Speed, Balding, et al.: “for a wide range of traits, common SNPs tag a greater fraction of causal variation than is currently appreciated”

I recently blogged about a nice lecture by David Balding at the 2015 MLPM (Machine Learning for Personalized Medicine) Summer School: Machine Learning for Personalized Medicine: Heritability-based models for prediction of complex traits. In that talk he discussed some results concerning heritability estimation and potential improvements over GCTA. A new preprint on bioRxiv has the …

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Machine Learning for Personalized Medicine: Heritability-based models for prediction of complex traits (David Balding)

Highly recommended talk by David Balding on modern approaches to heritability, relatedness, etc. in statistical genetics. (I listened at 1.5x normal speed, which worked for me.) MLPM (Machine Learning for Personalized Medicine) Summer School 2015 Monday 21st of September Heritability-based models for prediction of complex traits by David Balding Complex trait genetics has been revolutionised …

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The tipping point

This is only the beginning. To serious people who read this blog, but may have been confused over the past 5+ years about things like missing heritability, genomic prediction, complex genetic architecture, gloomy prospects: isn’t it about time to consider updating your priors? Read all about it here. FT.com: Genetic scoring predicts how children do …

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GCTA, Missing Heritability, and All That

Bioinformaticist E. Stovner asked about a recent PNAS paper which is critical of GCTA. My comments are below. It’s a shame that we don’t have a better online platform (e.g., like Quora or StackOverflow) for discussing scientific papers. This would allow the authors of a paper to communicate directly with interested readers, immediately after the paper …

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HaploSNPs and missing heritability

By constructing haplotypes using adjacent SNPs the authors arrive at a superior set of genetic variables with which to compute genetic similarity. These haplotypes tag rare variants and seem to recover a significant chunk of heritability not accounted for by common SNPs. See also ref 32: Yang, J. et al. Estimation of genetic variance from …

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Sparsity estimates for complex traits

Note the estimate of few to ten thousand causal SNP variants, consistent with my estimates for height and cognitive ability. Sparsity (number of causal variants), along with heritability, determines the amount of data necessary to “solve” a specific trait. See Genetic architecture and predictive modeling of quantitative traits. T1D looks like it could be cracked …

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