Forensic nanopore sequencing of STRs and SNPs using Verogen’s ForenSeq DNA Signature Prep Kit and MinION

Ren, Zilin; Zhang, Jiarong; Zhang, Xiaomeng; Xu, Lai; Lin, Yanfeng; Bai, Hua; Wang, Mengchun; Cheng, Feng; Liu, Jin-Ding; Kong, Lei; Bo, Xiaochen; Wang, Shengqi; Ni, Ming; Yan, Jiangwei

doi:10.1007/s00414-021-02604-0

Cited by 32 publications

(26 citation statements)

References 38 publications

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“…To assess the impact of amplification cycle number on stutter artifact formation we examined the prevalence of reads one repeat unit smaller and larger than the true allele (n ± 1) with the STRspy utility scripts (Supplementary File S1). Previous STR genotyping attempts have been complicated by the presence of stutter artifacts at D18S51 ([AGAA]n) in ONT sequencing data [30]. Consistent with the notion that stutter percentage increases with the number of PCR cycles, we observed higher normalized read counts for n ± 1 stutter at D18S51 when NISTAc (12,15) was amplified with 30 cycles (0.36, 0.38, 0.41) compared to 15 cycles (0.26, 0.28, 0.27).…”

Section: Impact Of Amplification Cycle Number On Stutter Artifactsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Few studies to date have assessed the use of the ONT MinION device for sequencing forensic STRs [30][31][32][33]. 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 [30]. These and other researchers have attributed the inability to obtain complete and accurate STR profiles to the high error rate of ONT platforms [30][31][32][33].…”

Section: Introductionmentioning

confidence: 99%

“…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 [30]. These and other researchers have attributed the inability to obtain complete and accurate STR profiles to the high error rate of ONT platforms [30][31][32][33]. The results obtained were used to identify locus-and allele-specific features (e.g., repeat number, motif complexity, presence of homopolymers) that prevent successful genotyping using nanopore sequencing data and provide guidelines for developing panels of ONT-compatible STR loci.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

Hall

Kesharwani

Phillips

et al. 2022

Forensic Science International: Genetics

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Section: Impact Of Amplification Cycle Number On Stutter Artifactsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Hall

Kesharwani

Phillips

et al. 2022

Forensic Science International: Genetics

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“…Currently, nanopore R9.4.1 has been used in multiple areas for rapid sequencing and showed a good performance, including cancer research [56], human genetics [57] and microbiology [58]. However, as R9.4.1 has only one reader head, it cannot accurately identify bases in some special sequences.…”

Section: Optimization Of Nanopore Typesmentioning

confidence: 99%

Nanopore Technology and Its Applications in Gene Sequencing

2021

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In recent years, nanopore technology has become increasingly important in the field of life science and biomedical research. By embedding a nano-scale hole in a thin membrane and measuring the electrochemical signal, nanopore technology can be used to investigate the nucleic acids and other biomacromolecules. One of the most successful applications of nanopore technology, the Oxford Nanopore Technology, marks the beginning of the fourth generation of gene sequencing technology. In this review, the operational principle and the technology for signal processing of the nanopore gene sequencing are documented. Moreover, this review focuses on the applications using nanopore gene sequencing technology, including the diagnosis of cancer, detection of viruses and other microbes, and the assembly of genomes. These applications show that nanopore technology is promising in the field of biological and biomedical sensing.

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Pilot validation of on‐field STR typing and human identity testing by MinION nanopore sequencing

Luo,

Zhang,

et al. 2024

Electrophoresis

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Nanopore sequencing technology has broad application prospects in forensic medicine due to its small size, portability, fast speed, real‐time result analysis capabilities, single‐molecule sequencing abilities, and simple operation. Here, we demonstrate for the first time that nanopore sequencing platforms can be used to identify individuals in the field. Through scientific and reasonable design, a nanopore MinION MK1B device and other auxiliary devices are integrated into a portable detection box conducive to individual identification at the accident site. Individual identification of 12 samples could be completed within approximately 24 h by jointly detecting 23 short tandem repeat (STR) loci. Through double‐blinded experiments, the genotypes of 49 samples were successfully determined, and the accuracy of the STR genotyping was verified by the gold standard. Specifically, the typing success rate for 1150 genotypes was 95.3%, and the accuracy rate was 86.87%. Although this study focused primarily on demonstrating the feasibility of full‐process testing, it can be optimistically predicted that further improvements in bioinformatics workflows and nanopore sequencing technology will help enhance the feasibility of Oxford Nanopore Technologies equipment for real‐time individual identification at accident sites.

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Forensic nanopore sequencing of STRs and SNPs using Verogen’s ForenSeq DNA Signature Prep Kit and MinION

Cited by 32 publications

References 38 publications

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

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

Nanopore Technology and Its Applications in Gene Sequencing

Pilot validation of on‐field STR typing and human identity testing by MinION nanopore sequencing

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