1) accelmed: Unveiled: 1 of coolest inventions @ Wyss/HMS: DNA Nanobot 4 Immune Programming http://t.co/LeEYghZ1 #tedmed #futuremed @hackmedmit #agbt
(1) pathogenomenick: sounds rattled! RT @neilhall_uk: Rothberg does not believe it. http://t.co/P29C99Aq Who would have thunk? #agbt #nanopore
(1) omespeak: I can see the joke about 'it is only a USB stick not a sequence' getting old pretty quick here. Jesse Gray does the first one. #AGBT
(1) djschlesinger: Gray: RNA-Seq densities across introns have negative slopes, why? #AGBT

11 - 12pm EST
+20m favenmarg: Next gen sequencing scientists are better-than-average scientist dancers. Seriously. #AGBT
+37m alansariim6: AGBT
+42m darissambaya: Nanopore is about to release a $900 #sequencing platform http://t.co/w20rylRb
+8m takkah: Oxford Nanopore to Begin Selling Two Low-Cost DNA Strand Sequencing Instruments this Year http://t.co/saNVe7dj
+4m hiro_h: @takkah togetterAGBT
+18m hiro_h: AGBT tweets 2012 (3) http://t.co/7KHmVFxg
+25m hiro_h: `not` AGBT tweets 2012 http://t.co/SjW8BOb3
+26m hiro_h: tweets aggregations for AGBT are available at http://t.co/5azXoai6 #nonAGBT
+0m fyallpwiq9: GnuBio all runs to date Q50 per base AGBT
+18m carolineqvcu0: AGBT Anthony Griswold: single variant association yielded a few hits, but do not pass cutoff after m
+22m UniverseAwake: Which technology won AGBT? http://t.co/NzsjJGcb
+37m djwhelan: Checking out. I went to bed at this time the other night.... #AGBT http://t.co/0xTja16U
+0m steffenss3: AGBT
+24m sjcockell: No big surprises here :) "Which technology won AGBT?" http://t.co/ePMMMtAs #greader

10 - 11pm EST
+33m suemiuehara_: Vo sai, agbt vai ouvi musica aqui vish tres retardadas dancando kkk
+43m MTomasson: @eugeneday Thanks for card in advance. On twitter crack--first conference in absentia #AGBT what t was made for.

9 - 10pm EST
+10m mbcf: #agbt star wars party getting hot http://t.co/UYwfgMUf
+11m cla8208: So happy to join the Dark side at #agbt http://t.co/cW2H5Kc5
+27m mbcf: #agbt star wars sand people. Cheating on the duck http://t.co/2qsjVXE7
+42m mbcf: #agbt no comment. http://t.co/Y9f8Q4Is
+48m amythewilliams: @cla8208 hope you're enjoying #AGBT!

8 - 9pm EST
+1m jgreid: Love the SW party theme at #AGBT
+6m omespeak: Based on main buzz of this meeting, people at the party should be saying 'may the nanopores be with you'd #AGBT
+17m marialy0: agbt
+26m sprytron: Storm trooper representing U of Washington @ #AGBT
+32m jgreid: Obi-Wan cupcake? Hell yeah. #AGBT http://t.co/9MXSWmFE
+40m Personal_RX_WI: #AGBT Star Wars Dinner. Chewbacca cupcake anyone? Mike's dessert. http://t.co/81LSUfJM

7 - 8pm EST
+15m Black_Badger: Many thanks to everyone tweeting from #agbt. It was great to follow and experience the (vicarious) excitement.
+28m Symbionticism: Back home from the exciting #AGBT mtg with 1 final thought - in an age of tight govnmt budgets, imo we should downsize from Marco. Thoughts?
+28m omespeak: Ready for the Star Wars party at #AGBT http://t.co/RPsYRVo3
+51m girlscientist: My new friend at #AGBT! http://t.co/Axm64l4i
+52m djschlesinger: Wish I would have known about the Star Wars dinner theme before I got here. I would have brought my slave-Leia costume #AGBT
+55m nygenome: The Force is with #nygenome at #AGBT! http://t.co/69LpLJs8

6 - 7pm EST
+23m Greeicy_PJL: ta tteno churras aq novamente rs ;)) . . daq a poco agbt vai la na praia nos shows q ta teno por la rs ..
+45m vervecoaching: Blending in with Next Gen Sequencing crowd at #AGBT in Marco Island.
+50m bffo: thank you all for the tweets & RT/MT ... It has been a great tweetfest, and a great meeting, I enjoyed the insightful comments #agbt

5 - 6pm EST
+10m SEQanswers: Spy pic of next gen @PacBio just arrived in my inbox.... #AGBT http://t.co/950CcUBg
+19m chloe46037: Final starwars reception #AGBT . Done with tweeter until #ABRF.
+25m jobsyo2: AGBT
+53m RainDanceTech: Congratulations to James Hadfield (Head of Genomics at CRUK) our #AGBT iPad 2 contest winner! http://t.co/DtaH8Mr8

4 - 5pm EST
+0m djschlesinger: Steven Bennet from the Foundation for Applied Molecular Evolution giving last talk of #AGBT - reagent innovations for DNA analysis
+1m omespeak: Ethanol powered, carbon fiber-based car as the door prize for next year's #AGBT?
+3m ElementoLab: #AGBT Gerald Tuskan: currently performing functional assays to find out lignin function of genes where 42 SNPs were found
+3m genome_gov: Last talk: Steve Benner on "Reagent innovations for sensitive, clean, and highly multiplexed analysis of DNA" #AGBT
+8m CRIgenomics: "China is a third world country", so says Steve Benner at #AGBT. Expect apologies later on!
+8m omespeak: Not next-generation sequencing but 'next-generation DNA':Steve Benner (famous for his reasoned arguments against the Arsenic-bacteria)#AGBT
+11m froggleston: Benner: "China is a third world country". Oops. #agbt
+15m dauserftk7: medicalcollege team from Personal_RX_WI hanging with top genomics experts at agbt
+19m CRIgenomics: @Agilent just left me in charge of 2 Apple TVs and an iPad 2, their prizes for #AGBT. See you all next year...
+22m illumina: Cheers 2 great #AGBT tweeters @djschlesinger @girlscientist @ElementoLab @omespeak @deannachurch @finchtalk @Massgenomics & many more!
+25m djschlesinger: Benner's use of bright blue and red in his slides reminds me of 3D movies from the 1980s #AGBT
+28m ribozyme: More like an iPad 5 with a nanopore in the home button! USB gone by then I hope :-) RT @ribozyme: @lexnederbragt: GATTACA #AGBT
+30m froggleston: @djschlesinger I find it more like a Geocities website circa 1997. #agbt
+34m omespeak: Yes, registration frustrations! #AGBT
+34m lykkebak: Dates for #AGBT 2013 - February 20-23
+35m Personal_RX_WI: #AGBT February 20-23 2013. New registration process will be in place.
+36m omespeak: RT @Personal_RX_WI: #AGBT February 20-23 2013. New registration process will be in place.
+37m Personal_RX_WI: #AGBT Coming to a close. Farewell dinner tonight. Jaime & Mike heading back to MCW tomorrow AM. Thanks for following our adventure!
+39m omespeak: Great #AGBT meeting. Thanks to the organizers and sponsors. Now to write up some of my thoughts. But Star Wars part first!
+55m Gavin_Oliver: Can anyone recommend a Marco Island company who does half day Everglades tours? Want to squeeze one in before 4pm flight tomorrow #AGBT

