Day 2

General twitter comments slowed down to a crawl in the morning, most likely due to most attendants suffering from the horrible WiFi connection or last night’s cocktail parties. Again, 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 as this is mostly for my own records. Thanks everyone for the excellent coverage!

General notes

• Pacific Biosciences CEO Hugh Martin previews “third-generation” sequencer. Other take on the new machine from Genetic Future with some more numbers and feature details
• Also from Genetic Future a general update
• MassGenomics’s update on cancer genomics at AGBT, and another MassGenomic’s article around the general topic. “In 2-3 years all ped leukemia patients will get a full genome sequencing along with parents and sibs at ST Jude’s” (J. Downing)
• VCFTools gets released

Talk notes

• Keynote from James Downing on cancer genomics at St Judes
• Elaine Mardis: use next-gen seq to find mutations present in a subset of cancer cells; more common mutations likely older. Testing PacBio. Accuracy 94% sites 6 fp and fn. Sensitivity. Detected low prev. Tumor cellularity. Prevalence. Tier 1 good. Tier 3 ok. PacBio proof of principal: cancer mutations tally pretty well with Illumina/454. Neither depth or cost mentioned. See MassGenomic’s previous coverage on pediatric cancers
• Levi Garraway, Harvard Med. Cancer transitioning from ‘where in the body is the primary’ to mutation-based diagnoses. Can (almost) give each cancer patient 1/10th of a lane of targetted Illumina: 100X coverage for ~250 cancer genes. Clinical oncologists will ‘shoot you or run away in terror’ if presented with a patient’s full genome sequence.
• Nicole Cloonan, The University of Queensland, Translation-State RNAseq of Human Embryonic Stem Cells using Paired-End Sequencing. Beyond the Plurinet.
• Shuro Sen, NHGRI, Transcriptome Profiling of ClinSeq Particpants by Massively Parallel Short-Read DNA Sequencing.
• Brian Haas, Broad, Genome annotation using mRNA-Seq: A case study of Schizosaccharomyces pombe. Overview of current algorithm and approaches for mRNA-seq assembly
• Manual Garber, Broad, Annotating LincRNA Transcripts Using Targeted Sequencing.
• Stan Nelson (UCLA), “Whole Human Cancer Genome Sequencing: Progress Towards Common Application”. Gold standard for SNP discovery isn’t longer reads at high-quality, but low coverage overall
• Dietrich Stephan (co-founder of @Navigenics, now CEO of the IGNITE Institute for Individualized Health) is discussing pers. medicine. There will be no market for targeted sequencing once whole-genome sequencing drops to a few hundred dollars.
• David Craig (TGen): Lower-coverage whole-genome seq can be more cost-effective than exome seq for Mendelian discovery.
• Kevin McKernan (Life Tech): sequencing your boss’ genome raises some serious career-ending possibilities. Announcing the improved SOLiD 4 technology: increased accuracy, increased output, changes to colour space encoding. Actually quite cool: some serious improvements in accuracy. By using both 2-base and 1-base encoding, SOLiD can bring error rates down to 1 in 10^6. Sequencing is so accurate that errors from library prep now dominate. Are working on gentler prep methods.
• Pacfic Biosciences Workshop with many more numbers, as well details from Jonas Korlach’s talk. Stephen Turner: Raised nearly $300M. Influenza work. 9hrs to data. Single molecule heat maps detect subspecies. With singe reads. Single read transcripts too. 10,351 Base reads. Strobe sequencing allows you to generate pulses of sequence separated by an arbitrary distance (mate pair equivalent). Circular consensus. Can give q40 reads. Coverage not gc biased. Can detect and discriminate C 5meC and OHMeC and 8-oxoG (Methylation assays take advantage of differential kinetcs of base incorporation at me-sites and measure different kinds of me-groups). V1 2010 to 2013. V2 2014. Human genome in 15 min for $100. Three questions about error rates, and still Turner has given us no hard numbers. Presentation was like watching Lost. You think you’ll finally get some answers but you end up w/even more questions.