Fig. 2
From: Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping
Diplotype concordance for pharmacogenes with complex alleles. Results of the TAS-LRS workflow for (a) reference cell lines (n = 11), (b) clinical research samples (n = 3) and (c) external quality assessment (EQA) samples (n = 3) were compared against reference truth sets. GeT-RM calls were used as the truth set for HG001, HG01190, NA18861, NA18966, NA19174, and NA19226 unless otherwise specified. Diplotype calls for HG00337, HG005, HG01097, HG01572, and HG03259 were compared to PyPGx diplotypes from 30x short-read data. For all samples, ABCB1, G6PD, NUDT15, and UGT1A1 calls were compared to PyPGx outputs, and HLA-A and HLA-B calls were evaluated against optitype v1.3.5. Calls matching the truth set were labelled as concordant, while mismatched calls were considered improved based on IGV read support or consensus across orthogonal methods.
