Characterizing stutter variants in forensic STRs with massively parallel sequencing

Li, Ran; Wu, Riga; Li, Haixia; Zhang, Yinming; Peng, Dan; Wang, Nana; Shen, Xuefeng; Wang, Zhiyuan; Sun, Hongyu

doi:10.1016/j.fsigen.2019.102225

Cited by 23 publications

(21 citation statements)

References 22 publications

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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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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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“…Sequence analyses of compound stutters could be helpful. The maturation of NGS-based STR sequencing and data analysis technologies have made stutter sequence analyses possible [18][19][20][28][29][30]. In this work, compound stutter sequences of eight STR loci were recorded and counted.…”

Section: Discussionmentioning

confidence: 99%

Massively parallel sequencing of STRs using a 29‐plex panel reveals stutter sequence characteristics

Liu

et al. 2020

Electrophoresis

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Massively parallel sequencing of forensic STRs simultaneously provides length‐based genotypes and core repeat sequences as well as flanking sequence variations. Here, we report primer sequences and concentrations of a next‐generation sequencing (NGS)‐based in‐house panel covering 28 autosomal STR loci (CSF1PO, D1GATA113, D1S1627, D1S1656, D1S1677, D2S441, D2S1776, D3S3053, D5S818, D6S474, D6S1017, D6S1043, D8S1179, D9S2157, D10S1435, D11S4463, D13S317, D14S1434, D16S539, D18S51, D18S853, D20S482, D20S1082, D22S1045, FGA, TH01, TPOX, and vWA) and the sex determinant locus Amelogenin. Preliminary evaluation experiments showed that the panel yielded intralocus‐ and interlocus‐balanced sequencing data with a sensitivity as low as 62.5 pg input DNA. A total of 203 individuals from Yunnan Bai population were sequenced with this panel. Comparative forensic genetic analyses showed that sequence‐based matching probability of this 29‐plex panel reached 2.37 × 10−29, which was 23 times lower than the length‐based data. Compound stutter sequences of eight STRs were compared with parental alleles. For seven loci, repeat motif insertions or deletions occurred in the longest uninterrupted repeat sequences (LUS). However, LUS and non‐LUS stutters co‐existed in the locus D6S474 with different sequencing depth ratios. These results supplemented our current knowledge of forensic STR stutters, and provided a sound basis for DNA mixture deconvolution.

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“…In STR analysis, ePIA and oPIA have the same definition as that in the analysis of SNPs, but the process of identifying alleles in plasma was more complicated. A novel strategy, inspired by our previous study about the characteristics of stutter variants in STR genotyping [23], was developed for the identification of STR alleles in plasma. Firstly, sequences with read counts of <1% were excluded for each locus, assuming that they were mainly PCR-derived noises or sequencing errors.…”

Section: Genotype Callingmentioning

confidence: 99%

“…All the alleles detected in nonplasma samples of both parents were added to the STR sequence database to avoid exclusion of novel alleles. Thirdly, a sequence simplification process for the remaining sequences was performed following Li et al's strategy [23]. According to this method, sequences with the same simplified architecture were categorized into one group and the sequence with the highest read count was considered as the parental allele of that group.…”

Section: Genotype Callingmentioning

confidence: 99%

“…Among MPS panels developed for forensic research, the ForenSeq DNA Signature Prep Kit (Verogen., San Diego, CA, USA), which is based on Illumina Miseq FGx platform, was widely used and evaluated [22]. Also, a sequence simplification method for MPS-based STR sequence polymorphism analysis was developed, which may bring improvement for mixture deconvolution under stutter interference [23]. For unbalanced mixtures, the minor contributor's alleles could be identified even when the ratios were as low as 1:1000.…”

Section: Introductionmentioning

confidence: 99%

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Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing

Shen

et al. 2021

Genes

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Cell-free fetal DNA (cffDNA) from maternal plasma has made it possible to develop noninvasive prenatal paternity testing (NIPPT). However, most studies have focused on customized single nucleotide polymorphism (SNP) typing systems and few have used conventional short tandem repeat (STR) markers. Based on massively parallel sequencing (MPS), this study used a widely-accepted forensic multiplex assay system to evaluate the effect of noninvasive prenatal paternity testing with a combination of well-established SNP and STR markers. Using a ForenSeq DNA Signature Prep Kit, NIPPT was performed in 17 real parentage cases with monovular unborn fetuses at 7 to 24 gestational weeks. Different analytical strategies for the identification of paternally inherited allele (PIA) were developed to deal with SNPs and STRs. Combined paternity index (CPI) for 17 real trios as well as 272 unrelated trios was calculated. With the combination of SNPs and A-STRs, 82.35% (14/17), 88.24% (15/17), 94.12% (16/17), and 94.12% (16/17) of real trios could be accurately determined when the likelihood ratio (LR) threshold for paternity inclusion was set to 10,000, 1000, 100, and 10, respectively. This reveals that simultaneous surveys of SNP and STR markers included in the ForenSeq DNA Signature Prep Kit offer a promising method for NIPPT using MPS technology.

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Characterizing stutter variants in forensic STRs with massively parallel sequencing

Cited by 23 publications

References 22 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

Massively parallel sequencing of STRs using a 29‐plex panel reveals stutter sequence characteristics

Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing

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