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Day-07 - polyphen2 screening for damaging SNPs

posted Jul 6, 2011, 9:19 AM by Colm O'Dushlaine   [ updated Oct 15, 2014, 10:02 AM ]
So imputation (day 6) revealed very little additional SNPs. To be honest, it's probably not a good idea given that I only have one individual.

Polyphen is another interesting way to look at you 23andMe genotypes. Here, I converted my data into a polyphen2 compatible file and ran the analysis. It took about 20 minutes or so. I then downloaded the results and filtered out only what I thought was most interesting - SNPs with a "probably damaging" label. Now it's one thing to do that, but don't rush to look at the results. I found some interesting mutations that caused alarm, e.g. "essential for sperm motility"...but when you look at the frequency of this mutation in Caucasians you find that it's at 100%...and we seem to be procreating without much difficulty! So it's very important to pull in some estimates of the frequency of your SNP in your population. I did this and then pulled out the 20 most rare SNPs. Some of these relate to MHC and olfactory genes, which not unsurprising I think. One or two genes involved in transcriptional regulation, etc.

Overall, I think this is a very useful endeavour, and it complements the established research presented by 23andMe and may give some interesting additional leads into your phenotype. Be careful when interpreting the findings though and especially be sure to interpret your mutation in the context of a matched population.
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