Reproducibility of SNP Testing, Part II

imageThe Quantified Self has a follow-up to last week’s post about the reproducibility of SNP testing by 23andMe and deCODEme using Illumina SNP chips (see the Quantified Self’s post and my post). In that post, it was revealed that two comparisons of the 560,000 overlapping SNP results from the two different companies had revealed differences of just 23 locations for one individual and 35 for another.

Soon after last week’s post, one of these individuals – Ann Turner – contacted The Quantified Self with new information that 4 of the SNPs on her list of 35 disagreeing results are also on the other person’s list of 23 disagreeing results (Antonio Oliveira). From Ann’s email to The Quantified Self:

Four of those (rs11149566, rs4458717, rs4660646, and rs754499) were also found in Antonio’s list. That’s more than you would expect by chance.

Interesting results, and as Kelly at TGS points out, “This is why sharing results is so valuable and a key to great quantified self understanding.” For anyone who might be interested in doing further comparison, here is Oliveira’s list (also available here):

rs4660646, rs4458717,rs754499, rs11149566, rs1934496, rs10933181, rs9881405, rs1064205, rs312330, rs11100437, rs2955195, rs7033246, rs1536928, rs10793963, rs10894749, rs3921012, rs510978, rs12296276, rs4965862, rs2290505, rs12960185, rs4814138, rs6615048

And here is Turner’s list (also available here):

rs4660646, rs4458717,rs754499, rs11149566, rs10435795, rs1045363, rs10743414, rs10945383, rs11179382, rs11707159, rs11915402, rs1209171, rs1221986, rs12907462, rs1303912, rs13422439, rs161381, rs17328647, rs1961196, rs1966357, rs2016461, rs2064034, rs2290516, rs2853981, rs3952469, rs4336661, rs4423481, rs4572718, rs6531490, rs6942478, rs7102702, rs7812884, rs845217, rs9332128, rs9476380

For everyone not familiar with SNPs, or Single Nucleotide Polymorphisms, see this brief introduction at Wikipedia, including the helpful diagram, or read the SNP Page at SNPedia (which links to a helpful YouTube video).