Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains

Elwick, Kyleen; Buś, Magdalena M.; King, Jonathan L.; Chang, Joseph; Hughes‐Stamm, Sheree; Budowle, Bruce

doi:10.1016/j.legalmed.2019.08.001

Cited by 25 publications

(14 citation statements)

References 41 publications

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“…In this study, DNA quantity and quality of the skeletal remain samples were assessed for library preparation during MPS run and STR allele recovery. Our data showed that the number of STR loci recovered was correlated with DNA input in the first round of PCR for samples <100 pg, which was also reported previously [10], which may be related to the library yield generated from the starting materials. DNA analysis using a low template DNA may still be a challenge in MPS‐based STR analysis similar to CE system.…”

Section: Discussionsupporting

confidence: 88%

“…The recovery rate of STR alleles in the in‐house MPS‐STR system was dependent on the amplicon size (Supporting Information Fig. S5), as shown in the CE system, but not for all STR loci detected in previous studies [9, 10]. Overall, a higher success rate of recovery was obtained using the in‐house MPS‐STR system (mean 57.4 ± 15.2 samples, min.…”

Section: Resultsmentioning

confidence: 72%

“…Currently, multiple commercial forensic STR kits are available in the MPS system (MPS‐STR system) and have been validated for intact DNA samples [5, 6]. Environmentally and artificially degraded samples also have been tested with the commercially available MPS‐STR system [7–11], which showed a higher success rate of amplification and sequencing of forensic markers compared with the CE system. Thus, the MPS‐STR system is a valuable tool for analysis of degraded DNA samples for human skeletal remains, and optimization of the protocol and panel can improve the assay.…”

Section: Introductionmentioning

confidence: 99%

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Improved STR analysis of degraded DNA from human skeletal remains through in‐house MPS‐STR panel

et al. 2020

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DNA analysis of degraded samples and low-copy number DNA derived from skeletal remains, one of the most challenging forensic tasks, is common in disaster victim identification and genetic analysis of historical materials. Massively parallel sequencing (MPS) is a useful technique for STR analysis that enables the sequencing of smaller amplicons compared with conventional capillary electrophoresis (CE), which is valuable for the analysis of degraded DNA. In this study, 92 samples of human skeletal remains (70+ years postmortem) were tested using an in-house MPS-STR system designed for the analysis of degraded DNA. Multiple intrinsic factors of DNA from skeletal remains that affect STR typing were assessed. The recovery of STR alleles was influenced more by DNA input amount for amplification rather than DNA degradation, which may be attributed from the high quantity and quality of libraries prepared for MPS run. In addition, the higher success rate of STR typing was achieved using the MPS-STR system compared with a commercial CE-STR system by providing smaller sized fragments for amplification. The results can provide constructive information for the analysis of degraded sample, and this MPS-STR system will contribute in forensic application with regard to skeletal remain sample investigation.

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Section: Discussionsupporting

confidence: 88%

Section: Resultsmentioning

confidence: 72%

Section: Introductionmentioning

confidence: 99%

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Improved STR analysis of degraded DNA from human skeletal remains through in‐house MPS‐STR panel

et al. 2020

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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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“…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]. Hence, on the basis of the sufficient validations of the stability and homogeneity, more essential data of worldwide populations are needed urgently at present to improve the standard experimental procedures, promote the efficiencies of MPS-based system, and strengthen and unify the contacts between capillary electrophoresis-based (CE-based) and MPS-based data for the basic and extended applications of forensic sciences and others.As the aborigines in Hainan island where was the entrances to East Asia (either the southern entrance from Indo-China peninsula or the northern entrance from Central Asia) [12,[69][70][71], Hainan...…”

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confidence: 99%

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

Fan

Wang

et al. 2020

Preprint

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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. Signature Prep Kit; Massively parallel sequencing. mass landings of the Han (since BC 214 in Qin Dynasty) and Lingao people (about BC 500 during the Spring and Autumn period) compressed the living space of Hainan Li, making Li from the north to the south of Hainan island [1,2,9,29,30]. (Nowadays, the main distributions of Hainan Li minority are shown in Fig. 1C.) In all ages, ever since the primordial settlements in Hainan island, Hlai language was the dominant language for the original migrants and their descendants, and the intangible cultural and spiritual heritages within Hainan Li were preserved by oral transmission without ancient writings to hand down. Hlai, which is one important branch of the Tai-Kadai languag...

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Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains

Cited by 25 publications

References 41 publications

Improved STR analysis of degraded DNA from human skeletal remains through in‐house MPS‐STR panel

Improved STR analysis of degraded DNA from human skeletal remains through in‐house MPS‐STR panel

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

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

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Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains

Cited by 25 publications

References 41 publications

Improved STR analysis of degraded DNA from human skeletal remains through in‐house MPS‐STR panel

Improved STR analysis of degraded DNA from human skeletal remains through in‐house MPS‐STR panel

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

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

Contact Info

Product

Resources

About

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