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Illumina Discovery Symposium at ASHG 2012, Part One

by
Abizar Lakdawalla
| Nov 14, 2012

ASHG2012 No.RegistrantsIt’s been a few years since I had attended the American Society of Human Genetics meeting, but I could not resist this year as it was in San Francisco, so close to home. I was very impressed with how well-organized it was, and especially how the society organizers have embraced mobile apps. This was one of the easiest-to-use conference apps that I have seen, with schedules, location maps of the conference venue, abstracts, and best of all, an area to input your own notes. This app worked incredibly well on the iPhone but even better on the iPad (no, not the 7-inch mini one, as I have not got my paws on it yet!)

With nearly 7,000 scientific registrants, the public meeting started off on Tuesday evening with a very nice presentation by the prominent human geneticist Dr. Mary-Claire King, who came across as understated and gently humorous. If you want to check out her entire presentation in full glory, check out the YouTube recording.

Earlier in the day, before the opening ASHG presentation, I attended the Illumina Discovery workshop up the street at Hotel Nikko, featuring a great lineup of speakers. I had also invited some Illumina engineers along to learn a bit of biology. And it always helps that there is a great free breakfast and lunch.

Jeff Barrett from the Sanger Institute presented an intriguing talk on what to do after establishing associations with genome-wide association studies (GWAS). Focusing on inflammatory bowel disease, a significant amount of meta analysis and follow-up with the Illumina Immunochip yielded 163 loci associations from about 75,000 worldwide samples. Jeff’s group performed GRAIL network analysis with NOD2 for Crohn’s disease. It seemed difficult to establish disease specificity (Crohn’s and ulcerative colitis), and many of the markers overlapped with primary immunodeficiency and with leprosy, due to a potentially interesting association with Mendelian susceptibility to mycobacteria. He also talked about the transition to post-GWAS sequencing, with high power attached to sequencing a large number of samples at low depth rather than a few samples at high depth. For the UK 10k project, consisting of 4,000 controls and 5,000 cases, they have initiated sequencing at about 6x depth, requiring a new analysis pipeline to handle the low-coverage BAM files. He concluded that locus mapping is now quite routine, and collaboration is key for nearly all aspects of genetic interpretation.

Juan Rodriguez-Florez from the Weill Cornell Medical College presented on the Qatari genome sequencing project. The Qatari population was genotyped with 43 diagnostic SNPs showing three different population clusters, The Illumina exome chip and exome sequencing on the Illumina platform at BGI, was used to asses mutational profiles to determine prevalence of genetic disorders resulting from high rate of consanguineous marriage. 38% of the populations showed Mendelian disorder mutations, of which only 11% are currently being tested. They are in the process of transitioning from exome to genome sequencing, with 108 Qatari samples at 38x coverage.

Jake Byrnes from Ancestry.com, gave a good overview of genealogical research. They have over 2 million subscribers, and over 2 billion records. The aims of the AncestryDNA group are to tell you where your DNA comes from in the world, and who you share it with. They have performed over 50,000 DNA tests to inform family tree maps, cousin matching, and most common ancestor identification. The challenge seems to be the lack of enough data from worldwide populations to get highly granular interpretations but accuracy should improve as they get more samples.

Stay tuned for more of my perspecitves on the Illumina Discovery Symposium at ASHG, in the next post!

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