3 - 4pm EST
+0m ElementoLab: #AGBT Vivian Cheung: audience member: single molecule seq showed that in population of cells, some genomes might be different
+0m girlscientist: ...your results be explained by mismatch repair in some cells and not in others yet? A: we would be v happy to look at single cells! #AGBT
+1m finchtalk: #AGBT VC, question about sequencing and cell purity. Are DNA and RNA sampling different sub-populations?
+3m genome_gov: Lior Pachter now on "Streaming algorithms for analyzing and maintaining RNA-seq data" #AGBT
+5m ElementoLab: #AGBT Lior Pachter: streaming algorithms for analyzing and maintaining RNA-seq data
+6m genomeresearch: Means piecemeal RT @genome_gov: Lior Pachter now on "Streaming algorithms for analyzing and maintaining RNA-seq data" #AGBT
+6m genome_gov: Pachter: will argue that batch algorithms are scalable #AGBT
+6m ElementoLab: #AGBT Lior Pachter: Nanopore talk yesterday highlighted a streaming approach to sequencing
+7m finchtalk: #AGBT Lior Pachter on streaming algorithms. Genomics is batch orientated, that's a problem. Need to stream the data. Right on!
+8m genome_gov: Correction - Pachter aregues that batch algorithms are NOT scalable #AGBT
+10m Wagnerizer: Are DNA sequencers really going to be in the same family as my USB coffee cup warmer? #AGBT #Nanopore http://t.co/Squ0aZ2g
+10m ElementoLab: #AGBT Lior Pachter: what Cufflinks do is to assign reads to transcripts using statistical modeling
+11m ElementoLab: #AGBT Lior Pachter: showed an RNA-seq map of the world based on Cufflinks download IP addresses
+12m genome_gov: Pachter: "My worst nightmare: the curse of deep sequencing" aka too much data. #AGBT
+13m ElementoLab: #AGBT Lior Pachter: curse of deep sequencing: the reliability of some algorithms (eg assembly) decreases when you use them on too much data
+15m Verbal_SeduXion: @bongopondit Hahaha why doesn't that surprise me! Also the Illumina summary of AGBT was a nice read, thanks :)
+16m genome_gov: Pachter: not a big believer in the cloud #AGBT
+18m genome_gov: Pachter: eXpress >> streaming algorithm >> process one read at a time #AGBT
+21m ElementoLab: #AGBT Lior Pachter: eXpress algorithm processes reads as they come from machine, assigns them probabilistically to transcripts on the fly
+23m westr: @MTomasson "10 Mistakes... " by @TrishaTorrey - Mistake 9: Thinking Medical Research Is Searching for Cures http://t.co/qLq184Pr #AGBT
+23m illumina: Speaking of cloud-based genomic analysis...check out HiSeq2500 data on BaseSpace #AGBT http://t.co/icjWUTyd
+24m ElementoLab: #AGBT Lior Pachter: online algorithm for assigning reads converges towards optimal solution as more and more reads are processed
+26m omespeak: Lior Pachter is making a relatively tough subject really easy to follow. Love the zooming into various parts of the slide. Great talk #AGBT
+26m finchtalk: @genome_gov: Pachter: not a big believer in the cloud #AGBT but not make a compelling case one way or another
+28m ElementoLab: #AGBT Lior Pachter: eXpress memory needs very low and do not change w read numbers; much much faster than Cufflinks
+30m ElementoLab: #AGBT Lior Pachter: eXpress only needs 1M reads to find biases in an RNA-seq experiment
+30m nanopore: Thank you all the amazing speakers at #AGBT and safe travels home! ps did you spot the clue in our Xmas card? http://t.co/csnL08oc
+31m genome_gov: Pachter: algorithm removes the need to store the alignment files #AGBT
+32m ElementoLab: #AGBT Lior Pachter: eXpress removes need to store alignment files; can also stop analysis when desired experimental accuracy is reached
+34m omespeak: Hmmm. Cheeky :) #AGBT MT @nanopore: ps did you spot the clue in our Xmas card? http://t.co/mknVpjKC
+35m genome_gov: Gerald Tuskan now on "Integrating population-scale resequencing and shotgun proteomics w/i the Populus Common Garden Experiment" #AGBT
+35m Copenhagenomics: Kevin McKernan from Courtagen Life Sciences will talk about the cannabis genome at #CPHx 2012 :) Video from #AGBT: http://t.co/PcsX3PFv
+37m ElementoLab: #AGBT Gerald Tuskan: cellulose and lignocellulose most abundant polymers on planet
+47m bffo: GT: a SNP every 30 bp in Populus ... you thought you had variation challenge! #agbt
+48m genome_gov: Tuskan: GWAS to identify genes associated with lignin formation #AGBT
+49m ElementoLab: #AGBT Gerald Tuskan: performed GWAS in Populus; found 42 SNPs associated with lignin content, 3-13% phenotypic variance explained in total
+54m notSoJunkDNA: same here. Thanks for the reports #agbt @nparmalee: @girlscientist This story boggles my mind.
+54m Perpilocution: Excitement hangover from yesterday's chaos following #nanopore's announcements at #AGBT
+56m lykkebak: Some people are sleeping during the last session (front row). Guess they partied to much last night.... :) #AGBT

