A comment from the current speaker (Vivian Cheung) inspired this post’s title, and it seems to me that the final day of AGBT 2012 has many elephants in the room. There’s the Roche hostile takeover, which has had relatively little chatter this week. I managed to meet Illumina CEO Jay Flatley after a talk yesterday (before Oxford’s announcement); he was polite and exuded nothing but cheerful, casual confidence.
The talks today have been spectacular. The morning session included Michel Georges on the genetic basis of “color-sidedness”, a coloration trait observed in Belgian blue cattle that was mapped to a duplication near the KIT gene in the bovine genome. Jesse Gray of Harvard Medical School presented his work on “steady-state” RNA-seq to decipher the kinetics of transcription and splicing. Patrick Schnable of Iowa State talked about gene loss during domestication of modern maize from its ancestor, Teosinte (tee oh sin tay) by Native Americans about 10,000 years ago.
Over the coffee break I met James Hadfield; he and Nick Loman are the creators of the next-generation sequencing maps, a visualization tool of NGS installations across the world.
After the break was one of my favorite talks, a survey of DNA methylation in hematopoietic stem cells, lymphoid cells, and myeloid cells given by Emily Hodges of CSHL. Then James Galagan walked us through systems biology approaches to study tuberculosis, whose pathogen has the unique ability to survive inside macrophages (in the face of hypoxia and even drug exposure) and does so by eating your cholesterol!
In the final session, chaired by Elaine Mardis, we heard about RNA-DNA differences in B-cells (Vivian Cheung) and streaming algorithms for RNA-Seq analysis from Lior Pachter, who related that someone had contacted him recently about processing 14 billion RNA-seq reads. That’s a lot.
The meeting is still abuzz with talk of Oxford Nanopore; which I think we can all agree is a disruptive technology, if the stock market is any indication:
My colleagues at Genomes Unzipped have a thorough take on this new technology, its promise, and what it could mean for the field. For my part, I remain cautious. I grew up in St. Louis, Missouri, the “show-me” state, and I’ll be convinced the moment I hold a minION in my hand.