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

Hall, Courtney L.; Kesharwani, Rupesh K.; Phillips, Nicole; Planz, John V.; Sedlazeck, Fritz J.; Zascavage, Roxanne R.

doi:10.1016/j.fsigen.2021.102629

Cited by 19 publications

(24 citation statements)

References 42 publications

(82 reference statements)

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“…The shift from a laboratorycentralised workflow to on-site DNA analysis overcomes the fundamental challenge of transporting biological material to a site where sequencing can be performed [42]. While only few studies to date have assessed the applicability of the ONT MinION device for sequencing forensic STRs [34,[49][50][51], recent findings suggest that STR panels can be compatible with ONT sequencing platforms [39], which opens up new opportunities in the field of wildlife forensics and conservation genetics.…”

Section: Discussionmentioning

confidence: 99%

“…Despite the advantages of MPS, the widespread adoption of high throughput sequencebased STR typing for wildlife conservation purposes is still hindered by high start-up costs (e.g. for equipment and reagents), labour-intensive sample preparation, and steep learning curves associated with MPS data analysis [39][40][41]. Additionally, the lack of well-established research facilities in biodiverse countries means that biological samples must be shipped to sites where sequencing can be performed [42].…”

Section: Discussionmentioning

confidence: 99%

“…Nevertheless, recent technological advances have circumvented these issues by greatly reducing the cost for the acquisition of sequencing and laboratory equipment, with positive repercussions for the implementation of wildlife conservation genomics initiatives [39, 40]. In this regard, the commercialisation of portable nanopore sequencing devices by Oxford Nanopore Technologies Plc.…”

Section: Discussionmentioning

confidence: 99%

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Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes

Fedele

Wetton

Jobling

2022

Preprint

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Background: Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). Here we assess in African great ape DNAs the human-based ForenSeq DNA Sequencing Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. Results: The Forenseq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges, but variation in repeat array structures and little relationship with the known phylogeny, suggesting stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity, indicating a possible mutational difference to humans. Conclusions: Despite some variability in amplification success, orthologs of most human aSTRs in the ForenSeq DNA Sequencing Prep Kit can be analysed in African great apes. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes

Fedele

Wetton

Jobling

2022

Preprint

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“…Příkladem mikrosatelitu je dinukleotidová repetice CTCTCTCTCTCT, která může být zkráceně zapsána jako (CT) 6 , nebo tetranukleotidová repetice ACTCACTCACTCACTC, zapsaná jako (ACTC) 4 . Pro současnou forenzní praxi byly vybrány takové mikrosatelity, jejichž alely nejsou natolik dlouhé, aby jejich typizace byla ohrožena u degradovaných vzorků, mají vysokou úroveň heterozygozity, nejsou navzájem ve vazbě, chovají se způsobně v multiplexu, mají nízkou úroveň zadrhávání neboli stutteru (viz níže) a nízkou frekvenci mutací.…”

Section: Mikrosatelityunclassified

“…Nejprve byla RFLP metoda nahrazena technikami rozlišujícími délkové polymorfismy typu krátkých tandemových repetic, Short Tandem Repeats (STR), které nevyžadují tak velké množství nedegradované vstupní DNA a jsou lépe standardizovatelné. V současné době probíhá postupný přechod na metody masivně paralelního sekvenování, o čemž bude napsáno více v kapitole 4 a 6 této knihy (4,5). Zároveň byly poznány limity genotypizačních metod a stanoveny požadavky pro zacházení 1 Nesmíme však zapomenout, že ani DNA není úplně rezistentní vůči klasickým snahám o znehodnocení důkazů, jako je podvržení vzorku, sanace místa činu prostředkem ničícím veškerou DNA, zpochybnění neporušenosti důkazního řetězce (chain of custody).…”

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Vybrané metody forenzní genetiky

2022

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

Cited by 19 publications

References 42 publications

Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes

Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes

Vybrané metody forenzní genetiky

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

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