Developmental validation of the GlobalFiler ® Express PCR Amplification Kit: A 6-dye multiplex assay for the direct amplification of reference samples

Wang, Dennis Y.; Gopinath, Siddhita; Lagacé, Robert; Norona, Wilma; Hennessy, Lori K.; Short, Marc L.; Mulero, Julio J.

doi:10.1016/j.fsigen.2015.07.013

Cited by 79 publications

(44 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2 and S1). In general, results for the ForenSeq DNA Signature Prep Kit aSTR sensitivity were comparable to CE-based STR kits [58][59][60][61] and in line with earlier published MPS studies [1,3,4,14,54].…”

Section: Sensitivitysupporting

confidence: 88%

Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA

et al. 2019

View full text Add to dashboard Cite

We present results from an inter-laboratory massively parallel sequencing (MPS) study in the framework of the SeqForSTRs project to evaluate forensically relevant parameters, such as performance, concordance, and sensitivity, using a standardized sequencing library including reference material, mixtures, and ancient DNA samples. The standardized library was prepared using the ForenSeq DNA Signature Prep Kit (primer mix A). The library was shared between eight European laboratories located in Austria, France, Germany, The Netherlands, and Sweden to perform MPS on their particular MiSeq FGx sequencers. Despite variation in performance between sequencing runs, all laboratories obtained quality metrics that fell within the manufacturer's recommended ranges. Furthermore, differences in locus coverage did not inevitably adversely affect heterozygous balance. Inter-laboratory concordance showed 100% concordant genotypes for the included autosomal and Y-STRs, and still, X-STR concordance exceeded 83%. The exclusive reasons for X-STR discordances were drop-outs at DXS10103. Sensitivity experiments demonstrated that correct allele calling varied between sequencing instruments in particular for lower DNA amounts (≤ 125 pg). The analysis of compromised DNA samples showed the drop-out of one sample (FA10013B01A) while for the remaining three degraded DNA samples MPS was able to successfully type ≥ 87% of all aSTRs, ≥ 78% of all Y-STRs, ≥ 68% of all X-STRs, and ≥ 92% of all iSNPs demonstrating that MPS is a promising tool for human identity testing, which in return, has to undergo rigorous in-house validation before it can be implemented into forensic routine casework.

show abstract

Section: Sensitivitysupporting

confidence: 88%

Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA

et al. 2019

View full text Add to dashboard Cite

show abstract

“…A few reproducible cross-reactivity peaks were observed in all three replicates for chicken, horse and porcine as summarized in Table 2. The peaks indicated in bold font for horse and porcine samples have previously been reported in a validation study of GlobalFiler 1 Express [19]. The presence of the additional reproducible peaks was confirmed by processing samples using Fig.…”

Section: Species Specificitysupporting

confidence: 65%

“…Table 2 Reproducible peaks present in species DNA (n = 3 per species DNA). In bold, peaks that were previously reported [19].…”

Section: Species Specificitymentioning

confidence: 99%

Validation of a rapid DNA process with the RapidHIT ® ID system using GlobalFiler ® Express chemistry, a platform optimized for decentralized testing environments

Salceda

Barican

Buscaino

et al. 2017

Forensic Science International: Genetics

View full text Add to dashboard Cite

The RapidHIT ID is a fully automated sample-to-answer system for short tandem repeat (STR)-based human identification. The RapidHIT ID has been optimized for use in decentralized environments and processes presumed single source DNA samples, generating Combined DNA Index System (CODIS)-compatible DNA profiles in less than 90min. The system is easy to use, requiring less than one minute of hands-on time. Profiles are reviewed using centralized linking software, RapidLINK™ (IntegenX, Pleasanton, CA), a software tool designed to collate DNA profiles from single or multiple RapidHIT ID systems at different geographic locations. The RapidHIT ID has been designed to employ GlobalFiler Express and AmpFLSTR NGMSElect™, Thermo Fisher Scientific (Waltham, MA) STR chemistries. The Developmental Validation studies were performed using GlobalFiler Express with single source reference samples according to Scientific Working Group for DNA Analysis Methods guidelines. These results show that multiple RapidHIT ID systems networked with RapidLINK software form a highly reliable system for wide-scale deployment in locations such as police booking stations and border crossings enabling real-time testing of arrestees, potential human trafficking victims, and other instances where rapid turnaround is essential.

show abstract

“…Automated CE is designed to separate, detect, and analyze fluorescently labeled DNA fragments, and allows for a wide range of applications such as standard PCR fragment analysis , minisequencing , amplified fragment length polymorphism , or Sanger sequencing (reviewed in ). Numerous commercial genotyping kits are available, either for identification of human individuals (e.g., Applied Biosystems' GlobalFiler™ PCR Amplification Kit , Promega's PowerPlex 21 , and Qiagen's Investigator DIPplex kits), domestic animals (e.g., Applied Biosystems' StockMarks ), cultivars (e.g., Labindia's Basmati Verifiler Kit ), or bacterial species (e.g., MseI Microbial AFLP Ligation/Amplification Module ).…”

Section: Introductionmentioning

confidence: 99%

Design, installation, and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis

et al. 2016

View full text Add to dashboard Cite

CE equipment detects and deconvolutes mixtures containing up to six fluorescently labeled DNA fragments. This deconvolution is done by the collection software that requires a spectral calibration file. The calibration file is used to adjust for the overlap that occurs between the emission spectra of fluorescence dyes. All commercial genotyping and sequencing kits require the installation of a corresponding matrix standard to generate a calibration file. Due to the differences in emission spectrum overlap between fluorescent dyes, the application of existing commercial matrix standards to the electrophoretic separation of DNA labeled with other fluorescent dyes can yield undesirable results. Currently, the number of fluorescent dyes available for oligonucleotide labeling surpasses the availability of commercial matrix standards. Therefore, in this study we developed and evaluated a customized matrix standard using ATTO 633, ATTO 565, ATTO 550, ATTO Rho6G, and 6-FAM dyes for which no commercial matrix standard is available. We highlighted the potential genotyping errors of using an incorrect matrix standard by evaluating the relative performance of our custom dye set using six matrix standards. The specific performance of two genotyping kits (UniQTyper™ Y-10 version 1.0 and PowerPlex® Y23 System) was also evaluated using their specific matrix standards. The procedure we followed for the construction of our custom dye matrix standard can be extended to other fluorescent dyes.

show abstract

Developmental validation of the GlobalFiler ® Express PCR Amplification Kit: A 6-dye multiplex assay for the direct amplification of reference samples

Cited by 79 publications

References 17 publications

Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA

Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA

Validation of a rapid DNA process with the RapidHIT ® ID system using GlobalFiler ® Express chemistry, a platform optimized for decentralized testing environments

Design, installation, and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis

Contact Info

Product

Resources

About