Automation and developmental validation of the ForenSeq™ DNA Signature Preparation kit for high-throughput analysis in forensic laboratories

Hollard, Clémence; Ausset, Lionel; Chantrel, Yann; Jullien, S.; Clot, Maéva; Faivre, Magalie; Suzanne, Elodie; Pène, Laurent; Laurent, François-Xavier

doi:10.1016/j.fsigen.2019.01.010

Cited by 36 publications

(31 citation statements)

References 34 publications

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“…Furthermore, the detail DoCs for all samples were presented in Supplementary Table S2 and Supplementary Figure S1-S3, which indicated that the DoCs for all samples were balanceable, with no differences for females and males. Our sequencing results were in accordance with other forensic MPS-related studies [40,41,43,45,[111][112][113][114][115]. No matter in females or males, the DoCl and DoCs had no differences at the same locus, and the DoC were unbalanced in different types of genetic markers.…”

Section: Resultssupporting

confidence: 90%

“…The ForenSeq™ DNA Signature Prep Kit, as the first commercial MPS-based and forensic related kit formally released in 2015, made full use of the MPS method's advantages by means of the simultaneous and compound amplification of either greater than 150 loci including various types of genetic markers. The large-scale performances and functional tests had been widely validated for the ForenSeq™ DNA Signature Prep Kit, the DNA Primer Set A (DPMA, 152 loci totally: 27 common, forensic autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 identity informative SNPs) and the DNA Primer Set B (in total 230 loci: DMPA plus 22 phenotypic informative SNPs and 56 biogeographical ancestry SNPs), which also include robustness, reproducibility, species specificity, consistency and sensitivity of detection [40][41][42][43][44][45][46][47]. In addition, the applicability of the DNA Signature Prep Kit had been evaluated and verified on challenging samples, DNA mixture, degradative DNA [48][49][50], formalin-fixed paraffin-embedded tissues [49,51], and remains of skeletons and bones [48,[52][53][54], to extend the applications for forensic sciences [55][56][57][58][59][60][61][62][63][64][65][66][67][68].…”

Section: Introductionmentioning

confidence: 99%

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The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

Fan

Wang

et al. 2021

Int J Legal Med

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Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai-language speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics, however, the forensic associated studies on Hainan Li population are still insufficient.Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DAPA, it demonstrated that the STRs and iiSNPs in DAPA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three Datasets, which included the genetic data of (Ⅰ). iiSNPs (27 populations, 2640 individuals), (Ⅱ). Y-STRs (42 populations, 8281 individuals), and (Ⅲ). Yhaplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives.In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.

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Section: Resultssupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

Fan

Wang

et al. 2021

Int J Legal Med

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“…These markers include identity single nucleotide polymorphisms (iSNPs), phenotype informative single nucleotide polymorphisms (piSNPs), autosomal STRs, YSTRs, and XSTRs. A total of 94 SNPs are used for identification purposes with an additional 76 SNPs which are used for phenotype/ancestry estimation [19]. In this research, we offer an alternative processing workflow optimized for both DNA extraction and amplification to increase positive outcomes with rootless hair samples without having to resort to less discriminatory mitochondrial DNA testing.…”

Section: Introductionmentioning

confidence: 99%

Novel extraction chemistry and alternative amplification strategies for use with rootless hair shafts

Gutierrez

LaRue²,

Houston

2021

Journal of Forensic Sciences

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Rootless hair shafts are often considered unsuitable for STR genotyping due to the known high failure rate. The same samples can be reliably processed with mitochondrial sequencing. However, the minimal discriminatory power of widely implemented control region mitochondrial sequencing techniques limits its utility in some forensic casework. In this research, multiple variables were tested to provide information on rootless hair shaft sample genotyping success. Results showed external decontamination procedures decreased drop-in alleles but also greatly reduced profile recovery. The novel InnoXtract ™ chemistry was comparable to automated EZ1 DNA Investigator extraction. With thoroughly decontaminated hairs, InnoTyper ® 21 amplification generated random match probabilities higher than STR chemistry in 71.875% of samples and 18.75% of samples benefitted from the use of InnoTyper ® 21 amplification compared with estimated mtDNA profile rarity. Compared with the capillary electrophoresis-based amplification chemistries tested, the ForenSeq™ DNA Signature Prep chemistry paired with massively parallel sequencing was the most discriminatory amplification strategy tested.

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“…Several commercial sequencing panels were developed for human identification, including the ForenSeq TM DNA Signature Prep Kit (Verogen V R , San Diego, CA, USA), the Precision ID GlobalFiler NGS STR Panel (Thermo Fisher Scientific, Waltham, MA, USA), and the PowerSeq TM 46GY System (Promega, Madison, WI, USA). These assays were tested rigorously by different forensic genetic laboratories, and they produced sequencing results that were concordant with CE-based STR typing assays at a level of sensitivity that is comparable to that of the currently used PCR-CE methods [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Sequencing of human identification markers in an Uyghur population using the MiSeq FGx^TMForensic Genomics System

Simayijiang

Morling

Børsting

2020

Forensic Sciences Research

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Massively parallel sequencing (MPS) offers a useful alternative to capillary electrophoresis (CE) based analysis of human identification markers in forensic genetics. By sequencing short tandem repeats (STRs) instead of determining the fragment lengths by CE, the sequence variation within the repeat region and the flanking regions may be identified. In this study, we typed 264 Uyghur individuals using the MiSeq FGx TM Forensic Genomics System and Primer Mix A of the ForenSeq TM DNA Signature Prep Kit that amplifies 27 autosomal STRs, 25 Y-STRs, seven X-STRs, and 94 HID-SNPs. STRinNGS v.1.0 and GATK 3.6 were used to analyze the STR regions and HID-SNPs, respectively. Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were 3-4 times larger than those of alleles determined by repeat length alone. A relatively large number of flanking region variants (28 SNPs and three InDels) were observed in the Uyghur population. Seventeen of the flanking region SNPs were rare, and 12 of these SNPs had no accession number in dbSNP. The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85EÀ36 and 1.49E þ 16, respectively. This was 10 000 times lower and 1 000 times higher, respectively, than the same parameters calculated from STR repeat lengths. HIGHLIGHTS Sequencing data on STRs and SNPs used for human identification are presented for the Uyghur population. STRinNGS v.1.0 was used to analyze the flanking regions of STRs. The concordance between PCR-CE and PCR-MPS results was 99.86%. Detection of sequence variation in STRs and their flanking regions increased the allelic diversity.

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Automation and developmental validation of the ForenSeq™ DNA Signature Preparation kit for high-throughput analysis in forensic laboratories

Cited by 36 publications

References 34 publications

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

Novel extraction chemistry and alternative amplification strategies for use with rootless hair shafts

Sequencing of human identification markers in an Uyghur population using the MiSeq FGx^TMForensic Genomics System

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Automation and developmental validation of the ForenSeq™ DNA Signature Preparation kit for high-throughput analysis in forensic laboratories

Cited by 36 publications

References 34 publications

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

Novel extraction chemistry and alternative amplification strategies for use with rootless hair shafts

Sequencing of human identification markers in an Uyghur population using the MiSeq FGxTMForensic Genomics System

Contact Info

Product

Resources

About

Sequencing of human identification markers in an Uyghur population using the MiSeq FGx^TMForensic Genomics System