Characterizing the genetic polymorphisms in 370 challenging medically relevant genes using long-read sequencing data from 41 human individuals among 19 global populations

Abstract

Numerous challenging medically relevant genes (CMRGs) cannot be adequately investigated using next-generation sequencing, hindering the detection of functional variation among these genes. In this study, long-read sequencing data from 41 human individuals across 19 populations were analyzed using the current version of the human reference genome assembly (GRCh38) and a telomere-to-telomere assembly of the human genome (T2T-CHM13). After excluding 142 CMRGs containing windows with a depth of coverage (DoC) significantly deviating from the average DoC value of proteincoding regions in the GRCh38 (138) or T2T-CHM13 (47) assemblies, 179 and 263 CMRGs exhibited copy number variation (CNV) signal in GRCh38 and T2T-CHM13, respectively. In addition, 451 high-impact short variants were detected in 188 CMRGs. Further, some genetic alterations were individual- or continental-superpopulation-specific, suggesting a strong need to consider genetic background differences in future genetic testing and drug design studies. Finally, side-by-side comparisons of short variant calls in CMRGs using NGS and LRS data from 13 samples indicated that 15.79% to 33.96% of high-impact short variants in different individuals could only be detected using LRS data. The results described herein will be an important reference for future clinical and pharmacogenetic studies to further improve precision medicine.