T2T-CHM13 reference genome reduces mapping bias and enhances alignment accuracy at disease-associated variants

The T2T-CHM13v2.0 reference genome added previously uncharacterized genomic sequences and improved the accuracy of repetitive stretches compared to former human genome assemblies. By comprehensive allelic variation analysis and read mapping statistics from sequencing reads aligned to hg38 and T2T-CHM13 assemblies in samples encompassing different sequencing designs, we observed that T2T-CHM13v2.0 assembly significantly reduces the reference mapping bias (RMB) and increases read mapping precision at clinically relevant sites, including BRCA1 pathogenic variants. We report the presence of sequence dissimilarities among reference genomes in the proximity of ClinVar annotated variants, suggesting the need for data re-analysis. Analyzing DNA sequencing data from cancer patients, we identified a mean 2.3% increase in variant allelic frequency (VAF) and 0.3% increase in coverage over clinically relevant variants for samples aligned to T2T-CHM13 compared to hg38. Overall, these findings support the implementation of T2T-CHM13 reference for the improvement of sequencing data analyses in the clinical genomic setting.