Forensic STR profiling using Oxford Nanopore Technologies’ MinION sequencer

Cornelis, Senne; Willems, Sander; Neste, Christophe Van; Tytgat, Olivier; Weymaere, Jana; Plaetsen, Ann-Sophie Vander; Deforce, Dieter; Nieuwerburgh, Filip Van

doi:10.1101/433151

Cited by 13 publications

(13 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Historical data obtained by our group using the R7 flow cell version resulted in lower genotyping accuracy [17], indicating that advancements were made. Moreover, the yield of sequencing runs is more than a 10-fold higher.…”

Section: Nanopore Sequencing-based Genotypingmentioning

confidence: 99%

“…The platform already evolved in such a way that the MinION sequencer is now capable of correctly genotyping forensic SNP loci [14,15]. The first attempts to assess nanopore sequencing for STR-profiling have been reported recently [16,17]. Unfortunately, results were suboptimal, which can be attributed to multiple factors, both on the chemistry, hardware, and the bioinformatics side.…”

Section: Introductionmentioning

confidence: 99%

“…R10 is characterized by pores with a longer barrel and a dual reader head, enhancing the accuracy of homopolymer regions. The gathered results are also compared to historical data obtained by our group using the R7 version of MinION flow cells [17]. On the other hand, we want to determine which STR loci are better suited for nanopore sequencing, by identifying characteristics of the STR loci that hinder accurate nanopore sequencing-based STR profiling.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling

Tytgat

Gansemans

Weymaere

et al. 2020

Genes

Self Cite

View full text Add to dashboard Cite

Nanopore sequencing for forensic short tandem repeats (STR) genotyping comes with the advantages associated with massively parallel sequencing (MPS) without the need for a high up-front device cost, but genotyping is inaccurate, partially due to the occurrence of homopolymers in STR loci. The goal of this study was to apply the latest progress in nanopore sequencing by Oxford Nanopore Technologies in the field of STR genotyping. The experiments were performed using the state of the art R9.4 flow cell and the most recent R10 flow cell, which was specifically designed to improve consensus accuracy of homopolymers. Two single-contributor samples and one mixture sample were genotyped using Illumina sequencing, Nanopore R9.4 sequencing, and Nanopore R10 sequencing. The accuracy of genotyping was comparable for both types of flow cells, although the R10 flow cell provided improved data quality for loci characterized by the presence of homopolymers. We identify locus-dependent characteristics hindering accurate STR genotyping, providing insights for the design of a panel of STR loci suited for nanopore sequencing. Repeat number, the number of different reference alleles for the locus, repeat pattern complexity, flanking region complexity, and the presence of homopolymers are identified as unfavorable locus characteristics. For single-contributor samples and for a limited set of the commonly used STR loci, nanopore sequencing could be applied. However, the technology is not mature enough yet for implementation in routine forensic workflows.

show abstract

Section: Nanopore Sequencing-based Genotypingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling

Tytgat

Gansemans

Weymaere

et al. 2020

Genes

Self Cite

View full text Add to dashboard Cite

show abstract

“…Beside biodiversity monitoring, the MinION platform is interesting for other conservation and biodiversity related fields, such as wildlife forensics [86]. However, due to its high error rate in homogeneous sequences, the current technology does not allow for reliable sequencing of microsatellites (STRs), a standard marker in forensics [87]. Techniques such as genome skimming using the MinION device have been shown to work well for species identifications [63].…”

Section: Discussionmentioning

confidence: 99%

Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

Krehenwinkel

Pomerantz

Prost

2019

Genes

View full text Add to dashboard Cite

We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology’s MinION portable sequencing platform, as well as summarize areas of recent development.

show abstract

“…Few studies to date have assessed the use of the ONT MinION device for sequencing forensic STRs [29][30][31][32]. Despite successful profiling of the SNPs interrogated, only 14 of the 27 autosomal STRs were correctly typed across all samples using the most recently developed pipeline [29].…”

Section: Introductionmentioning

confidence: 99%

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

Hall

Kesharwani

Phillips

et al. 2021

Preprint

View full text Add to dashboard Cite

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. In this proof-of-principle study, we evaluate the forensic applicability of the newest and smallest NGS platform available — the Oxford Nanopore Technologies (ONT) MinION device. Although nanopore sequencing on the handheld MinION offers numerous advantages, including 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. Here we present STRspy, a streamlined method capable of producing length- and sequence-based STR allele designations from noisy, long-read data. To demonstrate 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. Basecalled reads were 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% concordance based on both length and sequence. Furthermore, we were able to identify flanking region SNPs with >90% accuracy. These results demonstrate that nanopore sequencing platforms are capable of revealing additional variation in and around STR loci depending on read coverage. As the first long-read 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.

show abstract

Forensic STR profiling using Oxford Nanopore Technologies’ MinION sequencer

Cited by 13 publications

References 21 publications

Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling

Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling

Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

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

Contact Info

Product

Resources

About