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.
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.
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!