2 - 3pm EST
+7m BioMickWatson: Are people still at #AGBT? Didn't everyone just leave after the @nanopore announcement?
+10m omespeak: Still here for StarWars party? RT @BioMickWatson: Are people still at #AGBT? Didn't everyone just leave after the @nanopore announcement?
+15m Symbionticism: Lol "@Copenhagenomics: Here's a spy photo from a projected sequencing center, planned to open in early 2013: http://t.co/3Ctam3Lo #AGBT"
+16m CLCbio: Kevin McKernan, Medicinal Genomics: "Most assemblers gave up assembling the cannabis genome, but @CLCbio did the job" #AGBT
+25m Copenhagenomics: Good description of @nanopore's MinION potential with this tag: #DriveBySequencing (coined by @brynskov) #AGBT :)
+26m chloe46037: Great turn out for K.McKernan talk #AGBT but no tweets?
+28m Personal_RX_WI: Thanks to Geospiza @PerkinElmer for meeting with us today about your LIMS system. Very informative. #AGBT
+30m djschlesinger: Vivian Cheung, UPenn discussing RNA and DNA sequence differences in the human genome #AGBT
+31m nygenome: Great #nygenome #AGBT presentation this morning. Thanks to all who joined us! We'd love your feedback here or agbt@nygenome.org.
+32m girlscientist: Vivian Cheung of Penn kicking off last session. RNA:DNA differences. #AGBT
+32m deannachurch: Viburnum Chueng talking about RNA and DNA differences in the human genome. #AGBT
+34m girlscientist: In case you have been under a rock, Cheung's lab found much larger than expected numbers of sequence diff's bn RNA/DNA of same person. #AGBT
+34m deannachurch: Damn autocorrect Vivien! No more tweeting on my phone. #AGBT
+36m ElementoLab: #AGBT Vivian Cheung: looking for differences (not only editing) between DNA and RNA in B cells
+36m bongopondit: Vivien Cheung: Does not want to use the term RNA-editing, but call it RNA-DNA differences (RDD) since mechanism is unknown. #AGBT
+37m omespeak: Vivien Cheung: Does not want to use the term RNA-editing, but call it RNA-DNA differences (RDD) since mechanism is unknown. #AGBT
+37m djschlesinger: Cheung defining very strict requirements for determining differences between RNA and DNA #AGBT
+38m djschlesinger: Cheung: sequence must be unique, covered by at least 10 reads, must have two RNA reads with mismatch and must be found in two people #AGBT
+38m omespeak: Vivian Cheung: A to G RDD most common C to G and G to least common. #AGBT
+39m ElementoLab: #AGBT Vivian Cheung: after filtering, BLAT-based remapping, cov>=10X: 10,210 exonic sites differed between DNA and RNA
+39m djschlesinger: Cheung: base pair differences found between RNA and DNA are common between individuals #AGBT
+39m omespeak: Vivian Cheung: aware that this is unexpected, not ready to assign it to some systematic error. Must be some biological mechanism. #AGBT
+40m joe_pickrell: For background on Cheung RNA-DNA differences talk, see http://t.co/g65UAGHA http://t.co/oRzySH0q #AGBT
+41m Massgenomics: Vivian Cheung at #AGBT: found 10,210 RNA-DNA differences in 4,741 genes, of which 8,163 sites seen in >50% of samples examined.
+42m omespeak: RT @joe_pickrell: For background on Cheung RNA-DNA differences talk, see http://t.co/2JZtRsHN http://t.co/kLOgV71I #AGBT
+43m girlscientist: Original paper Cheung is describing with RNA:DNA differences: http://t.co/vWyBwCbY ($) #AGBT
+43m djschlesinger: Have they tried enriching for the variant allele in the DNA? Maybe as-PCR or COLD-PCR? #AGBT
+43m bigfeet5grl: Jelly RT @girlscientist Vivian Cheung of Penn kicking off last session. RNA:DNA differences. #AGBT
+43m ElementoLab: #AGBT Vivian Cheung: showing example of genes with differences eg CORO1C; coverages showed were high in DNA-seq, lower in RNA-seq (<20X)
+44m finchtalk: #AGBT Vivian Cheung on RNA editing. Found ~10k sites/~5k genes. Data show varied allele frequency, usually the RDD is lower, some complete
+44m omespeak: Vivian Cheung: RDDs observed in tissues other than B-cells as well. Prsent in skin cells too. #AGBT
+46m ElementoLab: #AGBT Vivian Cheung: showing examples of genes with DNA-RNA differences eg CORO1C; coverage shown higher in DNA-seq cmp to RNA-seq (<20X)
+46m djschlesinger: Cheung: very thorough in ruling out alternative non-biological explanations for RNA DNA differences #AGBT
+47m girlscientist: Cheung: since their paper, at least 5 others have come out with similar findings (did not comment on relative numbers of sites yet). #AGBT
+48m genome_gov: Cheung: RDDs tend to occur in patches #AGBT
+48m omespeak: Vivian Cheung: RDDs seem happens in patches. #AGBT
+48m ElementoLab: #AGBT Vivian Cheung: 41% RNA-DNA differences in coding exons, 71% of which lead to changes in aa (most freq are L>P, V>A, S>P)
+48m omespeak: Vivian Cheung: RDDs seem to happen in patches. #AGBT
+48m djschlesinger: Cheung: 71% of RNA DNA changes are nonsynonymous #AGBT
+49m girlscientist: Cheung: can they find peptides corresponding to RNA form? LC-MS/MS in B cells. Answer = yes, see both RNA and DNA forms in peptides. #AGBT
+49m omespeak: Vivien Cheung: Founds example of protein encoded by the RDD RNAs using LC-MS. #AGBT
+50m omespeak: Vivien Cheung: Found examples of protein encoded by the RDD RNAs using LC-MS. #AGBT
+50m ElementoLab: #AGBT Vivian Cheung: DNA-RNA differences present in translated proteins according to mass spec
+51m djschlesinger: @girlscientist , where does the DNA form come from? #AGBT
+52m omespeak: Vivien Cheung: RDD levels ~20% on an average. Bimodal distribution of RDD levels. #AGBT
+53m genome_gov: Cheung: levels of RDD vary across inidivduals #AGBT
+53m bongopondit: Vivien Cheung: RDD levels vary across individuals. #AGBT
+53m rnomics: RT @razZ0r: RT @ElementoLab: #AGBT Vivian Cheung: after filtering, BLAT-based remapping,... http://t.co/xae5m0K8 #GeneticSequence-bio @MyEN
+53m rnomics: RT @finchtalk: #AGBT Vivian Cheung on #RNA editing. Found ~10k sites/~5k genes. Data show... http://t.co/EtJqQyec #GeneticSequence-bio @MyEN
+53m rnomics: RT @finchtalk: #AGBT Vivian Cheung on #RNA editing. Found ~10k sites/~5k genes. Data show... http://t.co/EtJqQyec #rnomics-bioscience @MyEN
+53m rnomics: RT @genome_gov: RT @djschlesinger: Cheung: 71% of #RNA DNA changes are nonsynonymous #AGBT http://t.co/0YlIU6ef #rnomics-bioscience @MyEN
+53m ElementoLab: #AGBT Vivian Cheung: what mediates DNA-RNA differences not known
+54m girlscientist: Cheung: "the elephant in the room right now is" underlying mechanism. "Unfortunately don't have answer yet" but working on it, obv! #AGBT
+54m omespeak: Vivien Cheung: Elephant in the room 'what is the underlying mechanism'? No answer yet. #AGBT
+55m girlscientist: Cheung: ADAR siRNA KO does not explain all of RDD seen so far. Cells lose A to G, as expected, but not other changes. #AGBT
+55m finchtalk: #AGBT VC RDD (RNA DNA diff). Transcript abundance bimodal - 20% high, 100% low and variable wrt individuals. A phenotype?
+55m ElementoLab: #AGBT Vivian Cheung: knocking down ADAR decreases A to G editing, other DNA-RNA differences unaffected
+56m omespeak: Vivien Cheung: Twin concordance studies....RDD levels more similar among twins compared to different individuals. #AGBT
+56m genome_gov: Cheung: looked in twins; RDD distribution more similar in twins than to unrelated inidivduals #AGBT
+56m ElementoLab: #AGBT Vivian Cheung: DNA-RNA difference levels closer in twins than in unrelated individuals
+57m omespeak: Vivien Cheung: so RDD possibly genetically regulated. #AGBT
+58m genome_gov: Cheung: when doing genetic studies...should we expand to looking at variation in RNA? #AGBT
+59m finchtalk: #AGBT VC high concordance with levels in twins, indicating the RDD level in a transcript is inherited.
+59m girlscientist: First Q for Cheung: understatement of "your result is...intriguing." But we now see indiv cells have diff genomes even. Could... #AGBT

1 - 2pm EST
+13m ribozyme: More like GridIon, cause the sample goes to back room and takes 15 mins :) RT @lexnederbragt: I guess they used MinIONs for GATTACA #AGBT
+15m ribozyme: In a movie remake now she puts the hair root inside her USB stick at her computer :) RT @lexnederbragt: They used MinIONs for GATTACA #AGBT
+16m SEQanswers: My morning: #AGBT tweets, coffee and firing up an XL EC2 instance to align and call variants from yesterday's runs. (kids are very quiet!)
+18m pathogenomenick: #AGBT day 4 tweets http://t.co/gedbgq8q
+31m omespeak: Looking forward to Vivian Cheung's talk on RNA/DNA sequence differences coming up in the afternoon session at #AGBT.
+32m omespeak: The study was controversial originally (http://t.co/xwgPZGqI) but seems like more data will be present to validate the differences/ #AGBT
+40m bhalomanush: @bongopondit slightly envious. Would have loved to have attended AGBT. Too busy and unfortunately still under-crewed at present.

