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Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device

NCJ Number
303993
Journal
Forensic Science International: Genetics Volume: 56 Dated: January 2022
Author(s)
Courtney L. Hall; Rupesh K. Kesharwani; Nicole R. Phillips; John V. Planz; Fritz J. Sedlazeck; Roxanne R. Zascavage
Date Published
November 2021
Annotation

This proof-of-principle study evaluated the forensic applicability of the newest and smallest NGS platform available – the Oxford Nanopore Technologies (ONT) MinION device.

Abstract

The high variability characteristic of short tandem repeat (STR) markers is harnessed for human identification in forensic genetic analyses. Despite the power and reliability of current typing techniques, sequence-level information both within and around STRs are masked in the length-based profiles generated. Forensic STR typing using next generation sequencing (NGS) has therefore gained attention as an alternative to traditional capillary electrophoresis (CE) approaches. Although nanopore sequencing on the handheld MinION offers numerous advantages, including low startup cost and on-site sample processing, the relatively high error rate and lack of forensic-specific analysis software has prevented accurate profiling across STR panels in previous studies. The current study presents STRspy, a streamlined method capable of producing length- and sequence-based STR allele designations from noisy, error-prone third generation sequencing reads. To assess the capabilities of STRspy, seven reference samples (female: n = 2; male: n = 5) were amplified at 15 and 30 PCR cycles using the Promega PowerSeq 46GY System and sequenced on the ONT MinION device in triplicate. Base-called reads were then processed with STRspy, using a custom database containing alleles reported in the STRSeq BioProject NIST 1036 dataset. Resultant STR allele designations and flanking region single nucleotide polymorphism (SNP) calls were compared to the manufacturer-validated genotypes for each sample. STRspy generated robust and reliable genotypes across all autosomal STR loci amplified with 30 PCR cycles, achieving 100-percent concordance based on both length and sequence. Furthermore, researchers were able to identify flanking region SNPs in the 15-cycle dataset with > 90-percent accuracy. These results demonstrate that when analyzed with STRspy, ONT reads can reveal additional variation in and around STR loci depending on read coverage. As the first and only third-generation sequencing platform-specific method to successfully profile the entire panel of autosomal STRs amplified by a commercially available multiplex, STRspy significantly increases the feasibility of nanopore sequencing in forensic applications. (publisher abstract modified)

Date Published: November 1, 2021