Our Gene Sherpa Steve Murphy has a lot more to say about this, include a challenge to 23andMe to repeat the assays for all clients that have already been genotyped and compare the two data-sets. I personally don't think that's necessary, although it would be a powerful symbol of openness for the company to release some more detailed results of the comparisons between results between the old and new facilities (at least to its customers, if not to the rest of us riff-raff).
Disclaimers or no disclaimers, people are taking the results of these tests seriously. Failing to act quickly and strongly to reassure the community that their personal genomic data are sound would further undermine an industry that is already being subjected to considerable media scepticism.
That said, if I were in the first batch of customers I'd still be feeling pretty confident about my data. Steve suggests that the stated
<0.1% discrepancy between the old and new labs represents "a whole ton of SNPs"; I'd respond that it means that for any given SNP of interest, there's at most a 1 in 1000 chance that your data are incorrect. That strikes me as a thoroughly acceptable error rate given how small an emphasis I'm likely to place on any one SNP when considering making changes to my lifestyle.Update: In the comments, Ann Turner points to her recent comparison of 23andMe and deCODEme data from the same individual on RootsWeb. For the 560,128 SNPs for which both companies called a genotype, only 35 were different between the two platforms - that's an astoundingly low discrepancy rate of just 6.25 differences per one hundred thousand SNPs! Slightly more worrying is 23andMe's missing data rate of 3.5 per 1000 SNPs (for SNPs that were called successfully by deCODEme), which is uncomfortably high to my liking, and compares unfavourably to deCODEme's missing rate of less than 1 per 1000 SNPs.
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4 comments:
gawker media should buy you so you can turn into a gossip site for the personal genomics industry....
OK, OK... I'll be focusing on something other than scurrilous personal genomics gossip over the next few posts, I promise.
I suspect the laboratory switch has more to do with bureaucratic regulations and red tape than anything else. 23andMe originally sent their samples to Illumina for testing, while deCODEme has in-house capabilities.
DeCODEme originally interpreted laws in such a way that customers from certain states (e.g. California) could not receive any gene profile results because their laboratory was not CLIA certified. They later concluded that they were exempt, since they do not actually make diagnoses.
I compared results for a person who had tested at both 23andMe and deCODEme. For the SNPs that overlapped, the rate of discordant calls was .00624%.
http://archiver.rootsweb.ancestry.com/th/read/genealogy-dna/2008-01/1201224021
Ok...Ok....that's a pretty good read.....Maybe I overshot it?
But...it does stink when LabCorp is now locked in with 23andMe and now LabCorp is locking out others trying to get into the genomics game.
http://www.g2reports.com/issues/advisory/advisory/mark_terry/235-1.html
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