Systematic evaluation of the early access applied biosystems precision ID Globalfiler mixture ID and Globalfiler NGS STR panels for the ion S5 system

Müller, Petra; Alonso, Antonio; Barrio, Pedro A.; Berger, Burkhard; Bodner, Martin; Martı́n, Pablo; Parson, Walther

doi:10.1016/j.fsigen.2018.06.016

Cited by 34 publications

(29 citation statements)

References 38 publications

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“…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%

“…In line with these findings for the ForenSeq DNA Signature Prep Kit, Müller et al, 2018 [4] observed comparable results for TH01 and D19S443 evaluating both Globalfiler MPS-kits (i.e. the Early Access Applied Biosystems Precision ID Globalfiler Mixture ID and the Globalfiler NGS STR Panels) on the Ion S5 instrument [4]. Although using a centrally prepared sequencing library we observed locus coverage variation for single source samples sequenced on the eight MiSeq FGx sequencers (Tables 1 and S5).…”

Section: Locus Coveragementioning

confidence: 67%

“…Identity SNP results for FA10030T01A were fully concordant between runs, except for rs1294331, rs354439, and rs1382387 showing the drop-out of allele A, allele T and allele G, respectively (Table S13). Locus drop-out was observed at rs2920816 (all runs), rs719366 (runs 0, 2-8), rs13182883 (runs 0-2, 4, 6-8) and rs13218440 (runs [1][2][3][4][5][6]8). Overall, profile of FA10030T01A consisted of 87.3% (3.8%), 82.5% (6.3%), and 92.0% (2.3%) concordantly typed aSTRs, X-STRs, and iSNPs, respectively ( Table 3, Figure S3).…”

Section: Ancient Dna Samplesmentioning

confidence: 96%

“…Identity SNP results for FA10026B01A were fully concordant between sequencing runs, except for rs1015250 and rs722290 (Table S13). Manual revision of rs1015250 no-call iSNP revealed a potential G allele for runs [3][4][5][6][7] showing reads that accounted for 20%, 16%, 16%, 18%, and 14% of the called iSNP-allele reads, respectively. However, non-called iSNP, allele G, was found for rs1015250 for runs 0-2 and 8 too with reads ≤ 19.…”

Section: Ancient Dna Samplesmentioning

confidence: 99%

“…With the emergence of massively parallel sequencing (MPS) technologies, molecular genetic tools have been developed to characterise the nucleotide sequence of short tandem repeat (STR) markers that have so far been analysed using fragment sizing by capillary electrophoresis (CE) [1][2][3][4][5][6][7]. As is common practise in forensic genetics, such novel tools undergo detailed evaluation [3,[8][9][10][11][12] and validation [1,13,14] prior to their application in casework.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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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.

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Section: Sensitivitysupporting

confidence: 88%

Section: Locus Coveragementioning

confidence: 67%

Section: Ancient Dna Samplesmentioning

confidence: 96%

Section: Ancient Dna Samplesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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Short tandem repeat markers applied to the identification of human remains

Goodwin

Alsafiah

Aljanabi

2020

Forensic Science and Humanitarian Action

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Widens traditional concepts of forensic science to include humanitarian, social, and cultural aspects Using the preservation of the dignity of the deceased as its foundation, Forensic Science and Humanitarian Action: Interacting with the Dead and the Living is a unique examination of the applications of humanitarian forensic science. Spanning two comprehensive volumes, the text is sufficiently detailed for forensic practitioners, yet accessible enough for non-specialists, and discusses both the latest technologies and real-world interactions. Arranged into five sections, this book addresses the 'management of the dead' across five major areas in humanitarian forensic science.

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Isometric artifacts from polymerase chain reaction‐massively parallel sequencing analysis of short tandem repeat loci: An emerging issue from a new technology?

et al. 2022

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The recent introduction of polymerase chain reaction (PCR)‐massively parallel sequencing (MPS) technologies in forensics has changed the approach to allelic short tandem repeat (STR) typing because sequencing cloned PCR fragments enables alleles with identical molecular weights to be distinguished based on their nucleotide sequences. Therefore, because PCR fidelity mainly depends on template integrity, new technical issues could arise in the interpretation of the results obtained from the degraded samples. In this work, a set of DNA samples degraded in vitro was used to investigate whether PCR‐MPS could generate “isometric drop‐ins” (IDIs; i.e., molecular products having the same length as the original allele but with a different nucleotide sequence within the repeated units). The Precision ID GlobalFiler NGS STR panel kit was used to analyze 0.5 and 1 ng of mock samples in duplicate tests (for a total of 16 PCR‐MPS analyses). As expected, several well‐known PCR artifacts (such as allelic dropout, stutters above the threshold) were scored; 95 IDIs with an average occurrence of 5.9 IDIs per test (min: 1, max: 11) were scored as well. In total, IDIs represented one of the most frequent artifacts. The coverage of these IDIs reached up to 981 reads (median: 239 reads), and the ratios with the coverage of the original allele ranged from 0.069 to 7.285 (median: 0.221). In addition, approximately 5.2% of the IDIs showed coverage higher than that of the original allele. Molecular analysis of these artifacts showed that they were generated in 96.8% of cases through a single nucleotide change event, with the C > T transition being the most frequent (85.7%). Thus, in a forensic evaluation of evidence, IDIs may represent an actual issue, particularly when DNA mixtures need to be interpreted because they could mislead the operator regarding the number of contributors. Overall, the molecular features of the IDIs described in this work, as well as the performance of duplicate tests, may be useful tools for managing this new class of artifacts otherwise not detected by capillary electrophoresis technology.

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Systematic evaluation of the early access applied biosystems precision ID Globalfiler mixture ID and Globalfiler NGS STR panels for the ion S5 system

Cited by 34 publications

References 38 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

Short tandem repeat markers applied to the identification of human remains

Isometric artifacts from polymerase chain reaction‐massively parallel sequencing analysis of short tandem repeat loci: An emerging issue from a new technology?

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