12 - 1pm EST
+0m obahcall: Galagan: Showing latest TB regulatory network, with 51 TFs chipped, 2704 genes with binding, 5521 interactions. #AGBT
+0m ElementoLab: #AGBT James Galagan: some transcription factors in TB only bind to their own promoters !
+8m girlscientist: Galagan: in hypoxia, TB is in macrophage and relies on host immunomodulatory lipids and induction of foamy macrophages. #AGBT
+9m obahcall: Galagan: using their predictive model, show can accurately predict ~30% of differentially expressed genes #AGBT
+9m salisburymw: Galagan: big juicy lipid droplets. Eww. #agbt
+9m girlscientist: Galagan: in other words, TB another example of infection manipulating your immune system for its own ends. #AGBT #weareallatitsmercy
+9m ElementoLab: #AGBT James Galagan: all TB ChIP-seq data available at http://t.co/HUz7O7r4
+9m mbeisen: b/c nobody knows about overhyped and not ready for prime time sequencing tech like jonathan rothberg http://t.co/boqzG4uv #AGBT @nanopore
+10m obahcall: Galagan: Their TB ChiP-Seq data all available at http://t.co/69dYPJNy #AGBT
+18m bkmacy: Shawn Levy presenting how @ING_SYS variant analysis ID'd novel variant at @roche lunch #AGBT
+21m CrapBio: @mbeisen: nobody knows about overhyped and not ready for prime time sequencing tech like rothberg http://t.co/BqD5rtLq #AGBT apart from us
+21m drgitlin: Sad that I'm at neither #AGBT nor #AAASmtg.
+25m bkmacy: @ING_SYS variant analysis able to collaborate variant hypothesis in less than an hour #AGBT
+25m bioontology: RT @bffo: Birney also urges JG to look at encode data http://t.co/riAfjB6l #AGBT
+31m lexnederbragt: I guess they used MinIONs for GATTACA... #ONT #AGBT
+33m bkmacy: Levy: @ING_SYS variant analysis helps find needle in a haystack #AGBT
+33m GenomicsIo: Jonathan Roth has some serious doubts about @nanopore technology maturity http://t.co/s3fX4IgA via @forbes - perhaps not unfounded? #agbt
+35m bkmacy: Levy: @ING_SYS variant analysis helps find rare disease novel variants #AGBT
+37m bkmacy: Levy: @ING_SYS variant analysis finds new potential functional variant candidates #AGBT
+56m MTomasson: In the cold light of day, vaguely sad that tech vaporware stole the show from real biology at #AGBT
+57m westr: Hype = Happy! RT @MTomasson: In the cold light of day, vaguely sad that tech vaporware stole the show from real biology at #AGBT
+59m MTomasson: Caring for the ill with compassion not as sexy as selling snake oil with a good back story #AGBT

11 - 12pm EST
+10m gtyrelle: While ppl r fussing about technology @ #AGBT here at #EMBL Lee Hood, @timjph, Robert Gentleman et al. discuss implementation of P4 medicine.
+10m djschlesinger: Emily Hodges from HHMI & CSHL up next with a title too long to Tweet, subject: epigenetics #AGBT
+11m leonidkruglyak: A bit? RT @bioitworld: A bit harsh! Ion Torrent's Jonathan Rothberg compares @nanopore to cold fusion! #AGBT #nanopore http://t.co/1GwzYvCI
+13m WeigelWorld: Oxford Nanopore @pathogenomenick: I think wordles are often a bit lame, but this one from #AGBT tells a good story http://t.co/v4krjrI8
+13m djschlesinger: Hodges: jokes about being tall enough to see over the podium and about the length of her talk title #AGBT :p
+14m girlscientist: Emily Hodges will tell us stories from libraries of shotgun bisulfite sequencing. #AGBT [earlier comment correct: room = ghost town.]
+14m djschlesinger: Hodges: using shotgun busulfite sequencing to study methylomes in various cell types #AGBT
+16m Massgenomics: Now at #AGBT: Emily Hodges on genome-wide methylation studies of human blood cells. Shotgun bisulfite sequencing for hypomethylation.
+16m djschlesinger: Hodges: focusing on hypomethylation to identify areas of interest #AGBT
+18m girlscientist: Hodges: comparing methylomes from HSPCs, lymphoid and myeloid lineages. Looking for hypomethylated regions. #AGBT
+22m Massgenomics: Hodges: Very cool figure on hypomethylated regions vs CpG island declaration: arbitrary cutoffs make island definition quite arbitrary #AGBT
+23m bioinfosm: #agbt Hodges: 28k cpg islands and 50k hmr (unconventional tissue spec cpg islands)
+23m girlscientist: Hodges: no surprise, hypomethylated regions mostly at promoters. But strong subclass outside genes. Every tissue has unique set HMRs. #AGBT
+23m ElementoLab: #AGBT Emily Hodges: did full bisulfite-seq on hematopoietic stem/progenitor cells, lymphoid and myeloid lineage cells
+23m ElementoLab: #AGBT Emily Hodges: found 50-60K hypomethylated regions in each cell type, not restricted to CpG islands
+26m ElementoLab: #AGBT Emily Hodges: increasing lineage commitment is not unidirectional in terms of DNA methylation
+27m ElementoLab: #AGBT Emily Hodges: some hypomethylated regions are gained in more committed cell types, eg at CD19 in B cells
+28m ElementoLab: #AGBT Emily Hodges: boundaries of hypomethylated regions expand and contract in a cell type specific manner
+28m girlscientist: Hodges: at any region, differential methylation is "tidal" meaning boundaries expand and contract in cell-type-specific manner. #AGBT
+29m Massgenomics: Hodges at #AGBT: Differential methylation in HSC lineages is "tidal" near TSS - expanding/contracting in cell-type-specific manner.
+32m ElementoLab: #AGBT Emily Hodges: H3K4me1 and H3K4me3 are enriched at expanded hypomethylated regions (in ENCODE cell lines)
+34m girlscientist: Hodges: intergenic HMRs enriched for tissue specific transcription factor binding sites. [Similar to work from ENCODE.] #AGBT
+35m Massgenomics: Hodges: Intergenic hypomethylated regions (iHMRs) shared across subtypes are evol. conserved and enriched for TF binding sites. #AGBT
+36m ElementoLab: #AGBT Emily Hodges: shared intergenic hypomethylated regions tend to be bound by CTCF
+40m ElementoLab: #AGBT Emily Hodges: cell type-specific intergenic hypomethylated regions are enriched with H3K4me1; transcription occurs on both sides
+41m salisburymw: Ooh, TB regulatory network up next. Should be good. #agbt
+42m obahcall: And now James Galagan on regulatory network of tuberculosis #AGBT
+42m obahcall: Galagan: recently reported entirely drug resistant TB strains are quite scary #AGBT
+43m girlscientist: The wonderfully nice James Galagan now: TB, when faced with hypoxic environment, eats your cholesterol! Eww. #AGBT
+44m Massgenomics: James Galagan at #AGBT: The tuberculosis pathogen can persist inside of macrophages, in face of hypoxia and drugs, eating your cholesterol.
+46m djschlesinger: James Galagan from Boston Univ. speaking very very fast about the regulatory network of TB #AGBT
+46m djschlesinger: @girlscientist, better than Lipitor?? #AGBT
+46m pathogenomenick: better than eating benecol though? MT @girlscientist: ... TB, when faced with hypoxic environment, eats your cholesterol! Eww. #AGBT
+48m djschlesinger: Is it just me, or is Galagan's talk in fast forward mode? #AGBT
+49m obahcall: Galagan: start by comprehensive profiling generating tons of data including chip seq, proteomics, glycomics, and more.. #AGBT
+49m obahcall: Galagan: resolving binding site to single nt accuracy and resolution #AGBT
+50m robincoope: Eating cholesterol? That's why they used to call it Galloping Consumption. #agbt
+51m ElementoLab: #AGBT James Galagan: performing ChIP-seq on ALL transcription factors in TB
+51m obahcall: Galagan: see binding is exquisitely reproducible. #AGBT
+52m obahcall: Galagan: novel peaks enriched for known fxn. binding associated with motif strength #AGBT
+52m joalunatkthse: AGBT
+52m ElementoLab: #AGBT James Galagan: less than 30% of high affinity DNA motifs are actually bound in TB
+53m joalunatkthse: agbt 2012
+55m ElementoLab: #AGBT James Galagan: expression analysis shows that 25% of all TB ChIP-seq peaks are associated with gene regulation
+56m obahcall: Galagan: assign potential regulation to 25% of all peaks #AGBT
+59m girlscientist: Galagan: TB regulatory network quite a respectable hairball thanks to ChIP-seq data. #AGBT

