STRspy-ing hidden variation in forensic DNA profiles using the Oxford Nanopore Technologies MinION device

Forensic DNA examinations harness the high degree of repeat length variation characteristic of short tandem repeats (STRs) for human identification. Conventional approaches to STR profiling consist of PCR amplification followed by length-based separation and detection via capillary electrophoresis (CE). These well-established methods are used in forensic laboratories throughout the world to generate robust and reliable profiles that can discriminate between individuals based on differences in STR repeat length alone. The power of discrimination achieved with length-based allele designations across established panels of autosomal and YSTRs is often sufficient for routine DNA examinations. However, nucleotide-level variation within and around STRs has been shown to increase resolution and facilitate interpretation in more challenging casework scenarios such as those involving partial and mixed DNA profiles. The MinION is a DNA sequencer from Oxford Nanopore Technologies (ONT) that is small in both size and price tag. This portable device could provide an alternative for STR sequencing in forensic laboratories that cannot afford the initial investment or commitment of common next-generation sequencing (NGS) platforms. Despite this potential, the relatively high error rate and lack of STR analysis software have precluded accurate forensic profiling with nanopore sequencing in previous studies. This project aims to determine whether STRs amplified with a commercial kit can be sequenced and profiled on the ONT MinION device. To achieve our overall objective, we developed and tested a novel bioinformatic method known as STRspy that is designed to produce forensic STR profiles from third-generation sequencing data. The results presented herein demonstrate that STRspy can predict the correct sequence- and length-based allele designations across an entire panel of autosomal and Y-STRs using error-prone ONT reads as well as detect variation in the flanking regions with a high level of accuracy. Moreover, these data provide novel insight into how PCR-induced stutter and sample multiplexing impact STR profiling on the MinION. Ultimately, this work increases the feasibility of nanopore sequencing in forensic investigations and provides the foundation for future efforts that aim to harness the big potential of the small MinION device.