Throwing the baby out with the bathwater:Non-Synonymous and Synonymous Coding SNPs Show Similar Likelihood and Effect Size of Human Disease Association

I was literally having a 'oh shoot' moment when i saw this news in GenomeWeb

Synonymous SNPs Shouldn't Be Discounted in Disease, Study Finds

NEW YORK (GenomeWeb News) – Synonymous SNPs that don't change the amino acid sequence encoded by a gene appear just as likely to influence human disease as non-synonymous SNPs that do, according to a paper appearing online recently in PLoS ONE by researchers from Stanford University and the Lucile Packard Children's Hospital.

from the abstract of the paper

The enrichment of disease-associated SNPs around the 80^th base in the first introns might provide an effective way to prioritize intronic SNPs for functional studies. We further found that the likelihood of disease association was positively associated with the effect size across different types of SNPs, and SNPs in the 3′untranslated regions, such as the microRNA binding sites, might be under-investigated. Our results suggest that sSNPs are just as likely to be involved in disease mechanisms, so we recommend that sSNPs discovered from GWAS should also be examined with functional studies.

Hmmmm how is this going to affect your carefully crafted pipeline now?