Forensic SNP Genotyping using Nanopore MinION Sequencing

Senne Cornelis,Yannick Gansemans,Filip Van Nieuwerburgh,Lieselot Deleye,Dieter Deforce

doi:10.1038/srep41759

Senne Cornelis, Yannick Gansemans + Show 3 more

Open Access

https://doi.org/10.1038/srep41759

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Abstract

One of the latest developments in next generation sequencing is the Oxford Nanopore Technologies’ (ONT) MinION nanopore sequencer. We studied the applicability of this system to perform forensic genotyping of the forensic female DNA standard 9947 A using the 52 SNP-plex assay developed by the SNPforID consortium. All but one of the loci were correctly genotyped. Several SNP loci were identified as problematic for correct and robust genotyping using nanopore sequencing. All these loci contained homopolymers in the sequence flanking the forensic SNP and most of them were already reported as problematic in studies using other sequencing technologies. When these problematic loci are avoided, correct forensic genotyping using nanopore sequencing is technically feasible.

Highlights

Short tandem repeats (STRs) have been the golden standard in forensic DNA casework for many years
The 52 single nucleotide polymorphism (SNP) containing regions were individually amplified via PCR using a protocol based on the forensic SNP multiplex developed by the SNPforID consortium[1]
This study demonstrates proof-of-concept forensic SNP genotyping using the Oxford Nanopore MinION sequencing platform and shows the current capabilities of the system

Summary

Introduction

Short tandem repeats (STRs) have been the golden standard in forensic DNA casework for many years. The SNPforID consortium developed a 52-SNP multiplex which matches the discrimination power of routinely used 10–15 STR multiplexes[1] This SNP multiplex was initially designed to be analyzed via Single Base Extension (SBE) combined with capillary electrophoresis (CE)[6]. Oxford Nanopore developed a pocketsize MPS device called MinION This low cost, highly portable sequencer uses nanoscopic pores through which DNA strands are translocated. The quasi real time strand sequencing allows for an on-the-fly base calling and a ‘run until’ analysis, i.e. running the device until a required amount of data has been produced. In this proof-of-principle study the potential of the MinION sequencer to generate data allowing the deduction of a 52 SNP profile was investigated. A first assessment of the performance of the MinION sequencer to analyze a forensic SNP multiplex, as well as identifying criteria for selecting MinION compatible SNP markers was made

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Results

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