Bio::Newsletter - Issue Q4, 2008

Terry's Corner

Report from American Society of Human Genetics (ASHG) meeting in Philadelphia, PA. Nov 13, 2008

If you have never attended an ASHG meeting, it is a relatively large meeting with more than 5,000 attendees. The plenary sessions are held in a cavernous room with 5,000 seats, 4 large screen projections of the speaker's presentation slides and an additional screen showing video of the speaker. Even larger is the poster and exhibits hall, where more than 2,300 posters are presented (covering topics including genetics, disease mapping, genomics, and new techniques and analyses), and various vendors are presenting their products and services. There are multiple smaller concurrent sessions as well. Few other experiences can provide you with such a comprehensive overview of the current trends in research concerning genetics and genomics.

No single person could be expected to cover or absorb the multitude of talks, topics, ideas, and results. Here I have attempted to provide impressions and samplings of some of the best and brightest existing research projects — at least for the sessions that I attended. My research interests are in genomics, bioinformatics, mutation identification and disease gene mapping so the talks that I attended were biased towards these topics. You can visit the ASHG 2008 meeting website (http://www.ashg.org/2008meeting/) and click on the “Abstract Book” link if you are interested in trying to get a sampling of the other exciting topics from this years meeting.

It is clear to me that next-generation sequencing technology (and in many cases coupled with existing technology — oligo chips, SNP chips, etc) is taking over as the dominant technology for genetics and genomics. However, this is currently limited to the largest institutions and genome sequencing centers due to the cost of both the technology and the assay run costs. It will be interesting to see if the technology will come down in price enough to be ubiquitous or if it will be replaced by something better before that happens. I should point out that the transition from capillary sequencing to next-generation technologies is more than a 100–fold increase in capacity. One of the early sessions aggregated many of the larger sequencing projects into one session. These included: Stacey Gabriel presenting on a “hybrid selection” technique using beads to capture DNA that is sequenced with Illumina/Solexa; Richard Wilson presented the discovery of 8 new genes that cause cancer found by re-sequencing; Richard Gibbs referenced a paper that describes a new company (“Complete Genomics”) that is promising a $5,000 whole genome sequencing service in the next year; Michael Stratton presented the identification of a startling number (305 rearrangements) of copy number polymorphisms (CNVs) in breast cancer cells (these were called “genomic shards” which would be very difficult to assemble with the short read technologies); In another session, David Altshuler discussed the 1000 Genomes project, whose goal is to create the most detailed and medically useful map of human genome variation by sequencing 1000 or more people in two years. In the month of September alone, the 1000 genomes project generated as much sequence data as is stored in GenBank; and then they did it again in October.

The application of massive sequencing appeared in many other talks, including: variation of expression of mice genes in CNVs, bisulfide sequencing to identify methylation sites, re-sequencing of X-linked mental retardation mutations, and hybrid capture and re-sequencing of lung cancer tumors. These exciting projects, as well as any projects related to next-gen sequencing, are generating even more data than what was considered 'enormous amounts' just a few years ago.

It is clear that advanced software to manage, present, and analyze this data will play a very important role in the years to come. If you are considering a new project that will utilize these technologies, feel free to contact Bio::Neos to see how your research could benefit from our software design and data analysis services.

I could not possibly pass on all of the exciting discoveries that were presented at ASHG, but hopefully I've provided a small sampling. If you ever get the chance to attend an ASHG annual meeting, I encourage you to do so.