Fig 1.
(a) Allele frequency distributions in different ethnic groups of 282 variants in 153 genes (b) differences in allele frequencies relative to EUR samples.
Fig 2.
CYP2D6 allele frequencies for three MVP HARE groups, MVP Local Ancestry Inference (LAI) and two publicly available data sets: 1000 genome project and gnomAD.
Only consensus Tier 1 alleles [9] are shown. We note that we did not perform LAI in HARE EUR samples. Thus LAI frequencies are identical by default to HARE EUR frequencies. For HARE HIS, LAI corresponds to the AMR track allele frequencies (3-way deconvolution). We estimate imputation quality per site and ethnicity. We do not present allele frequencies for poorly imputed sites.
Fig 3.
Copy number variation in CYP2D6.
Results are shown just for the HARE AFR cohort; clusters were derived using UMAP [13].
Table 1.
Allele frequencies for allele CYP2D6*5 (whole gene deletion) in different HARE groups.
In addition, we show allele frequencies in the three components of the HARE HIS group (EUR, AFR, AMR) calculated using individuals ancestry-homozygous at CYP2D6.
Fig 4.
HLA allele distribution in 4 ethnic groups.
Allele imputation was performed through HIBAG using the Axiom UK Biobank model and Axiom MVP genotypes.
Table 2.
Allele frequencies for HLA alleles with known large effects in pharmacogenomics.