Extended Data Fig. 1: Evaluation and quantification of allele-specific expression in the GoCAR cohort.
From: LILRB3 genetic variation is associated with kidney transplant failure in African American recipients
a) Overall work flow of eSNP identification and allele expression fraction (AEF) calculation. (b-d) The distribution of AEF of homozygous genotype of reference allele (0/0) (b), heterozygous genotype (0/1) (c) and homozygous genotype of alternative allele (1/1) (d) in the GoCAR cohort. Most alleles showing a balanced expression of reference and alternative alleles (AEF around 50%) while some alleles showed a higher expression of either the reference allele or the alternative allele (AEF > 50% or AEF < 50%), and a few sites exhibited mono-allelic expression at both ends (AEF=0 or AEF=1). This distribution aligns with previous studies on allele-specific expression. (e) The sensitivity and specificity of RNAseq-based genotyping by comparing to the SNP array-based genotyping for heterozygous (upper) and homozygous (lower) calls with various read coverage depths in the GoCAR cohort (n = 153 with both RNA-seq and SNP array data). Each dot represents a sample and box and whiskers plot showing the distribution (thick bar, median; box, 25th to 75th percentile, whiskers reach to the largest/smallest observations within 1.5 box-heights of the box). Overall, the RNAseq-based genotyping strategy achieved over 90% sensitivity and specificity for both heterozygous and homozygous detection with more than 10 reads. With 5-10 reads, we achieved over 75% sensitivity and 100% specificity for heterozygous calls, and 100% sensitivity and over 99% specificity for homozygous calls. These data indicate that our informatic pipeline effectively detected exonic SNPs from RNA-seq data in the GoCAR cohort with high sensitivity and specificity.
