Complete Genomics User Group Meeting 2011

[Michael.James.Clark]

Anyone else here in San Francisco for this?

So far the talks have been quite good, I think. If anyone's interested but can't attend, I'm blogging some of it at Mendelian Disorder.

In short, the presenters were clearly hand-picked because they've got strong findings using CGI. I want to also say that it's good to see some genuine academics presenting here... people using RealTimeGenomics for analysis, people pairing the CG data with exome-seq off an Illumina, et cetera. I do have to say that a lot of the findings seem to be stuff that can be identified solely through exome-seq, which makes one wonder why they would invest in whole genome sequencing. That said, for the sake of copy number, SVs, et cetera in cancer genomes it makes sense to go with whole genome.

[Michael.James.Clark]

People might be interested in this:

http://community.completegenomics.com/

Forum.
Wiki-ish "knowledge base" (at least I hope it's going to be wiki-ish).
Tools section that hosts CGAtools, community-created tools, etc.

[Michael.James.Clark]

Also, Jay Kaufman just announced an interesting "Cancer Grant" from Complete.

Copying from my blog:

Will be officially announced week of June 20th. Basically, it'll be an abstract plus some simple questions. There will be two winners in US and Europe. Applications will be due July 29th, winners decided by August 12th and samples will need to be submitted by September 16th.
Bonus: All applicants will get a future discount regardless.

Pretty cool... time to find some cancer samples to sequence.

[Michael.James.Clark]

Updated blog with info from some more of the talks. Some of the last ones were both interesting and generally relevant. In particular, the one about "gKnome", a new variant annotation tool from the Kong lab at Harvard, info about how to cut down on false positive de novo variants and HuVariome, an effective alternative (we hope) to using dbSNP as a filter.

Overall, I thought it was quite a strong conference. It was not overly biased despite being hosted and paid for by CG. The speakers were nearly all academics and shared some very good info with us. Plus, there were "breakout" sessions where we had smaller group chats that were great. Kudos to CG. (Also, the venue--San Francisco Fairemont, top floor overlooking the bay--was awesome, and pretty decent food the whole time too! Props!)

[Geneus]

Overall, I thought it was quite a strong conference.

I agree. CG brought their A-game out for this meeting.

[Len Trigg]

I want to also say that it's good to see some genuine academics presenting here... people using RealTimeGenomics for analysis, people pairing the CG data with exome-seq off an Illumina, et cetera.

For those interested in processing Complete Genomics data themselves, Real Time Genomics have now released the RTG Investigator tools for mapping and variant detection free for individual use. Give it a try and let us know how you get on!