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PCA

This repository contains code and other resources associated with the manuscript:

Grinde, K., Browning, B., Reiner, A., Thornton, T., Browning, S. "Adjusting for principal components can induce spurious associations in genome-wide association studies in admixed populations." In Revision at PLOS Genetics.

If you use any of these resources, please cite our preprint: https://www.biorxiv.org/content/10.1101/2024.04.02.587682v1.

Of particular interest may be the following directories:

  • code
  • data/highLD

code

This directory contains an example of the code we used to perform PCA, as well as associated pre-processing steps (e.g., LD pruning) and diagnostics (plotting SNP loadings), in TOPMed COPDGene whole genome sequence data.

Our analysis leans heavily on the UW GAC TOPMed Analysis Pipeline.

data/highLD

This directory contains a list of high LD regions (identified via an extensive literature review) that are often recommended for exclusion prior to running PCA. Lists are available in builds 36 (exclude_b36.txt), 37 (exclude_b37.txt), and 38 (exclude_b38.txt). See Table 1 in our paper for more details.