Saturday, December 15, 2012

(A;A) Christmas Platypus

rs55705857 is strongly associated with the most common form of primary brain cancer, glioma, but it also achieves a distinction of being one of the most strongly cancer-associated SNPs ever found in a SNP survey.

The study published in Nature Genetics this fall [PMID 22922872] by researchers at UCSF and the Mayo Clinic found that rs55705857(G) allele carriers are at 6 times higher risk for glioma formation than non-carriers, and in particular, for subtypes known to harbor IDH1 or IDH2 somatic mutations. It is comforting that while the mutation is common (between 2 - 8% of us harbor this allele), gliomas are rare (diagnosed in around 3 people per 100,000 every year) so most carriers will never develop such tumors. Unfortunately, for those that do, it’s often fatal, as it was for a good friend and colleague, Neil Ghiso.

The chromosomal region (8q24) this SNP is located in has previously yielded SNPs associated with ovarian and prostate cancer, but with much lower odds ratios. And while it’s clear the region is important in some regulatory manner, it’s not yet clear how.  Perhaps another one of 2012’s top scientific stories – the first major release by the ENCODE project of data on functional elements in the genome  – will help explain this.

And here’s where the platypus comes in.  Even though it’s far from a coding region, sequencing shows that the common rs55705857(A) allele is invariant in all mammals, from humans through to, yes, the platypus. Here’s to the Christmas Platypus!

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