APOL1 single gene view methods
The single gene lookup page combines results from multiple analyses. Methods for each analysis can be found here:
The single gene lookup page combines results from multiple analyses. Methods for each analysis can be found here:
Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease.
Lu X, et al.
Nat Genet. 2017 Dec;49(12):1722-1730. doi: 10.1038/ng.3978.
Tutorial for the Differential Expression View
We conducted the differential expression analysis with the R package DESeq2. We first filtered for protein-coding genes with more than 10 counts in at least 14 samples (our smaller group size). Fourteen low-risk (LR) samples were compared to 16 high-risk (HR) samples adjusting for age, sex, and RNA-Seq batch. Cook’s distance was used to flag associations influenced by sample outliers.
The APOL1 Portal was created to facilitate sharing and secondary use of analyses and data related to APOL1 associated kidney disease in order to parallelize and accelerate discovery for this condition.
Summary statistics are available for download at the CARDIoGRAMplusC4D Consortium website.
A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease.
Nikpay M, et al.
Nat Genet. 2015 Oct;47(10):1121-1130. doi: 10.1038/ng.3396.
PMID: 26343387
Summary statistics are available for download at the GIANT Consortium website.