Disclaimer: All notes, comments and links are just cut’n‘pasted from Twitter (#AGBT), FF and RSS feeds, blog posts are attributed, Twitter comments are not.

In general, people seem to be cautious over the niche that PacBio is likely to fit in, have written off Helicos, and seem to be excited about the single-mindedness of Complete Genomics and the new technologies such as Ion Torrent’s machine.

General notes

• Summary of the current state of sequencing technology at Genetic Inference. Helicos is noticeably absent.
• Slide used to describe Complete Genomic’s sequencing process
• Details on Ion Torrent’s sequencing chemistry using an ion-sensitive layer (essentially a pH-meter); no light/scanning/cameras required.
• Omics! take on the Pacific Biosciences release, and more coverage from MassGenomics. Lots of skepticism given the lack of hard data.
• From Omics!, something already discussed on the SAM mailing list: “SAM/BAM stores all sorts of information on read pairs, and the strobe sequencing can generate many more than 2 tags per DNA fragment.”
• IBM timed their press release on a new data analysis method well

The workshops and New Technologies session

Illumina

Tons of data. 2 billion bases per run, 25GB/day with the HiSeq 2000. Work in progress: total human transcriptome, 16 tissues. Massive throughput, plug-and-play reagents, remote access (e.g. iPhone). Two human genomes in one run.

Elliot Margulies: Using 2 HiSeq flowcells rather than 1 moves >10 read coverage from 97% to 98%. Not worth using both; bsically, we’re now at the point where one run is overkill for sequencing a genome. SNP chip concordances: 98.2% for GAIIx, 99.7% for one HiSeq FC, >99.9% for both. Depths: 34X, 39X, 77X

Complete Genomics

1 million genomes in the next five years, 500 genomes/month this year.Customers are delivered software and data – nothing else. The company will take care of the steps between DNA sample and genetic variant calls. Wants to build 10 sequencing centers worldwide. 50 genomes completed so far. Rade Drmanac from Complete: Read errors very low (0.05%) Errors come from bubbles, dust, DNA damage, somatic variation. RD calls GCs offering “cloud sequencing”. Throughput per run is now approaching 2 trillion bases. That’s utterly insane. 20-instrument facility could do 100,000 genomes per year.

Jared Roach (ISB): four genomes from Complete from same family. Combining info across samples —> 99.9997% accuracy.

Dr. Zemin Zhang (Genentech): 1 mutation for every 3 cigarettes smoked… good to know. Cancer genomes. Aml norm and tumor. Had array data. Seq data>90% coverage above 10x. 40 and 60x avg coverage. Signed up for more genomes.

Helicos

ChIP-seq, direct-RNA. Runs with over 1e9. Single molecule. Helicos has short reads, high indel error rates, weighs 900 kg and costs $800K. Yeah, this talk is a tough sell.

PacBio

Eric Schadt: sequencing to explore energy-producing bacteria. Added 13X PacBio seq to 19X Illumina seq to assemble a bacterial genome. Strobed reads powerful for spanning repeats. Can integrate DNA variation, molecular traits and phenotypes to construct a probabilistic causal gene network.

LifeTech

Joseph Beechem (Life Tech) just got applause for having the longest talk title of the session. JB is introducing Life Tech’s new single molecule sequencing instrument based on quantum dots. Portable Nanometer sequencer. Tunable read lenght, tunable accuracy. Table top instrument. Can replenish a batch of polymerase mid-way through a run to replace dead molecules; effectively unlimited read length. Beta instruments will be available to a small set of collaborators by the end of 2010.

Ion Torrent

Jonathon Rothberg of Ion Torrent is a student of history. He sees Second Generation tech as a minicomputer. The box is just a box: Ion Torrent is a chip. Measures H+ as a base is incorporated. No lights, no moving parts. Not a single complexity.

Can leverage developments in the semiconductor industry, not reliant on optical technology like other platforms. Offering two free Ion Torrent instruments to researchers who come up with the best possible applications. Can sequence in hotels and on the backs of donkeys. With wireless you can analyze your data in GeneSifter.

Talk notes

• Joseph Puglisi, Stanford University School of Medicine, The Molecular Choreography of Translation. Using the PacBio system to track translation.
• Bing Ren, UCSD, Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells.
• Jesse Gray, Harvard Medical School, Widespread RNA Polymerase II Recruitment and Transcription at Enhancers During Stimulus-Dependent Gene Expression.
• Keynote: Henry Erlich, Roche Molecular Systems, Applications of Next Generation Sequencing: HLA Typing With the GSFLX System.
• Christopher Mason, Weill Cornel Medical College, Developmental Changes in Human Neocortical Transcriptome Revealed by RNA-Seq. No visible end to gene discovery. The more you sequence the more you see.
• Yardena Samuels, NHGRI, Mutational Analysis of the Melanoma Genome.