Posted by: shrikantmantri | October 10, 2009

Scientists call for changes to personal genomics based on comparison of test…

via Genetic Future on 10/7/09


Four scientists – including the omnipresent J. Craig Venter (left) – have penned an opinion piece in the latest issue of Nature based results from five individuals genotyped by two separate personal genomics companies. The article highlights some deficiencies in the way that genetic data are currently used by direct-to-consumer companies to generate risk predictions and to present them to customers.

The identity of the tested individuals isn’t made explicit in the article, except to note that there were two males and two females from the same family and one unrelated female. All of the individuals were tested by the companies 23andMe and Navigenics, which examine ~580,000 and ~923,000 sites of common genetic variation (SNPs), respectively. It’s worth noting that in both cases the scans were performed before the companies were required to comply with CLIA standards (meaning that genotyping accuracy may have improved somewhat since these scans were done).

The first result is reassuring: the concordance between the genotype calls from the companies was excellent, with disagreements at fewer than one in every 3,000 sites. Previous comparisons (see comments on this article) between 23andMe and deCODEme have found even smaller discrepancy rates, closer to one error in every 25,000 sites – the difference appears to be due to a substantially higher error rate on the Navigenics platform compared to 23andMe (compared to research-quality typing performed on the same samples, Navigenics had a 0.29% discordance compared to 0.01% for 23andMe). Overall, though, it’s clear that the levels of technical accuracy being achieved by the genotyping platforms used by major personal genomics companies are perfectly acceptable.

The real challenge is not with generating the raw genetic data, but rather with converting it into disease risk predictions – and here, the authors argue, the results of the comparison are less than ideal:

Read the rest of this post… | Read the comments on this post…

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Responses

  1. Hello from Russia!
    Can I quote a post in your blog with the link to you?


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