Next-generation sequencing approaches to short-tandem repeat sequence variation

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Human short tandem repeats (STRs) have been widely used as markers in linkage and population-genetic studies, and remain the prime tools for forensic individual identification. However, remarkably little is known about STR sequence variation in human populations; this is due to genotyping via PCR fragment length, which ignores internal variants and STR-allele linkage to flanking variation, thus hiding alleles identical-by-descent (IBD) under apparent identity-by-state. The past decade has seen the emergence of next-generation sequencing (NGS), which can provide simultaneous sequence data for multiple PCR amplicons. This promises access to STR sequences and flanking variants, and thanks to its high throughput and suitability for fragmented DNA, is being developed for new forensic assays. Note that low-coverage whole-genome approaches yield only STR length information.