10 - 11am EST
+0m ElementoLab: #AGBT Jesse Gray: transcription initiation rates can be estimated from 3' read densities of introns, distribution bimodal too
+0m djschlesinger: Gray: mRNA stability is not bimodal #AGBT
+1m djschlesinger: Gray: what explains bimodal gene expression ? Structure of the genome? #AGBT
+2m bffo: JG RNA degradation rate is as important as transcription rate #agbt
+2m djschlesinger: Gray: genes where no reads are detected are far from high expressions #AGBT - neat
+4m chloe46037: Don't forget to come and see Kevin McKernan in palms ballroom #AGBT .
+7m bffo: JG Birney asks about the 1st intron, and JG tells us he actually excluded 1st introns in his analysis #agbt 1st intron is different
+8m genomeresearch: RT @Massgenomics: Jesse Gray on RNA-Seq kinetics in vivo: splicing occurs during transcription. Intron size no effect on rate #AGBT
+9m djschlesinger: Patrick Schnable from Iowa State University up next to talk about gene loss during domestication bottleneck in maize #AGBT
+9m bffo: Birney also urges JG to look at encode data http://t.co/PNEDOtZI #AGBT
+10m obahcall: Patrick Schnable talks next on gene loss during domestication of maize #AGBT
+10m djschlesinger: Schnable: regarding tweeting policy, his talk is so secretive he doesn't even want us to listen to him #AGBT :p
+11m Copenhagenomics: Patrick Schnable is doing a talk that is so secret that we can't even hear it! ;) Tweet away :) #sharingiscaring #AGBT
+15m djschlesinger: Schnable: allelic diversity is lost during domestication, are genes lost too? #AGBT
+16m ElementoLab: #AGBT Patrick Schnable: 250+ genes present in wild maize lines, have been lost in domesticated maize genome
+16m djschlesinger: Schnable: short answer: yes, genes are missing. #AGBT
+17m obahcall: Schnable: asking if if whole genes were lost during maize domestication #AGBT
+17m Massgenomics: Patrick Schnable: Corn was domesticated from Teosinte by native Americans 10k hrs ago. What genes were lost? #AGBT
+19m obahcall: Schnable: yes... 1ks of expressed genes in teosinte are missing from B73 ref #AGBT
+20m ElementoLab: #AGBT: Patrick Schable: 1,000s genes expressed in teosinte alone, not in domesticated B73 line
+20m obahcall: Schnable: validate by seq capture 74% of potential 2800 PAVs not present in B73 #AGBT
+22m rnomics: RT @bffo: JG #RNA degradation rate is as important as transcription rate #agbt http://t.co/wv7NPbSd #phylogenomics-gen @MyEN
+24m ElementoLab: #AGBT: Patrick Schable: teosinte genome not sequenced, used genetic mapping to find teosinte-specific genes, arranged in clusters
+25m antolikykab2: AGBT Rong Chen: calc a likelihood ratio of disease for personal genome from multiple allele risks
+26m ElementoLab: #AGBT: Patrick Schnable: teosinte genome not sequenced, used genetic mapping to find teosinte-specific genes, arranged in clusters
+26m illumina: New blog post from Abizar Lakdawalla recapping Friday at #AGBT http://t.co/py652hSN
+27m pathogenomenick: I think wordles are often a bit lame, but this one from #AGBT tells a good story http://t.co/6gGV6Bbs
+29m Massgenomics: Schnable at #AGBT: selection for or against alleles likely drove gene loss during domestication. e.g. selection against seed shattering
+29m omespeak: Great summary of yesterday's talks: RT @illumina: New blog post from Abizar Lakdawalla recapping Friday at #AGBT http://t.co/Sqlk2Nuc
+30m bffo: RT @illumina: New blog post from Abizar Lakdawalla recapping Friday at #AGBT http://t.co/XWPrwJOj
+30m illumina: Missed "Eliminating the Sequencing Informatics Bottleneck" workshop this morning? Another one in 5 min, Illumina Lounge (Capri Ballrm) #AGBT
+31m bffo: RT @pathogenomenick: I think wordles are often a bit lame, but this one from #AGBT tells a good story http://t.co/RPfETLOG
+32m ElementoLab: #AGBT: Patrick Schnable: some imp teosinte genes may have been lost due to proximity to neg selected genes, potential for crop improvement
+34m obahcall: Schnable: some these genes lost during domestication may have potential for crop improvement #AGBT
+37m ramblingmuse: Meanwhile over on Marco island, people are hugging thumb drives and having wet dreams #AGBT
+50m bioitworld: A bit harsh! Ion Torrent's Jonathan Rothberg compares @nanopore technology to cold fusion! #AGBT #nanopore Forbes http://t.co/HCcEgmIk
+52m assemblathon: Such a good twitter buzz yesterday! RT @pathogenomenick: All the tweets (and there are a lot of them) from #AGBT day 3 http://t.co/WHBX6nY4
+55m assemblathon: RT @CRIgenomics: Knock knock, can we come in? There are 1000 attendees at #AGBT that want a new sequencer. http://t.co/OK1m1HtK
+56m assemblathon: Awesome! RT @pathogenomenick: I think wordles are often a bit lame, but this one from #AGBT tells a good story http://t.co/E52aWhuT
+56m kbradnam: RT @pathogenomenick: I think wordles are often a bit lame, but this one from #AGBT tells a good story http://t.co/Zdftxaxf

