High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing

Abstract

Background: Tandem repeats (TRs) are highly prone to variation in copy numbers due to their repetitive and unstable nature, which makes them a major source of genomic variation between individuals. However, population variation of TRs has not been widely explored due to the limitations of existing approaches, which are either low-throughput or restricted to a small subset of TRs. Here, we demonstrate a targeted sequencing approach combined with Nanopore sequencing to overcome these limitations. Methods: We selected 142 TR targets and enriched these regions using Agilent SureSelect target enrichment approach with only 200 ng of input DNA. We barcoded the enriched products and sequenced on Oxford Nanopore MinION sequencer. We used VNTRTyper and Tandem-genotypes to genotype TRs from long-read sequencing data. Gold standard PCR sizing analysis was used to validate genotyping results from targeted sequencing data.  Results: We achieved an average of 3062-fold target enrichment on a panel of 142 TR loci, generating an average of 97X coverage per sample with 200 ng of input DNA per sample. We successfully genotyped an average of 75% targets and genotyping rate increased to 91% for the highest-coverage sample for targets with length less than 2 kb, and GC content greater than 25%. Alleles estimated from targeted long-read sequencing were concordant with gold standard PCR sizing analysis and highly correlated with alleles estimated from whole genome long-read sequencing. Conclusions: We demonstrate a targeted long-read sequencing approach that enables simultaneous analysis of hundreds of TRs and accuracy is comparable to PCR sizing analysis. Our approach is feasible to scale for more targets and more samples facilitating large-scale analysis of TRs.