Forensic tri-allelic SNP genotyping using nanopore sequencing

Senne Cornelis; Yannick Gansemans; Ann-Sophie Vander Plaetsen; Jana Weymaere; Sander Willems; Dieter Deforce; Filip Van Nieuwerburgh

doi:10.1016/j.fsigen.2018.11.012

Forensic tri-allelic SNP genotyping using nanopore sequencing

Forensic Sci Int Genet. 2019 Jan:38:204-210. doi: 10.1016/j.fsigen.2018.11.012. Epub 2018 Nov 12.

Authors

Senne Cornelis¹, Yannick Gansemans², Ann-Sophie Vander Plaetsen³, Jana Weymaere⁴, Sander Willems⁵, Dieter Deforce⁶, Filip Van Nieuwerburgh⁷

Affiliations

¹ Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Gent, Belgium; Department of Life Sciences and Imaging, imec, 3001 Leuven, Belgium. Electronic address: Senne.Cornelis@UGent.be.
² Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Gent, Belgium. Electronic address: Yannick.Gansemans@UGent.be.
³ Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Gent, Belgium. Electronic address: AnnSophie.VanderPlaetsen@UGent.be.
⁴ Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Gent, Belgium. Electronic address: Jana.Weymaere@UGent.be.
⁵ Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Gent, Belgium. Electronic address: Sander.Willems@UGent.be.
⁶ Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Gent, Belgium. Electronic address: Dieter.Deforce@UGent.be.
⁷ Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Gent, Belgium. Electronic address: Filip.VanNieuwerburgh@UGent.be.

PMID: 30448528
DOI: 10.1016/j.fsigen.2018.11.012

Abstract

The potential and current state-of-the-art of forensic SNP genotyping using nanopore sequencing was investigated with a panel of 16 tri-allelic single nucleotide polymorphisms (SNPs), multiplexing five samples per sequencing run. The sample set consisted of three single-source human genomic reference control DNA samples and two GEDNAP samples, simulating casework samples. The primers for the multiplex SNP-loci PCR were taken from a study which researched their value in a forensic setting using conventional single-base extension technology. Workflows for multiplexed Oxford Nanopore Technologies' 1D and 1D² sequencing were developed that provide correct genotyping of most SNP loci. Loci that are problematic for nanopore sequencing were characterized. When such loci are avoided, nanopore sequencing of forensic tri-allelic SNPs is technically feasible.

Keywords: Forensic; MinION; Next generation sequencing; Oxford nanopore technologies; SNP.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
DNA Primers
Genotyping Techniques / methods*
High-Throughput Nucleotide Sequencing*
Humans
Multiplex Polymerase Chain Reaction
Nanopores*
Polymorphism, Single Nucleotide*
Sequence Analysis, DNA*

Substances

DNA Primers