| 23andMe's genotyping chip is based on the Illumina Infinium beadarray technology. ( http://www.illumina.com/technology/beadarray-technology/infi... ) There is a nice animation of the technology on Illumina's website. It's a single base extension assay where you have hybridization of a probe, then add a labeled nucleotide where the SNP is that you are studying. For a A/T SNP, if you basepair and add an 'A' you get a green signal, if you add a 'T' you get a red signal. If you end up with a mix of green/red, you have a heterozygous variant. Illumina has a tech note on the call rate and error rate here: http://www.illumina.com/Documents/products/technotes/technot...
At a minor allele frequency of 0.5% their minor allele homozygous error rate was 0.1%. The nice thing about this technology is that the more data you have, the better your calls get, and 23andMe has real world data on over 1 million customers. (Illumina tech note used data from 2,000 genotyped samples) I think 23andMe has enough data to know which of the SNPs on their genotyping chip are accurate, but they don't exactly open up their data for public inspection. If you are a 23andMe customer you can see the improvements to the raw data they have made over the years here: ( https://www.23andme.com/you/download/revisions/ ) If you can't see it, it says things like: "July 28th, 2014. Analysis of our data has allowed us to improve the interpretation of over 10,000 SNPs genome-wide on the V4 chip." When they get more data, they are improving their calls. Finally, the FDA document about 23andMe's approved Bloom Syndrome carrier test says that "all homozygous variant genotype samples receive a 'no-call' result, since the calling software was designed not to detect homozygous variant genotypes." It sounds to me like they designed the software to ignore and throw out homozygous data.
http://www.accessdata.fda.gov/cdrh_docs/reviews/DEN140044.pd... |