An evaluation of the PowerSeq™ Auto System: A multiplex short tandem repeat marker kit compatible with massively parallel sequencing

Zeng, Xiangpei; King, Jonathan L.; Hermanson, Spencer; Patel, Jaynish; Storts, Douglas R.; Budowle, Bruce

doi:10.1016/j.fsigen.2015.07.015

Cited by 62 publications

(39 citation statements)

References 25 publications

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“…Zeng et al. 's work indicated that partial STR profiles of the minor contributor could be detected up to 19:1 mixture. Our data confirmed that NGS genotyped most alleles from a minor contributor, even at ratios of 1:19 and 19:1 (Fig.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…The ForenSeq™ DNA Signature Prep Kit (Illumina, San Diego, CA) includes two primer mixes: Primer Mix A tests for 27 autosomal STRs, 24 Y‐STRs, 7 X‐STRs, as well as 94 single nucleotide polymorphisms (SNPs) for identity, and Primer Mix B includes the loci of Mix A with an additional 24 phenotypic SNPs and 56 ancestry SNPs, of which two SNPs overlap . The PowerSeq™ Auto System (Promega, Madison WI) includes 23 STRs (22 autosomal and one Y‐STR) plus Amelogenin . Both the Promega and Illumina kits run on the Illumina MiSeq platform.…”

Section: Introductionmentioning

confidence: 99%

“…Recent studies evaluating Illumina MiSeq platform using ForenSeq TM Primer Mix B showed that STR profiles could be obtained from input DNA as low as 50 pg, which is in the range of other platforms such as the prototype of PowerSeq TM Auto System and STR kits using the Ion PGM™ System .…”

Section: Introductionmentioning

confidence: 99%

Systematic assessment of the performance of Illumina's MiSeq FGx™ forensic genomics system

et al. 2017

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This study assesses the performance of Illumina's MiSeq FGx System for forensic genomics by systematically analyzing single source samples, evaluating concordance, sensitivity and repeatability, as well as describing the quality of the reported outcomes. DNA from 16 individuals (9 males/7 females) in nine separate runs showed consistent STR profiles at DNA input ≥400 pg, and two full profiles were obtained with 50 pg DNA input. However, this study revealed that the outcome of a single sample does not merely depend on its DNA input but is also influenced by the total amount of DNA loaded onto the flow cell from all samples. Stutter and sequence or amplification errors can make the identification of true alleles difficult, particularly for heterozygous loci that show allele imbalance. Sequencing of 16 individuals' STRs revealed genetic variations at 14 loci at frequencies suggesting improvement of mixture deconvolution. The STR loci D1S1656 and DXS10103 were most susceptible to drop outs, and D22S1045 and DYS385a-b showed heterozygote imbalance. Most stutters were typed at TH01 and DYS385a-b, while amplification or sequencing errors were observed mostly at D7S820 and D19S433. Overall, Illumina's MiSeq FGx System produced reliable and repeatable results. aSTRs showed fewer drop outs than the Y- and X-STRs.

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“…The samples, extraction, PCR amplification, library preparation, and sequencing are described in Zeng et al (14). …”

Section: Methodsmentioning

confidence: 99%

“…Using data from Zeng et al (14), the noise and stutter distribution were characterized for 23 STRs included in PowerSeq TM Auto System (CSF1PO, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D1S1656, D21S11, D22S1045, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, DYS391, FGA, Penta D, Penta E, TH01, TPOX, and vWA) (Promega Corporation, Madison, WI, USA). While the sample size is small (as this is a preliminary study to describe the main artifacts), the results show that multiple stutter species can be observed.…”

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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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An evaluation of the PowerSeq™ Auto System: A multiplex short tandem repeat marker kit compatible with massively parallel sequencing

Cited by 62 publications

References 25 publications

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

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

Systematic assessment of the performance of Illumina's MiSeq FGx™ forensic genomics system

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

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