Whole-Genome Sequencing of African Americans Implicates Differential Genetic Architecture in Inflammatory Bowel Disease. H.K Somineni, S. Nagpal, et al. AJHG (2021).

Please cite if using the code/method: https://www.sciencedirect.com/science/article/pii/S0002929721000434?via%3Dihub

The analysis is divided into the following parts:

Genetic landscape and PRS transferibility between Africans and Europeans:

• Liability scale measurements
• Comparison of effect sizes between Africans and Europeans
• Generation of pseudo-control genotype from 1644 real controls of AA
• PVE of IBD loci using effect sizes and allele frequencies of AA and EUR
• PRS of AA and UKB as a function of discovery ancestry group

Common Variant Analysis:

• Include GWAS on WGS African American cohort using PLINK

Rare Variant Analysis: R SKAT code for gene-level rare variant analysis

Fine Mapping