Genomics

How did I inherit my prostate cancer highest risk SNP?


In a previous entry for this blog, I wrote that my highest risk factor in my 23andMe genotype is the rs10993994 SNP, which produces a 1.3 increase in odds for me to develop prostate cancer. Navigating my genome using myKaryoView I was able to learn that this gene is located 56 base pairs before the start of the MSMB gene. As it happens, this gene is a tumor suppressor that has been involved in prostate cancer. The rs10993994 SNP is located in the promoter region and the TT genotype, the one I contain, seems to down-regulate this tumor’s suppressor gene, increasing the chances of developing prostate cancer.

The most contributing SNP (highest column in red) corresponds to rs10993994 SNP.

Up to that point I was not able to learn anything else from my genome. Making use of last Christmas’ offer in 23andMe, that offered genome analyses from $99 and the keen collaboration of my family, I was able to buy 23andMe analysis kits for my Mum, Dad, Sister and Aunt. It was only last week when I finally got the results back. I have now uploaded all of these genomes in the DAS protocol and hence can query them using myKaryoView.

Region around rs10993994 SNP using myKaryoView. Pop up windows show the genotype of this SNP for the three individuals

The first thing I did was to establish how I inherited my TT genotype for rs10993994 SNP. I learnt that my mum and dad both have CT for the genotype of this SNP. So in fact I was unlucky enough to inherit one T from each parent. My sister was luckier, well she does not have a prostate, but at least the genotype she inherited, CT, is not the one that has been related to the greater health risk.

Categories: Genomics

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