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