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Day 14 - CNVs

posted Jul 22, 2011, 7:54 AM by Colm O'Dushlaine   [ updated Jul 22, 2011, 8:56 AM ]
I am keen to look at my CNVs. Unfortunately, it isn't that easy. Ideally, I'd like my beadstudio file from 23andme and then I would run Kai Wang's PennCNV to call CNVs. I would then look up pubmed and the database of genomic variants to get a feel for the potentially damaging effects of any CNVs I have.
...but I don't have the files. There's a great article at http://www.genomesunzipped.org/2010/08/dude-where-are-my-copy-number-variants.php that goes through 2 interesting methods to detect CNVs from array data. I'm in the process of convincing my parents to do 23andme, which would allow me one way to look for CNVs. I was also intrigued by the imputation method described at the above link. In the end, however, I just did a really quick-and-dirty analysis using an April 2010 Conrad et al. article. The table I used is here. It summarizes CNVs highly correlated with SNPs and likely to be the causal variant. So I pulled these from the table and searched them against my genome, taking care to check strandedness (SNPedia).     

- e.g. pull out SNPs from my genome
  grep -P "rs10492927|rs11809207|..." mygenome
- look at the genotypes (not all SNPs were in there)
- how frequent in a Caucasian population? Does this tell me anything about which of my SNPs, if any, are likely to tag deleterious CNVs?

In general, most of my genotypes were common in HapMap CEU. So even though these are associated with some traits, they don't appear to be under major selective constraint. However, three SNPs that I have were rare in HapMap CEU - rs9291683, rs3129934 and rs2705293. These are associated with bone mineral density, multiple sclerosis and Schizophrenia respectively. My genotypes have a frequency of about 20, 5 and 15% respectively. So the multiple sclerosis variant seems to be potentially the most damaging. (Interesting that I have strong bones though!) The reported gene is HLA-DRB1. The risk increase is 3.3 fold, based on SNPedia. Now, based on 23andme data, I have 0.2% risk of MS, which is ~the same as the average, albeit with a slight decrease in risk of 0.77x (0.34 per 100 on average, 0.2 with my genotype). Note that this is coming from 2 SNPs - one in IL7RA and one in HLA-DRB1. Even though it's the same gene, the references are different. The 23andme results are pretty good and have a 4-star rating, with multiple reference sources from large populations. The SNPedia reference here was for work done on a reasonably small cohort of 242 individuals, so less likely to be as credible (though they did replicated their findings).

So it's nice to get stuck into you data in this way and to consider some of the literature that might not be directly apparent when you first look at your results. I have protective and risk variants for MS, some in the same gene. This is interesting, but given the odds ratios represents only very modest effects on risk.




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