New review paper on GWAS

Comput Struct Biotechnol J. 2015 Nov 23;14:28-34
Uncovering the Genetic Architectures of Quantitative Traits.
Lee JJ, Vattikuti S, Chow CC.

Abstract
The aim of a genome-wide association study (GWAS) is to identify loci in the human genome affecting a phenotype of interest. This review summarizes some recent work on conceptual and methodological aspects of GWAS. The average effect of gene substitution at a given causal site in the genome is the key estimand in GWAS, and we argue for its fundamental importance. Implicit in the definition of average effect is a linear model relating genotype to phenotype. The fraction of the phenotypic variance ascribable to polymorphic sites with nonzero average effects in this linear model is called the heritability, and we describe methods for estimating this quantity from GWAS data. Finally, we show that the theory of compressed sensing can be used to provide a sharp estimate of the sample size required to identify essentially all sites contributing to the heritability of a given phenotype.
KEYWORDS:
Average effect of gene substitution; Compressed sensing; GWAS; Heritability; Population genetics; Quantitative genetics; Review; Statistical genetics

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One thought on “New review paper on GWAS

  1. very good article — though i can say i barely understand alot of it. many equations are quite recognizable. some less so. has a pretty complete reference list—eg missing heritability, lp model. i’m a bit of a dissident, if anything at all, so in your equation 7 the last term on the right E i would say cannot be ignored or set to 0 even for tractability—if i understand it correctly. besides gwas studies one might need ewas studies. people live in microenvironments, which will or may interact with genetic variations. they are likely harder to define or measure.

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