Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform

Guo, Fei; Zhou, Yajuan; Liu, Feng; Yu, Jiao; He, Song; Shen, Haihong; Zhao, Bi; Jia, Fei; Hou, Guangwei; Jiang, Xiaobei

doi:10.1016/j.fsigen.2016.04.004

Cited by 48 publications

(29 citation statements)

References 21 publications

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“…and Supporting Information Table S1). While full STR profiles could also be detected using ForenSeq™ Primer Mix A at 50 pg DNA input (consistent with other MPS platforms ), sensitivity for some loci were affected at this low DNA input.…”

Section: Discussionsupporting

confidence: 82%

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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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Section: Discussionsupporting

confidence: 82%

“…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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“…In addition, NGS has potential advantages with challenging samples and complicated familial testing (6,8,9). Therefore, increasing numbers of research groups are dedicating substantial efforts to studying NGS-based STR genotyping (10)(11)(12)(13)(14)(15)(16).…”

mentioning

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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“…9,10,11]. The allele category represents correctly sequenced DNA template and any sequencing method with reasonable fidelity will produce sequence types of this category.…”

Section: Resultsmentioning

confidence: 99%

A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis

Young¹,

King

Budowle

et al. 2017

PLoS ONE

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Amplicon (targeted) sequencing by massively parallel sequencing (PCR-MPS) is a potential method for use in forensic DNA analyses. In this application, PCR-MPS may supplement or replace other instrumental analysis methods such as capillary electrophoresis and Sanger sequencing for STR and mitochondrial DNA typing, respectively. PCR-MPS also may enable the expansion of forensic DNA analysis methods to include new marker systems such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) that currently are assayable using various instrumental analysis methods including microarray and quantitative PCR. Acceptance of PCR-MPS as a forensic method will depend in part upon developing protocols and criteria that define the limitations of a method, including a defensible analytical threshold or method detection limit. This paper describes an approach to establish objective analytical thresholds suitable for multiplexed PCR-MPS methods. A definition is proposed for PCR-MPS method background noise, and an analytical threshold based on background noise is described.

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Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform

Cited by 48 publications

References 21 publications

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

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

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

A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis

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