Genome-wide association studies

Univariate GWAS

In this project we used both univariate and multivariate GWAS. For univariate GWAS we used PLINK 2^1,2, a popular toolbox in population genetics. It provides functionality to perform a number of tasks, which includes preprocessing of genetic data, conducting a GWAS, and performing a meta-analysis. In this study we only used the functionality in PLINK to perform univariate GWAS on a number of continuous or dichotomous traits.

1.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007 Sep;81(3):559–75.

2.

Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: Rising to the challenge of larger and richer datasets. Gigascience [Internet]. 2015 Feb 25;4:7–7. Available from: https://pubmed.ncbi.nlm.nih.gov/25722852