9 - 10am EST
+0m omespeak: #AGBT Equally unsurprising, a doubting voice: MT @matthewherper: Who Doubts The USB Thumb Drive Sequencer? A Rival http://t.co/qxI7zTN3
+0m djschlesinger: Morning session of last day at #AGBT - it's like a ghost town. Must have been a rough night.
+2m djschlesinger: Michael George's from University of Liege giving morning keynote address #AGBT
+6m CrapBio: HELLO! #AGBT anyone awake or are you all sleeping of your nanpore hangover.?
+7m obahcall: Starting the last day of #AGBT right with keynote from Michel Georges
+8m omespeak: +the strong drinks at IonTorrent party last night RT @CrapBio: HELLO! #AGBT anyone awake or are you all sleeping of your nanpore hangover?
+9m CRIgenomics: There is nowhere to put your hand in these cows, unlike last years #AGBT!
+10m Massgenomics: First session at #AGBT today: Genetic basis of "color-sidedness" in Belgian Blue cattle. Bovines! Presenter said, "Please don't run away."
+10m neilhall_uk: @CRIgenomics: There is nowhere to put your hand in these cows, unlike last years #AGBT! I am not even going to try and understand...
+15m CRIgenomics: Google image search on "fistulated cow"...it was one of the best talks of last years #AGBT. Maybe the Zebra shaving video was better?
+16m p_hi1: "80% of the genome is expressed in the form of a primary transcript: 90.7% of exon, 79.3% of intron, and 35.5% of intergenic bases." #agbt
+20m p_hi1: Good review: AGBT 2012 Day 2: Cancer, Technology, and Oxford Nanopore: http://t.co/sDKc1phY
+24m robincoope: Domestic yaks! #agbt
+28m pathogenomenick: sounds rattled! RT @neilhall_uk: Rothberg does not believe it. http://t.co/P29C99Aq Who would have thunk? #agbt #nanopore
+28m pathogenomenick: "sequence A bacteria??" ughh #fail RT @neilhall_uk: Rothberg does not believe it. http://t.co/P29C99Aq Who would have thunk? #agbt #nanopore
+30m ElementoLab: #AGBT Michel Georges: color sidedness in cow due to circular bubble containing Kit gene moving from 1 chr to another, partially coming back!
+34m djschlesinger: Jesse Gray from Harvard Medical School up next to tell us about mRNA dynamics from unperturbed cells at steady state using RNA-Seq #AGBT
+35m djschlesinger: Gray: doesn't want to disappoint everyone but his USB stick only contains his PowerPoint slide #AGBT
+36m obahcall: Jesse Gray up next: this may be disappointing, but all I have on this usb is my talk #AGBT
+36m omespeak: I can see the joke about 'it is only a USB stick not a sequence' getting old pretty quick here. Jesse Gray does the first one. #AGBT
+37m bffo: Jesse Gray: next: "after yesterday's talk, you may be disappointed, but all I have on my USB stick is my talk" #agbt
+38m bffo: JG Kinetic analysis of RNA important, on patient tissues, yes, I strongly agree! #agbt
+38m ElementoLab: #AGBT Michel Georges: genetic bubble that came back inserted near Kit, did not contain Kit but piece of chr6-chr29
+39m djschlesinger: Gray: existing methods for studying RNA kinetics alter transcription, RNA-Seq is better method #AGBT
+40m djschlesinger: Gray: RNA-Seq densities across introns have negative slopes, why? #AGBT
+41m djschlesinger: Gray: negative slope is not simply due to RNA polymerase falling off #AGBT
+42m djschlesinger: Gray: negative slope is due to the intermediate steps in RNA synthesis, starting from first exon and proceeding to further exons #AGBT
+43m djschlesinger: Gray: negative slope is proportional to transcription initiation rate #AGBT
+43m bffo: JG introns have negative slope 1st principles: transcription, splicing & degraded steady state #agbt cool to go back to 1st principles!
+44m obahcall: Jesse Gray on RNA-seq for in vivo mRNA dynamics from unperturbed cells at steady state #AGBT
+45m djschlesinger: Gray: some transcripts are longer than diameter of the nucleus, how then do splice sites find each other? #AGBT
+46m djschlesinger: Gray: splicing of long introns requires waiting for transcription of intron to finish #AGBT
+47m bffo: JG Large introns are processed as efficiently as short ones #agbt
+47m djschlesinger: Gray: actually, he disproved that. Splicing does not wait for transcription of next intron. #AGBT
+49m ElementoLab: #AGBT Jesse Gray: a lot of mRNA dynamics information can be extracted from RNA-seq read densities across gene bodies and especially introns
+50m djschlesinger: Gray: describing relationship between RNA-Seq read densities and mRNA processing time #AGBT - too much calculus this early in the morning
+50m ElementoLab: #AGBT Jesse Gray: for example splicing of an intron does not have to wait from next intron to be transcribed
+51m ElementoLab: #AGBT: but splicing of long introns waits for transcription of the intron to finish, no pre-splicing
+52m Massgenomics: Jesse Gray on RNA-Seq kinetics in vivo: splicing occurs during transcription. Intron size no effect on rate #AGBT
+52m ElementoLab: #AGBT Jesse Gray: but splicing of long introns waits for transcription of the intron to finish, no splicing of partially transcribed introns
+54m djschlesinger: Gray: Lariat formation = 2 minute, exon ligation = 1 minute, intron degradation = 30 seconds #AGBT
+55m ElementoLab: #AGBT Jesse Gray: overall intron processing times: lariat formation takes 2mins, exon ligation 1min, intron degradation 0.5min
+56m djschlesinger: Gray: gene expression by RNA-Seq is bimodal #AGBT
+57m ElementoLab: #AGBT Jesse Gray: gene expression by RNA-seq is typically bimodal, low mode is 1-2 copies per cell
+58m CRIgenomics: Knock knock, can we come in? There are 1000 attendees at #AGBT that want a new sequencer. http://t.co/Un5TZO3n

8 - 9am EST
+5m illumina: #AGBT Workshop: Eliminating the Sequencing Informatics Bottleneck -- starts in 10 min, Illumina Lounge (Capri Ballroom 2/3)
+6m wimufi: I'm way behind, too MT @mrrizkallah It's been 2 hours and I am half way thru #AGBT tweets. This is a 500X coverage :-)
+18m wimufi: Doesnt $ILM own stake? MT @Matt_Francis #AGBT obi-wan: I felt a disturbance in the force, as if a million $ILM investors cried out in pain
+21m neilhall_uk: Rothberg does not believe it. http://t.co/bAPfYKXJ Who would have thunk? #agbt #nanopore
+25m accelmed: Unveiled: 1 of coolest inventions @ Wyss/HMS: DNA Nanobot 4 Immune Programming http://t.co/LeEYghZ1 #tedmed #futuremed @hackmedmit #agbt
+38m deannachurch: Not sure I can chair session and tweet at the same time, but I'm sure @girlscientist will be all over it! #AGBT
+57m omespeak: As expected, the New York Times picks up on the Oxford Nanopore story: http://t.co/FFOo7EdS #AGBT
+57m bongopondit: As expected, the New York Times picks up on the Oxford Nanopore story: http://t.co/EI0suLLp #AGBT
+59m Personal_RX_WI: Last day of #AGBT. Genomics Studies morning session about to get under way.

7 - 8am EST
+33m chloe46037: Here we go. Day 4 #AGBT .

6 - 7am EST
+4m hinksonzxgzyq0: Personal_RX_WI tweeting latest and greatest from world of agbt have fun Jaime and Mike!
+56m Chris_Evelo: Happily providing tutorials "@girlscientist: Boland final conclusion: he needs to go back to school for bioinformatics. Don't we all? #AGBT"
+57m Chris_Evelo: Happy 2 provide tutorials RT @girlscientist: Boland final conclusion: he needs to go back to school for bioinformatics. Don't we all? #AGBT

5 - 6am EST
+2m nanopore: RT @genomesunzipped: Making sequencing simpler with nanopores: Our take on the new Oxford @Nanopore machines #AGBT http://t.co/pqWhsQYp
+28m simonbayly: MT @pathogenomenick: Oxford Nanopore megaton announcement: Why do you need a machine? http://t.co/wqwZlHRP #AGBT"
+29m pathogenomenick: Well here you go, #AGBT day 4 tweets http://t.co/gedbgq8q - I guess we're not expecting announcements today.
+51m mannersuwnwe4: Rehm: discusses creating single database for clinical data, with tiered levels of curation AGBT

4 - 5am EST
+26m kevinltweets: diluting rabbit's blood in water = your sample prep I.M.P.R.E.S.S.E.D. Oxford @Nanopore machines #AGBT http://t.co/RoarVw4d
+45m mincle: @ElementoLab: #AGBT Scott Grimmond: axon guidance genes eg Robo2, Slt2, Sema3A often mutated in pancreatic adenocarcinomaoops sean
+54m phospho3d: A disposable USB pocket-sized nanopore sequencer. http://t.co/dRl8NV8R #AGBT #science #cool

All the Oxford Nanopore Videos

The Oxford Nanopore website is struggling a bit due to the huge interest generated by their announcement earlier today, so I've embedded their new videos in this post for you to view:

[vimeo clip_id="36907534"]

[vimeo clip_id="36905672"]

[vimeo clip_id="36903016"]

[vimeo clip_id="36906993"]

[vimeo clip_id="36909115"]

The last one entitled "Run Until": DNA sequencing informatics on the GridION and MinION systems doesn't seem to want to embed properly ... but you can view it on Vimeo.com

[vimeo clip_id="36903904"]

Oxford Nanopore megaton announcement: "Why do you need a machine?" - exclusive interview for this blog!

