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Day-15 - More CNVs

posted Oct 24, 2011, 4:36 PM by Colm O'Dushlaine   [ updated Oct 15, 2014, 9:54 AM ]
I found a list of CNVs reported by the Wellcome trust a while ago (http://www.wtccc.org.uk/wtcccplus_cnv/supplemental.shtml). This study was interesting, even though it didn't find anything amazing. The last line of the abstract says it all really (!) "We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases"
....nevertheless, I decided to check if I have an SNPs that are (a) rare in HapMap CEU and (b) tag CNVs. 

Very simply I obtained minor allele frequency for my genotypes from HapMap and just filtered <=10%. I then cross-references with the CNV table listed here. I took care to use the bestLocalIlluminaTagRSID column because this is the platform my data is on. Clearly this is a quick and dirty analysis. For example, I could have expanded to a list of imputed genotypes perhaps. Anyway, long story short I found just 3 genes found within CNVs tagged by rare genotypes in my genome:
          Gene CTGLF3 chr 10 51418083 51418083 within CNVR4732.1 chr10:51403541-51447456 loss rs17178655
                 - Putative GTPase-activating protein .. low expression everywhere, so probably not interesting

          Gene OR52N5 chr 11 5755465 5755465 within CNVR5049.1 chr11:5741435-5765861 gain rs1453415
                - Olfactory receptor, we know these vary in all sorts of ways

          Gene CHST5 chr 16 74119928 74119928 within WTCCC1_181 chr16:74096937-74132230 unknown rs11149841
                - Catalyzes the transfer of sulfate to position 6 of non-reducing N-acetylglucosamine (GlcNAc) residues and O-linked sugars of mucin-type acceptors.
                - not sure about this. It doesn't interact with anything according to http://string-db.org. Maybe a connection with poor eyesight, http://www.ncbi.nlm.nih.gov/pubmed/21440637 http://www.ncbi.nlm.nih.gov/pubmed/16938851 (though I might be clutching at straws here). Some interesting pharmacogenetic possibilities also, http://www.ncbi.nlm.nih.gov/pubmed/11829137

That's all I could find! Besides, this is not an ideal CNV dataset given the lack of any convincing disease association.