Characterization of genetic sequence variation of 58 STR loci in four major population groups

Novroski, Nicole M.M.; King, Jonathan L.; Churchill, Jennifer D.; Seah, Lay Hong; Budowle, Bruce

doi:10.1016/j.fsigen.2016.09.007

Cited by 142 publications

(168 citation statements)

References 68 publications

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“…Recently, MPS technology has attracted much interest in the field of forensic science. Multiple studies have been carried out to study various forensic markers using MPS technology . All of these studies imply that MPS holds promise for forensic applications.…”

Section: Introductionmentioning

confidence: 99%

“…In forensic applications, sequence‐based data are expected to increase the effective number of alleles in many STR loci, which will improve the discrimination power and may aid in mixture interpretation . To date, several commercial STR sequencing kits have been released, for example, the Ion Torrent HID STR 10‐plex ; the Early Access STR Kit , and the Precision ID GlobalFiler NGS STR Panel version 1 by Thermo Fisher Scientific (Waltham, MA, USA); the PowerSeq Auto System by Promega Corporation (Madison, WI, USA); and the ForenSeq DNA Signature Prep Kit by Illumina (San Diego, CA, USA). Related studies support that multiplex STR profiling by MPS has gained a higher power of discrimination and exclusion rate; moreover, reliable STR genotypes could be obtained at a relevant sensitivity level .…”

Section: Introductionmentioning

confidence: 99%

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Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Wang

Liu

et al. 2020

Electrophoresis

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Massively parallel sequencing (MPS) technologies have the ability to reveal sequence variations within STR alleles as well as their nominal allele lengths, which have traditionally been detected by CE instruments. Recently, Thermo Fisher Scientific has updated the MPS-STR panel, named the Precision ID GlobalFiler next-generation sequencing (NGS) STR Panel version 2, with primers redesigned to add two pentanucleotide tandem repeat loci and profile interpretation supported by the Converge software. Using the Ion Chef System, the Ion S5XL System, and the Converge software, genetic variations were characterized within STR repeat and flanking regions of 30 autosomal STR markers in 115 unrelated individuals from two Chinese population groups (58 Tibetans and 57 Hans). Nineteen STRs demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. In total, 390 alleles were identified by their sequences compared with 258 alleles that were identified by length. Of these 92 sequence variants found within the STR repeat regions, 40 variants were located in STR flanking regions. Additionally, the agreement of the results with CE data was evaluated, as was the ability of this new MPS panel to analyze case-type (11 samples) and artificially degraded samples (seven samples in triplicate). The results generated from this study illustrate that extensive sequence variation exists in commonly used STR markers in the selected population samples and indicate that this NGS STR panel has the potential to be used as an effective tool for human forensics.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Wang

Liu

et al. 2020

Electrophoresis

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“…Bornman et al's (5) study on short-read STR genotyping was an exception. Since 2015, the research community has shifted work to Miseq (7,11,12,14,16,(23)(24)(25)(26)(27) and Ion Torrent NGS machines (9,10,13,15,28) because 454 sequencers are no longer supported by their producer. Typing results for 48 autosomal STR markers (11,12,22,24), 29 Y-STR markers (10,24,25), and 9 X-STR markers (24) have been reported.…”

mentioning

confidence: 99%

“…Sample types including commercial genomic DNA (12,24), blood (4,7,8,10,23), saliva (5,17,23,28), buccal swabs (4,8,24), semen (9,24,28), vaginal secretions (28), skin (28), bone (9,23), and muscle (9) have been successfully genotyped with NGS. Population data for African American, Caucasian, Hispanic (11,25,27), Danish (6), and East Asian (10,27) are documented.…”

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confidence: 99%

Massively Parallel Sequencing of Forensic STRs Using the Ion Chef™ and the Ion S5™ XL Systems,

Wang

Chen

et al. 2018

Journal of Forensic Sciences

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Next-generation sequencing (NGS) has been used to genotype forensic short tandem repeat (STR) markers for individual identification and kinship analysis. STR data from several NGS platforms have been published, but forensic application trials using the Ion S5™ XL system have not been reported. In this work, we report sensitivity, reproducibility, mixture, simulated degradation, and casework sample data on the Ion Chef™ and S5™ XL systems using an early access 25-plex panel. Sensitivity experiments showed that over 97% of the alleles were detectable with down to 62 pg input of genomic DNA. In mixture studies, alleles from minor contributors were correctly assigned at 1:9 and 9:1 ratios. NGS successfully gave 12 full genotype results from 13 challenging casework samples, compared with five full results using the CE platform. In conclusion, the Ion Chef™ and the Ion S5™ XL systems provided an alternative and promising approach for forensic STR genotyping.

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“…Several studies already have revealed the potential value of MPS for STR typing (1-16). MPS technology enables characterization of a locus based on sequence instead of length-based differences as in CE, so it can increase the discrimination power of some STRs (2,9). MPS is able to detect repeat motif variation (RMV) within STRs, and single nucleotide polymorphisms (SNPs) residing within repeats and within the flanking regions.…”

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confidence: 99%

Investigation of the STR loci noise distributions of PowerSeq™ Auto System

Zeng¹,

King²,

Budowle³

2017

Croat Med J

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AimTo characterize the noise and stutter distribution of 23 short tandem repeats (STRs) included in the PowerSeqTM Auto System.MethodsRaw FASTQ files were analyzed using STRait Razor v2s to display alleles and coverage. The sequence noise was divided into several categories: noise at allele position, noise at -1 repeat position, and artifact. The average relative percentages of locus coverage for each noise, stutter, and allele were calculated from the samples used for this locus noise analysis.ResultsStutter products could be routinely observed at the -2 repeat position, -1 repeat position, and +1 repeat position of alleles. Sequence noise at the allele position ranged from 10.22% to 28.81% of the total locus coverage. At the allele position, individual noise reads were relatively low.ConclusionThe data indicate that noise generally will be low. In addition, the PowerSeqTM Auto System could capture nine flanking region single nucleotide polymorphisms (SNPs) that would not be observed by other current kits for massively parallel sequencing (MPS) of STRs.

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Characterization of genetic sequence variation of 58 STR loci in four major population groups

Cited by 142 publications

References 68 publications

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Massively Parallel Sequencing of Forensic STRs Using the Ion Chef™ and the Ion S5™ XL Systems,

Investigation of the STR loci noise distributions of PowerSeq™ Auto System

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