Sometimes this genome blogging lark really pays off. Yesterday was one of those days as I got a sneak preview of the big announcement at AGBT, and 20 minutes to speak with Oxford Nanopore's Dan Turner (Director of Applications), Clive Brown (Chief Technical Officer) and Zoe McDougall (Director of Comms). The downside of course was that I couldn't tell anyone what they said until the embargo was lifted at 5pm today!

I asked as many questions as I could without knowing the contents of the AGBT talk. I probably should have asked a bunch more. I do remember saying "wow" quite a lot.

First, go and read the press release!

Executive Summary

  • Nanopore have announced a strand sequencing method, made possible by a heavily modified biological nanopore and an industrially-fabricated polymer
  • DNA passes through the nanopore and tri-nucleotides in contact with the pore are detected through electrochemistry
  • Demonstrated 2x50kb sense & anti-sense of same molecules (lambda phage) - no theoretical read length limit
  • Can sequence direct from blood without need for sample preparation
  • Two products announced:
    • MinIon - USB disposable sequencer for ~ $900 has 512 nanopores - target 150mb/hour
    • MinIon can run at 120-1000 bases/minute per pore for up to 6 hours
    • GridIon - two versions of rack-mountable sequencer with 2000 nanopores (2nd half 2012), 8000 nanopores (2013)
    • GridIons can be racked in parallel, 20 could do a whole human genome in 15 minutes
    • Each GridIon can do "tens of gigabases" over 24 hours </ul>
    • Both machines commercially available 2nd half 2012
    • Sequencing can be paused, sample recovered, replaced, started again
    • Accuracy is 96%, errors are deletions, error profile will improve through software </ul>

      The MinIon

      Firstly you need to know this is pronounced "min, ion" rather than "min-yon". The MinIon is an array of nanopores - 512 to be precise - and circuitry housed in a USB stick. Why a USB stick? "The form factor is determined by the requirements" - as there are no fluidics you don't need a big machine. There are no fluidics. "Your fluidics is a Gilson", said Brown. The prototype version has an ugly battery pack attached to it but it will eventually use USB power. The USB stick is disposable. "Why do you need an instrument?" he says. We wander into the realms of sci-fi at this point. DNA molecules pass through the nanopore and nucleotide sequence is detected by the electronics. Bases are streamed - live - to your laptop as FASTQ (bases with qualities). This is where the "run until" makes sense, if you are interested in a particular gene just wait until the sequence comes out and shut it down to preserve the circuitry.

      "Hungry Hippo" sequencing


      The sample lives in solution and the DNA floats around, there is no attachment to beads or solid surfaces. Brown says the nanopore functions "like a Hungry Hippo", grabbing DNA as it bumps up against the pore. Only about 0.001% of the starting DNA is processed and the sample is unadulterated and can be recovered at the end. Do some sequencing, then literally "pause" it, remove the sample - mess around with it - replace it and continue sequencing. This is an iterative approach - how will it change our way of doing sequencing experiments? Can you run forever? "Right now this is limited by the circuits which burn out after about 6 hours."

      Fast-Slow Sequencing

      Nanopore can ratchet down the speed of the DNA passing through the pore. Right now they are running "about 120-150 bases per minute", but this can be sped up to give 150 megabases per hour of sequence from the MinION. It can be sped further, even as far as 1000 bases per minute per pore, although running above 500 bases per minute starts to impact the accuracy.

      Read lengths

      Read length reflects the fragment size in the sample. They've sequenced sense and antisense of lambda phage - giving a 100kb read from same molecule. "We've tried 5, 10, 15, 20kb etc. without problems" says Dan Turner. You could bung an Illumina library in there should you wish.

      Accuracy

      A huge question. They are talking about a 4% raw read error rate. The errors are mainly deletions. "We know what the problem is and we can fix it" said Turner. He explained the signal comes from the interaction of DNA with the pore barrel. The barrel is in contact with three nucleotide bases at one time, then the strand is moved along one base by a "special processive enzyme". Each tri-nucleotide gives a specific signal. A regular Viterbi algorithm turns that into bases, and the Markov model can be improved through better training. Notably the quality does not drop off over the length of the read and substitution errors are infrequent.

      The Breakthrough

      A major problem with turning biological nanopores into DNA sequencers is that they are often embedded in fragile lipid bilayers which are unstable to pH and temperature (see James Hadfield's great nanopore primer for more information). The major break-through is that Oxford Nanopore can make this membrane in an industrial process in a factory and the result remains stable, meaning it can be shipped to the customer at room temperature. The nanopore itself has over 300 modifications to make it work efficiently, these were found through random mutation during a series of high-throughput screening experiments.

      Bioinformatics

      With the MinIon - bases are streamed off in FASTQ straight to your laptop. You can set up your workflow to "run until ..." a particular sequence is read, and then shut it off to protect the circuitry.

      The GridIon

      The GridIon has already been announced and is a rackable sequencer which takes disposable cartridges for massively parallel sequencing. It will be available in 2000 and 8000 nanopore versions. There are four wells to one circuit.

      Sample Preparation

      The example given at the presentation was sequencing of whole blood. "You add blood, and some buffer and some enzymes", presumably to nick the DNA strands which don't need to be denatured. That's it. But you could process your sample in a million different ways first, as long as dsDNA is presented to the pore. "You could even put an Illumina library in". No amplification required. At the presentation Brown said they "had a look at RNA" and found they could read it just like DNA, no reverse complementation necessary.

      The Illumina Connection

      This is an Oxford Nanopore product, being marketed by Oxford Nanopore. Illumina have a stake in the company.

      Is this a game changer?

      This is a very different product to the existing suite of sequencers. It's also rather dissimilar to PacBio despite being single molecule (but apparently superior in all respects).

      For those chasing the goal of doing tens of thousands of $1,000 human genomes, this may not seem to be the obvious solution. The cost per base is competitive with existing systems. But I think we need to think differently about this machine:

      • how will access to a disposable sequencer change the way we do biology and medicine? With no capital costs, this certainly has the power to democratise sequencing even further. But does the $900 price point make it a tough sell for near-patient testing or field applications, or will clever use of the technology make it economical? Immediately you imagine that you could load a sample, sequence for 10 minutes, remove, put another sample in to get a kind of barcode-free multiplexing
      • how will 100kb+ reads change your research? It seems to me this will solve the very gritty problem of trying to reconstruct microbial communities through assembly of short-reads. Large chromosomal variations should be detectable with ease. Certainly de novo assembly will become trivially easy for many organisms. Should be amazing for 'unculturable' microbes too.
      • how will "run until" change your research? If you are looking for something specific, you just wait until you have got that particular bit of chromosome 7 running through the pore and stop - no need to oversample the whole genome to 100x.
      • we can now take the sequencer out into the field. How will this transform microbial ecology? You can go and pipette in some sewage water and be a 21st-century John Snow and detect cholera. Does this help with the "disease weather map" ? You can imagine a sexy Kate Winslet / Marion Cotillard style epidemiologist armed with one of these and a laptop.
      • what experiments can you do with iterative sequencing? What are the benefits of taking a sample on and off and manipulating it? Will this change the way we do RNA & ChIP-Seq type research? </ul>

        I'm still processing this announcement and would love to hear your thoughts below.

