Linkage Disequilibrium and Heterozygosity Modulate the Genetic Architecture of Human Complex Phenotypes
bioRxiv preprint doi: https://doi.org/10.1101/705285; this version posted August 11, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Linkage Disequilibrium and Heterozygosity Modulate the Genetic Architecture of Human Complex Phenotypes Dominic Hollanda,b,∗, Oleksandr Freid, Rahul Desikanc, Chun-Chieh Fana,e,f, Alexey A. Shadrind, Olav B. Smelanda,d,g, Ole A. Andreassend,g, Anders M. Dalea,b,f,h aCenter for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA 92037, USA, bDepartment of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA, cDepartment of Radiology, University of California, San Francisco, San Francisco, CA 94158, USA, dNORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo 0424 Oslo, Norway, eDepartment of Cognitive Sciences, University of California at San Diego, La Jolla, CA 92093, USA, fDepartment of Radiology, University of California, San Diego, La Jolla, CA 92093, USA, gDivision of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway, hDepartment of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA, Abstract We propose an extended Gaussian mixture model for the distribution of causal effects of common single nucleotide polymorphisms (SNPs) for human complex phenotypes, taking into account linkage disequilibrium (LD) and heterozy- gosity (H), while also allowing for independent components for small and large effects. Using a precise methodology showing how genome-wide association studies (GWAS) summary statistics (z-scores) arise through LD with underlying causal SNPs, we applied the model to multiple GWAS.
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