Validation results using qPCR for the most frequent somatic deletions identified by WGS in WM patients. Five patient samples, 3 from the paired and 2 from the unpaired WGS cohorts, were selected for validation studies using qPCR copy number assays. All assays were run in at least triplicate. Results represent median values and ranges. (A) Validation of deletion in the known 6q deletion in 2 patients at HINT3 (6q22.32). (B) Representative validation results normalized to germline as determined by qPCR. Deletions deemed significant by Welch’s t test are denoted by asterisk (*). (C) Somatic relative copy number needs to be interpreted in context. Significant germline copy number variation was noted in both HIVEP2 and MKLN1. (D) Comparison of whole genome and qPCR validation estimates of relative somatic copy number demonstrating similar clonal estimates.