        But to sum up, this is the megaton sequencing announcement we've been waiting for.

Oxford Nanopore introduces DNA 'strand sequencing' on the high-throughput GridION™ platform and presents MinION™, a sequencer the size of a USB memory stick

EMBARGO: Friday 17 February, noon EST/5pm UK
Oxford Nanopore introduces DNA 'strand sequencing' on the high-throughput GridION™ platform and presents MinION™, a sequencer the size of a USB memory stick

- New generation of sequencing technology uses nanopores to deliver ultra long read length single molecule sequence data, at competitive accuracy, on scalable electronic GridION platform. Miniaturised version of technology, MinION, will make nanopore sequencing universally accessible -

17 February 2012, Oxford, UK/FL, US. Oxford Nanopore Technologies Ltd. today presented for the first time DNA sequence data using its novel nanopore 'strand sequencing' technique and proprietary high performance electronic devices GridION and MinION. These data were presented by Clive G Brown, Chief Technology Officer, who outlined the Company's pathway to a commercial product with highly disruptive features including ultra long read lengths, high throughput on electronic systems and real-time sequencing results. Oxford Nanopore intends to commercialise GridION and MinION directly to customers within 2012. Oxford Nanopore's GridION system consists of scalable instruments (nodes) used with consumable cartridges that contain proprietary array chips for multi-nanopore sensing. Each GridION node and cartridge is initially designed to deliver tens of Gb of sequence data per 24 hour period, with the user choosing whether to run for minutes or days according to the experiment.

Oxford Nanopore will introduce a new model of versatile pricing schemes designed to deliver a price per base that is as competitive as other leading systems at launch. Further substantial pricing improvements are expected with future development to the technology, in particular with increases in nanopore processing speed and higher density electronic sensor chips.

Oxford Nanopore has also miniaturised these devices to develop the MinION; a disposable DNA sequencing device the size of a USB memory stick whose low cost, portability and ease of use is designed to make DNA sequencing universally accessible. A single MinION is expected to retail at less than $900.

"The exquisite science behind nanopore sensing has taken nearly two decades to reach this point; a truly disruptive single molecule analysis technique, designed alongside new electronics to be a universal sequencing system. GridION and MinION are poised to deliver a completely new range of benefits to researchers and clinicians," said Dr Gordon Sanghera, CEO of Oxford Nanopore. "Oxford Nanopore is as much an electronics company as a biotechnology company, and the development of a high-throughput electronics platform has been essential for us to design and screen a large number of new candidate nanopores and
enzymes. Our toolbox is customer-ready and we will continue to develop improved nanopore devices over many years, including ongoing work in solid state devices.

Summary of presentation

At the Advances in Genome Biology and Technology conference (AGBT), FL, US, Oxford
Nanopore presented:
 A novel method of DNA 'strand sequencing' that uses an array of proprietary protein nanopores embedded in a robust polymer membranes. Each nanopore sequences multiple strands of DNA from solution in succession, as individual strands are passed through the nanopore by a proprietary processive enzyme. Base calling is performed by identifying characteristic electronic signals (disruptions in current through the nanopore),
created by unique combinations of DNA bases as they pass through a specially engineered region inside the nanopore. DNA and enzyme are mixed in solution, engage with the nanopore for sequencing and once the strand has been completed a new strand is loaded into the nanopore for sequencing.
 Genomes that have been sequenced as contiguous reads comprising both complementary strands of the entire genome. An example was shown of 100 kilobases in a single continuous measurement of sense and antisense strands. Read lengths mirror fragment sizes in the sample with no exponential loss of processivity. Accuracy levels competitive with existing market-leading systems were shown. No deterioration of accuracy is seen throughout the sequencing of individual strands. A development pathway was presented that is expected to achieve accuracy exceeding current market-leading platforms through further design iteration of Oxford Nanopore's custom-made nanopores.
 Oxford Nanopore's GridION platform was presented, consisting of a scalable network device - a node - designed for use with a consumable cartridge. Each cartridge is initially designed for real-time sequencing by 2,000 individual nanopores at any one time. Alternative configurations with more processing cores will become available in early 2013 containing over 8,000 nanopores.
 Nodes may be clustered in a similar way to computing devices, allowing users to increase the number of nanopore experiments being conducted at any one time if a faster time-to-result is required. For example, a 20-node installation using an 8,000 nanopore configuration would be expected to deliver a complete human genome in 15 minutes.
 A variety of sample preparation options were presented. No sample amplification is required and any user-derived sample preparation resulting in double stranded DNA (dsDNA) in solution is compatible with the system. With nanopores embedded in robust polymer membranes, dsDNA can be sensed directly from blood and in some cases with no sample preparation.
 Oxford Nanopore's disruptive "Run Until..." informatics workflow:. Nanopores allow the analysis of data in real time, as the experiment happens. Each GridION node contains all the computing hardware and control software required for primary analysis of data as it is streamed from each nanopore, resulting in full length real time delivery of complete reads so that the user can perform secondary analyses as the experiment progresses. This allows the user to pre-determine an experimental question and continue the sequencing experiment until sufficient data have been accumulated to answer the question and move on to the next experiment.
 Oxford Nanopore intends to introduce a new pricing model for its GridION sequencing system, which moves away from the traditional instrument price and consumable price. This is designed as a series of packages that allow the user to tailor a scheme to their budget structure, whether more flexible with capital or consumable expenditure. Transparent pricing schemes are designed for online ordering and fulfilment, with
discounts applying to larger packages. Overall the schemes are designed to deliver a competitive 'price per base' compared to other systems on the market based on like-forlike user settings.

Further information is available at the Company's website www.nanoporetech.com. While orders are not yet being taken for the GridION and MinION systems, interested users may register their interest at the website.

-ends
Contact: Zoe McDougall, Communications. media@nanoporetech.com

Notes to editors
Oxford Nanopore Technologies Ltd is developing a novel technology for direct, electronic detection and analysis of single molecules using nanopores. The modular, scalable GridION technology platform is designed to offer substantial benefits in a variety of applications. The miniaturised MinION device is the size of a USB memory stick, designed for portable analysis of single molecules. Oxford Nanopore intends to commercialise GridION and MinION directly to customers for DNA 'strand sequencing' in 2012. In addition to DNA sequencing, the system is also compatible with the direct analysis of RNA. Oxford Nanopore is also developing a Protein Analysis technology that combines target proteins with ligands for direct, electronic analysis using protein nanopores. These nanopore sensing techniques are combined with the Company's proprietary array chip within the GridION system and MinION.The Company is also developing the subsequent generation of nanopore sensing devices based on solid-state nanopores.

Oxford Nanopore has licensed or owns more than 300 patents and patent applications that relate to many aspects of nanopore sensing including fundamental nanopore sensing patents, analysis using protein nanopores or solid state nanopores and for the analysis of DNA, proteins and other molecules, including the analysis of probe molecules on DNA The Company has collaborations and exclusive licensing deals with leading institutions including the University of Oxford, Harvard and UCSC. Oxford Nanopore has funding programmes in these laboratories to support the science of nanopore sensing. This includes the use of
functionalised solid-state nanopores for molecular characterisation, methods of fabricating solid-state nanopores and modifications of solid-state nanopores to adjust sensitivity or other parameters