Genetic analysis of Southern Brazil subjects using the PowerSeq™ AUTO/Y system for short tandem repeat sequencing

Silva, Deborah S.B.S.; Sawitzki, Fernanda R.; Scheible, Melissa; Bailey, Sarah F.; Alho, Clarice Sampaio; Faith, Seth A.

doi:10.1016/j.fsigen.2017.12.008

Cited by 17 publications

(5 citation statements)

References 21 publications

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“…Locus coverage ranged from 0× (dropout) to 5356× (1 ng), with the average coverage between 358× (0.125 ng) and 698× (1 ng) (Figure 4), which is approximately 5×-8× lower than the average coverage obtained using the TruSeq kit and SPBs. Of the loci that amplified using the KAPA kit, Y-GATA-H4 yielded the highest average coverage and DYS448 yielded the lowest average coverage, the latter being similarly observed in Moura-Neto et al [36] and Silva et al [34] (Figure 3, orange bars). Excluding dropout (heterozygote balance of zero), heterozygote balance otherwise ranged from 0.40 (0.125 ng) to 1 (1 ng).…”

Section: Kapa Hyperprep Library Preparationsupporting

confidence: 59%

“…Several publications have reported on the use of the ForenSeq DNA Signature Prep Kit [18,28,29] and Precision ID GlobalFiler NGS STR Panel [30][31][32], among other panels. The PowerSeq ® 46GY System (previously the PowerSeq™ Auto/Y System) was evaluated for use with human population identification [7,[33][34][35][36], STR analysis of forensic-type samples [37], standard reference materials [38], and modifications of individual steps within the PowerSeq ® workflow [37,39]. However, there are no published works on the optimization of the entire workflow of the PowerSeq ® 46GY System.…”

Section: Introductionmentioning

confidence: 99%

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Evaluation of Library Preparation Workflows and Applications to Different Sample Types Using the PowerSeq® 46GY System with Massively Parallel Sequencing

Elwick

Rydzak

Robertson

2023

Genes

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This project evaluated the prototype PowerSeq® 46GY System using donor DNA and casework-type samples. The goal of this study was to determine whether modifications to the manufacturer’s protocol could increase read coverage and improve sample results. Buccal and casework-type libraries were prepared using the TruSeq® DNA PCR-Free HT kit or the KAPA HyperPrep kit. Both kits were evaluated unmodified, and by substituting AMPure® XP beads for the beads of the most optimal kit. Two qPCR kits, the PowerSeq® Quant MS System and KAPA Library Quantification Kit, were also evaluated along with a KAPA size-adjustment workbook, which was compared as a third quantification method. Libraries were sequenced using the MiSeq® FGx and data were analyzed with STRait Razor. Results suggested that all three quantification methods overestimated library concentration, but the PowerSeq kit was most accurate. Samples prepared with the TruSeq library kit provided the highest coverage and the fewest instances of dropout and below-threshold alleles compared with the KAPA kit. Additionally, all bone and hair samples demonstrated full profile completeness, with bone samples yielding a higher average coverage than hair samples. Overall, our study demonstrated that the 46GY manufacturer’s protocol produced the best quality results compared to alternative library preparation options.

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Section: Kapa Hyperprep Library Preparationsupporting

confidence: 59%

Section: Introductionmentioning

confidence: 99%

Evaluation of Library Preparation Workflows and Applications to Different Sample Types Using the PowerSeq® 46GY System with Massively Parallel Sequencing

Elwick

Rydzak

Robertson

2023

Genes

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“…The advantage of MPS for STR typing lies in the fact that additional information can be obtained from the same sample input currently used with capillary electrophoresis technologies. This additional information, which takes the form of added markers and insight into sequence variations within those markers, could aid the resolution of complex cases with degraded or low amounts of DNA [11,12], assist with mixture deconvolution [13,14], help resolve kinship scenarios [15] as well as strengthen the statistics in population databases [16,17].…”

Section: Introductionmentioning

confidence: 99%

A closer look at Verogen's Forenseq™ DNA Signature Prep kit autosomal and Y‐STR data for streamlined analysis of routine reference samples

Moreno¹,

Galusha²,

Just³

2018

Electrophoresis

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Massively parallel sequencing (MPS) provides forensic DNA laboratories an option to overcome the limitations associated with CE and current STR assays. Verogen's MPS Forenseq DNA Signature kit concomitantly amplifies 27 autosomal, 7 X-, and 24 Y-STRs. In addition, 94 identity, 56 ancestry, and 22 phenotypic-informative SNPs are included for a total of over 200 markers in one multiplex. An internal validation of this platform was conducted using reference samples to investigate whether the Forenseq™ DNA Signature Prep kit, specifically primer panel B, has the capability to provide consistent and accurate typing/sequencing data. The data presented in this report is limited to that corresponding to autosomal and Y-STRs. Results suggest that the system can consistently generate accurate genotyping data when up to 40 high-quality, high-quantity (i.e. 1 ng) single source samples are pooled into a sequencing reaction. The results generated were used to determine appropriate analysis parameters and thresholds for streamlined data interpretation of reference samples.

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“…As users access this intuitive GUI through a web browser, it requires no bioinformatic expertise. The software is capable of processing MPS data of a predefined set of STRs (autosomal, X-and Y-STRs) [52,53] generated by different platforms, including the MinION. The analysis is robust and is ready to accommodate batch data processing [25].…”

Section: Altiusmentioning

confidence: 99%

An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

Huszar

Gettings

Vallone

2021

Genes

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The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and validate such methods locally. In the case of next-generation sequencing, in the last decade, several specifically forensic commercial options became available, offering reliable and validated solutions. Despite this, the readily available expertise to analyze, interpret and understand such data is still perceived to be lagging behind. This review gives an introductory overview for the forensic scientists who are at the beginning of their journey with implementing next-generation sequencing locally and because most in the field do not have a bioinformatics background may find it difficult to navigate the new terms and analysis options available. The currently available open-source and commercial software for forensic sequencing data analysis are summarized here to provide an accessible starting point for those fairly new to the forensic application of massively parallel sequencing.

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Genetic analysis of Southern Brazil subjects using the PowerSeq™ AUTO/Y system for short tandem repeat sequencing

Cited by 17 publications

References 21 publications

Evaluation of Library Preparation Workflows and Applications to Different Sample Types Using the PowerSeq® 46GY System with Massively Parallel Sequencing

Evaluation of Library Preparation Workflows and Applications to Different Sample Types Using the PowerSeq® 46GY System with Massively Parallel Sequencing

A closer look at Verogen's Forenseq™ DNA Signature Prep kit autosomal and Y‐STR data for streamlined analysis of routine reference samples

An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

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