Reverse Complement-PCR, an Innovative and Effective method for Multiplexing Forensically Relevant Single Nucleotide Polymorphism Marker Systems

Buś, Magdalena M.; Jong, Erik A.C. de; King, Jonathan L.; Vliet, Walter van der; Theelen, Joop; Budowle, Bruce

doi:10.2144/btn-2021-0031

Cited by 9 publications

(3 citation statements)

References 20 publications

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“…Additionally, throughput for the OmniSNP panel could be increased by using an instrument with higher output, such as a NextSeq (Illumina, San Diego, CA). A publication describing the development of this assay showed most of the SNP alleles were detected with DNA input of 60 pg [24]. The OmniSNP workflow does not have an intended bioinformatic software; however, STRait Razor Online v.0.1.7 and STRait Razor v3 were previously used for data analysis [24][25][26].…”

Section: Idseek Omnisnp Identity Informative Snp Typing Kitmentioning

confidence: 99%

“…A publication describing the development of this assay showed most of the SNP alleles were detected with DNA input of 60 pg [24]. The OmniSNP workflow does not have an intended bioinformatic software; however, STRait Razor Online v.0.1.7 and STRait Razor v3 were previously used for data analysis [24][25][26].…”

Section: Idseek Omnisnp Identity Informative Snp Typing Kitmentioning

confidence: 99%

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SNP assays for DVI: cost, time, and performance information for decision-makers

Gettings,

Tillmar,

Sturk-Andreaggi

et al. 2024

Preprint

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In mass disaster events, forensic DNA laboratories may be called upon to quickly pivot their operations toward identifying bodies and reuniting remains with family members. Ideally, laboratories have considered this possibility in advance and have a plan in place. Compared with traditional short tandem repeat (STR) typing, single nucleotide polymorphisms (SNPs) may be better suited to these disaster victim identification (DVI) scenarios due to their small genomic target size, resulting in an improved success rate in degraded DNA samples. As the landscape of technology has shifted toward DNA sequencing, many forensic laboratories now have benchtop instruments available for massively parallel sequencing (MPS), facilitating this operational pivot from routine forensic STR casework to DVI SNP typing. Herein, we review the commercially available SNP sequencing assays amenable to DVI, we use data simulations to explore the potential for kinship prediction from SNP panels of varying size, and we give an example DVI scenario as context for presenting the matrix of considerations: kinship predictive potential, cost, and throughput of current SNP assay options. This information is intended to assist laboratories in choosing a SNP system for disaster preparedness.

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Section: Idseek Omnisnp Identity Informative Snp Typing Kitmentioning

confidence: 99%

Section: Idseek Omnisnp Identity Informative Snp Typing Kitmentioning

confidence: 99%

SNP assays for DVI: cost, time, and performance information for decision-makers

Gettings,

Tillmar,

Sturk-Andreaggi

et al. 2024

Preprint

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show abstract

“…RC‐PCR has proven its strong value, for example, in SARS‐CoV‐2 whole genome sequencing (Coolen et al, 2021; Schwarzer et al, 2021) and forensics (Bus et al, 2021). Most recently, the EasySeq™ 16S rRNA bacterial ID kit was applied in a clinical setting for the detection of bacterial pathogens in patient samples.…”

Section: Introductionmentioning

confidence: 99%

Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection

Leontidou,

Abad‐Recio,

Rubel

et al. 2023

Environmental Microbiology

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Environmental DNA sequencing is the gold standard to reveal microbial community structures. In most applications, a one‐fragment PCR approach is applied to amplify a taxonomic marker gene, usually a hypervariable region of the 16S rRNA gene. We used a new reverse complement (RC)‐PCR‐based assay that amplifies seven out of the nine hypervariable regions of the 16S rRNA gene, to interrogate bacterial communities in sediment samples collected from different coastal marine sites with an impact gradient. In parallel, we employed a traditional one‐fragment analysis of the hypervariable V3–V4 region to investigate whether the RC‐PCR reveals more of the ‘unseen’ diversity obtained by the one‐fragment approach. As a benchmark for the full deck of diversity, we subjected the samples to PCR‐free metagenomic sequencing. None of the two PCR‐based approaches recorded the full taxonomic repertoire obtained from the metagenomics datasets. However, the RC‐PCR approach detected 2.8 times more bacterial genera compared to the near‐saturation sequenced V3–V4 samples. RC‐PCR is an ideal compromise between the standard one‐fragment approach and metagenomics sequencing and may guide future environmental sequencing studies, in which bacterial diversity is a central subject.

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DNA and protein analyses of hair in forensic genetics

Simayijiang

Wang

et al. 2023

Int J Legal Med

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Reverse Complement-PCR, an Innovative and Effective method for Multiplexing Forensically Relevant Single Nucleotide Polymorphism Marker Systems

Cited by 9 publications

References 20 publications

SNP assays for DVI: cost, time, and performance information for decision-makers

SNP assays for DVI: cost, time, and performance information for decision-makers

Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection

DNA and protein analyses of hair in forensic genetics

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