Thursday, May 11, 2006

Common structural variants are like SNPs   posted by the @ 5/11/2006 06:05:00 PM

Three papers in the January issue of Nature genetics, "Common deletions and SNPs are in linkage disequilibrium in the human genome", "Common deletion polymorphisms in the human genome" and "A high-resolution survey of deletion polymorphism in the human genome" each examine common structural variation in the human genome.

A number of papers have previously reported that intermediate-scale "structural" (e.g. insertions, deletions, rearrangements) variations "are prevalent enough to be an important source of genetic variation between individuals". One question was whether these intermediate-sized variations occured once during human history and shared by descent (like most SNPs) or whether they are like a class of recurring mutations that delete, insert or rearrange large portions of the genome and subseqently cause disease.

The Perlegen paper gives the best summary:
common deletions and SNPs ascertained with similar criteria have essentially the same distribution of linkage disequilibrium with surrounding SNPs, indicating that these polymorphisms may share evolutionary history and that most deletion polymorphisms are effectively assayed by proxy in SNP-based association studies.