Tag Archive for 'height'

Friday Links

The largest genome-wide association study ever undertaken was published in Nature this week. The appropriately named Genetic Investigation of ANthropocentric Traits (GIANT) consortium combined data from 183,727 individuals and identified around 180 loci influencing human height. The loci were enriched with genes underlying skeletal growth and other relevant biological pathways. Interestingly, these 180 loci are estimated to only account for 10% of the phenotypic variation in height (or around 12.5% of the heritability). [CAA]

Christophe Lambert from Golden Helix has an excellent, thorough post looking at the importance of careful experimental design in large-scale genetic association studies. In particular, Lambert focuses on the need for randomising samples across experimental batches: if you have some batches containing entirely cases and others entirely controls, then the all-too-pervasive spectre of batch effects can easily create false positive associations. In many cases batch effects can be recognised and corrected for post hoc (Lambert cites a good example from the original WTCCC study), but in other cases a failure to perform the right quality controls can have devastating consequences (Lambert cites the recent longevity GWAS paper in Science). I’d be interested to hear from my more GWAS-savvy colleagues (Carl, Jeff) whether randomisation is standard procedure in most large GWAS now. [DM]

We managed to miss this out last week, but the current issue of Nature Genetics has a strange and wonderful paper on breast cancer genetics. The study looked at 2838 individuals with BRCA1 mutations that strongly predispose to breast cancer, and looked for non-BRCA1 variants associations with breast cancer in this group. They found an associated variant of chromosome 19, and replicated it in another 5986 BRCA1 carriers (where do they find this many BRCA1 carriers?). To top it all off, they looked at this variant in another 6800 breast cancer patients without BRCA1 mutations, and found no association. However, when they stratified their samples into ER+ and ER- associations, they found associations in both, but going in opposite directions! The variant predisposes people to ER- cancer, but is protective against ER+, and taken together they pretty much perfectly balance out. [LJ]

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