title: Estimation and partitioning of polygenic variation captured by common SNPs for Alzheimer's disease, multiple sclerosis and endometriosis.
abstract: Common diseases such as endometriosis (ED), Alzheimer's disease (AD) and multiple sclerosis (MS) account for a significant proportion of the health care burden in many countries. Genome-wide association studies (GWASs) for these diseases have identified a number of individual genetic variants contributing to the risk of those diseases. However, the effect size for most variants is small and collectively the known variants explain only a small proportion of the estimated heritability. We used a linear mixed model to fit all single nucleotide polymorphisms (SNPs) simultaneously, and estimated genetic variances on the liability scale using SNPs from GWASs in unrelated individuals for these three diseases. For each of the three diseases, case and control samples were not all genotyped in the same laboratory. We demonstrate that a careful analysis can obtain robust estimates, but also that insufficient quality control (QC) of SNPs can lead to spurious results and that too stringent QC is likely to remove real genetic signals. Our estimates show that common SNPs on commercially available genotyping chips capture significant variation contributing to liability for all three diseases. The estimated proportion of total variation tagged by all SNPs was 0.26 (SE 0.04) for ED, 0.24 (SE 0.03) for AD and 0.30 (SE 0.03) for MS. Further, we partitioned the genetic variance explained into five categories by a minor allele frequency (MAF), by chromosomes and gene annotation. We provide strong evidence that a substantial proportion of variation in liability is explained by common SNPs, and thereby give insights into the genetic architecture of the diseases.
authors.affiliation: The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia.
authors.forename: S Hong
authors.initials: SH
authors.lastname: Lee
authors.forename: Denise
authors.initials: D
authors.lastname: Harold
authors.forename: Dale R
authors.initials: DR
authors.lastname: Nyholt
authors.forename: Michael E
authors.initials: ME
authors.lastname: Goddard
authors.forename: Krina T
authors.initials: KT
authors.lastname: Zondervan
authors.forename: Julie
authors.initials: J
authors.lastname: Williams
authors.forename: Grant W
authors.initials: GW
authors.lastname: Montgomery
authors.forename: Naomi R
authors.initials: NR
authors.lastname: Wray
authors.forename: Peter M
authors.initials: PM
authors.lastname: Visscher
mesh_terms: D000544:Alzheimer Disease / Q000235:genetics*; D016022:Case-Control Studies; D002877:Chromosomes, Human; D004715:Endometriosis / Q000235:genetics*; D005260:Female; D005787:Gene Frequency; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008297:Male; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D020412:Multifactorial Inheritance; D009103:Multiple Sclerosis / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide