Machine learning in genome‐wide association studies

S Szymczak, JM Biernacka, HJ Cordell… - Genetic …, 2009 - Wiley Online Library
Recently, genome‐wide association studies have substantially expanded our knowledge
about genetic variants that influence the susceptibility to complex diseases. Although …

Polygenic scores via penalized regression on summary statistics

TSH Mak, RM Porsch, SW Choi, X Zhou… - Genetic …, 2017 - Wiley Online Library
Polygenic scores (PGS) summarize the genetic contribution of a person's genotype to a
disease or phenotype. They can be used to group participants into different risk categories …

[HTML][HTML] PredictABEL: an R package for the assessment of risk prediction models

S Kundu, YS Aulchenko, CM van Duijn… - European journal of …, 2011 - Springer
The rapid identification of genetic markers for multifactorial diseases from genome-wide
association studies is fuelling interest in investigating the predictive ability and health care …

[HTML][HTML] Power analysis of transcriptome-wide association study: Implications for practical protocol choice

C Cao, B Ding, Q Li, D Kwok, J Wu, Q Long - PLoS genetics, 2021 - journals.plos.org
The transcriptome-wide association study (TWAS) has emerged as one of several promising
techniques for integrating multi-scale 'omics' data into traditional genome-wide association …

[HTML][HTML] Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer

G Covarrubias-Pazaran - PloS one, 2016 - journals.plos.org
Most traits of agronomic importance are quantitative in nature, and genetic markers have
been used for decades to dissect such traits. Recently, genomic selection has earned …

[HTML][HTML] Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies

S Song, W Jiang, L Hou, H Zhao - PLoS computational biology, 2020 - journals.plos.org
Genetic risk prediction is an important problem in human genetics, and accurate prediction
can facilitate disease prevention and treatment. Calculating polygenic risk score (PRS) has …

Pitfalls of predicting complex traits from SNPs

NR Wray, J Yang, BJ Hayes, AL Price… - Nature Reviews …, 2013 - nature.com
The success of genome-wide association studies (GWASs) has led to increasing interest in
making predictions of complex trait phenotypes, including disease, from genotype data …

[HTML][HTML] Modeling linkage disequilibrium increases accuracy of polygenic risk scores

BJ Vilhjálmsson, J Yang, HK Finucane, A Gusev… - The american journal of …, 2015 - cell.com
Polygenic risk scores have shown great promise in predicting complex disease risk and will
become more accurate as training sample sizes increase. The standard approach for …

Bayesian variable selection regression for genome-wide association studies and other large-scale problems

Y Guan, M Stephens - 2011 - projecteuclid.org
Abstract We consider applying Bayesian Variable Selection Regression, or BVSR, to
genome-wide association studies and similar large-scale regression problems. Currently …

[HTML][HTML] Further improvements to linear mixed models for genome-wide association studies

C Widmer, C Lippert, O Weissbrod, N Fusi, C Kadie… - Scientific reports, 2014 - nature.com
We examine improvements to the linear mixed model (LMM) that better correct for
population structure and family relatedness in genome-wide association studies (GWAS) …