Sunday, August 31, 2008

Counter-intuitive results using SNP chips

Two recent papers use of high density SNP chips to show counter intuitively that you can locate the geographic origin of a person to within a few hundred miles using only genetic data (Novembre et al., hat tip to gnxp), and that you can detect whether a person has contributed to the pooled data of a genome-wide association (GWA) scan (homer et al, hat tip to gnxp and the The Spitoon). Both of these papers testify to the power of large amounts of data for detecting very subtle signals. I think we are currently not use to how tiny effects can be multiplied across the hundreds of thousands of SNPs in these studies. It will be interesting to see what other counter intuitive results emerge, especially as we move towards whole genome resequencing. It is interesting to note that the current concern about learning whether someone has been involved in a GWA scan (see Spitoon) should decrease as the size of these studies increase. The statistical fluctuations away from the population mean frequency due to sampling relied upon by this method will decrease with large sample sizes. Although resequencing studies might once again be a cause for concern as rare variants will be diagnostic of a person's presence in a study.

Updated: link.