Monday, December 3, 2007

We need more Samples/Sherpas!!!

Genetic Research is a hard business. You have to fight and IRB to get your I's Dotted and Your T's crossed. You have to write and write and write grants to get funding for your ideas. You have to manage the project and work to keep everything on track. But what will the rate limiting step be in genomic research?

Perhaps it is the lack of samples?

From Medical News Today, an exciting announcement regarding Lupus. Lupus is a terrible disease where the immune system attacks the body's DNA. It can cause horrible things including, stroke, skin disease, kidney disease, brain inflammation. In fact a whole host of persons who have this disease are unable to function in society.

A new finding includes the discovery (Not Validation) of a gene implicated in Lupus' pathogenesis (disease cause) OX40L. These researchers have identified other risks as well. His findings are only mildly interesting as replication will be needed. But what is more telling is his plea to the British people

"Without DNA samples from people with Lupus, we would be unable to study the disease," he says. "Despite the disease being relatively common, DNA samples are in short supply. I would encourage patients to discuss with their GP or consultant about providing a blood sample to help further our understanding."

With all of these companies looking at your SNPs or your Exomes or your Genomes and the vigor with which they launch PR campaigns. One would hope they could donate their datasets to these Scientists in need.

I perosnally have been trying for months to help a friend donate her genome to a sequencing project. Hope fully the Delaware Valley project will take her code. I think that genome sequencing will ultimately win the day over some of this SNP Chip technology. Why? SNPs are not enough. Copy Number Variation will slowly be found to play as large a role...if not more. You can read about some of this here.

The Sherpa Says: Did anyone watch the 60 Minutes special on Sherpas in The City. Turns out that for their health Sherpas are moving to New York. Any Gene Sherpas in the batch? I sure hope so. The Gene Sherpas of the world are coming together for one big collaboration and I can't wait till we all can guide the genomic tourists of the world!!! Stay Tuned for the Sister services soon to show up on the scene. Heads Up L.A., S.F., CHI!!! Are you a Sherpa? Want to join the team? We would love to have you. Can't wait to see you all in NY!


Keith Robison said...

SNP chips can read out copy number variation, as the signal for the probes varies with the amount of DNA probed -- albeit noisily. There are a lot of algorithms out there to convert SNP chip data into CNV calls.

That isn't to say full sequence doesn't trump SNP calls -- there is a lot you can't read from SNP chips.

Steve Murphy MD said...

Keith, Great points about the algorithms. I agree there are some pretty decent ones out there. Still, I'd take George's sequencing over others any day. Once of course I can make heads or tails of my sequence.