In a previous post I discussed copy number variation, a form of genetic variation not broadly reported by DTC companies. In today’s post I provide a very simple program that allows one to identify potential deletions on the basis of high density SNP genotypes from a parent-offspring trio, and report on the results of running this program on data from my own family.
The program uses an approach that I applied as a graduate student to mine deletions from the very first release of data from the International HapMap Project in 2004. The idea, explained in my last post, is to look for stretches of homozygous genotypes interspersed with mendelian errors, which might indicate the transmission of a large deletion. Let’s be clear, this is a simple analysis that most programmers and computational biologists would find straightforward to implement. It is probably a good practice problem for graduate students and would-be DIY personal genomicists.
I obtained 23andMe data from both my mom and dad, and, with their consent, ran the three of us through the program. I was mildly surprised to find only two potential deletions; I had previously speculated that one would find 5-10 deletions per trio with the 550K platform used by 23andMe.