Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success

Zeng, Xiangpei; Elwick, Kyleen; Mayes, Carrie; Takahashi, Maiko; King, Jonathan L.; Gangitano, David; Budowle, Bruce; Hughes‐Stamm, Sheree

doi:10.1007/s00414-018-1955-9

Cited by 25 publications

(6 citation statements)

References 30 publications

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“…Moreover, current MPS-kits provide the option to multiplex various loci simultaneously within one reaction, such as STRs (autosomal, Y-and X-chromosomal), mitochondrial DNA (control region) as well as single nucleotide polymorphisms (SNPs) that provide estimates of identity, phenotypic traits, biogeographical and ancestry information [21][22][23][24]. The inclusion of SNPs adds the benefit [25][26][27] that these markers allow for shorter amplicon design, which can support human identification of degraded or challenging DNA samples [28][29][30]. Although published studies have demonstrated that MPS is a promising tool for forensic applications, little is known about the method's variability and potential differences in the limit of detection between sequencing platforms from the same supplier.…”

Section: Introductionmentioning

confidence: 99%

Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA

et al. 2019

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We present results from an inter-laboratory massively parallel sequencing (MPS) study in the framework of the SeqForSTRs project to evaluate forensically relevant parameters, such as performance, concordance, and sensitivity, using a standardized sequencing library including reference material, mixtures, and ancient DNA samples. The standardized library was prepared using the ForenSeq DNA Signature Prep Kit (primer mix A). The library was shared between eight European laboratories located in Austria, France, Germany, The Netherlands, and Sweden to perform MPS on their particular MiSeq FGx sequencers. Despite variation in performance between sequencing runs, all laboratories obtained quality metrics that fell within the manufacturer's recommended ranges. Furthermore, differences in locus coverage did not inevitably adversely affect heterozygous balance. Inter-laboratory concordance showed 100% concordant genotypes for the included autosomal and Y-STRs, and still, X-STR concordance exceeded 83%. The exclusive reasons for X-STR discordances were drop-outs at DXS10103. Sensitivity experiments demonstrated that correct allele calling varied between sequencing instruments in particular for lower DNA amounts (≤ 125 pg). The analysis of compromised DNA samples showed the drop-out of one sample (FA10013B01A) while for the remaining three degraded DNA samples MPS was able to successfully type ≥ 87% of all aSTRs, ≥ 78% of all Y-STRs, ≥ 68% of all X-STRs, and ≥ 92% of all iSNPs demonstrating that MPS is a promising tool for human identity testing, which in return, has to undergo rigorous in-house validation before it can be implemented into forensic routine casework.

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Section: Introductionmentioning

confidence: 99%

Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA

et al. 2019

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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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“…Zeng et al () found the ForenSeq™ library preparation was not affected when testing three commercial DNA extraction kits and one organic extraction method on the removal of common inhibitors; all methods sufficiently removed inhibitors from blood samples spiked with hematin, hair samples spiked with melanin, and bone samples spiked with calcium and humic acid.…”

Section: Validationmentioning

confidence: 99%

A review of the method and validation of the MiSeq FGx™ Forensic Genomics Solution

England

Harbison

2019

WIREs Forensic Science

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The MiSeq FGx™ Forensic Genomics Solution (MFGS; Verogen Inc.) is a massively parallel sequencing workflow using Illumina sequencing technology. The workflow includes the ForenSeq™ DNA Signature Prep kit, the MiSeq FGx™, and the ForenSeq™ Universal Analysis Software (UAS). This review explores the molecular biology and bioinformatic methods used during the preparation of samples into sequencing libraries, the MiSeq FGx™ sequencing process, and the data analysis. We highlight what happens during each of these steps and how they influence the final results, while identifying limitations and possible improvements. After initial evaluations established its suitability for forensic applications, a number of studies have completed forensic validation studies. We review this work, and find the MFGS has shown to be a reliable and robust technology. The successful validation of the solution has allowed its implementation into forensic casework in a number of jurisdictions. Some questions still remain around the normalization of the sequencing libraries, and the bioinformatic processing and analysis of the sequencing results. In particular, the markers for biogeographical ancestry and externally visible characteristics require further research into their performance, and the ForenSeq™ UAS, in its current form, is limited in its ability to accurately predict these characteristics. We suggest a number of alternative bioinformatic tools that could be used instead.

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Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success

Cited by 25 publications

References 30 publications

Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA

Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA

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

A review of the method and validation of the MiSeq FGx™ Forensic Genomics Solution

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