Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

Eduardoff, Mayra; Gross, T.E.; Santos, C.; Puente, M. de la; Ballard, David J.; Strobl, Christina; Børsting, Claus; Morling, Niels; Fusco, L.; Hussing, Christian; Egyed, Balázs; Souto, L.; Uacyisrael, J.; Court, Denise Syndercombe; Carracedo, Ángel; Lareu, M.V.; Schneider, Peter M.; Parson, Walther; Phillips, C.

doi:10.1016/j.fsigen.2016.04.008

Cited by 55 publications

(61 citation statements)

References 42 publications

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“…Universal Analysis Software (UAS) called alleles and genotypes based on the number of reads by applying a specified analytical (AT; 1.5%) and interpretation threshold (IT; 4.5%), except for DYS398II (AT: 5%; IT: 15%), DYS448 (AT: 3.3%; IT: 10%) and DYS635 (AT: 3.3%; IT: 10%) [45]. Single nucleotide polymorphism (SNP) analysis of aDNA samples were manually revised and no-call genotype corrected according to [11]. For example, no-call SNPs that fell below the manufacturer's default IT but in the range of 20 to 29 reads were manually corrected and genotype results put in brackets.…”

Section: Universal Analysis Softwarementioning

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. Recent population studies have shown that sequencing of STRs lead to an increased power of discrimination compared to commonly used CE sizing by a) illustrating micro-variant structures and b) identifying sequence variations located in the repeat-(isometric variants; alleles of identical size but different in internal sequence) or flanking region [15][16][17][18][19][20].…”

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: Universal Analysis Softwarementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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“…Recently, MPS technology has attracted much interest in the field of forensic science. Multiple studies have been carried out to study various forensic markers using MPS technology . All of these studies imply that MPS holds promise for forensic applications.…”

Section: Introductionmentioning

confidence: 99%

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Wang

Liu

et al. 2020

Electrophoresis

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Massively parallel sequencing (MPS) technologies have the ability to reveal sequence variations within STR alleles as well as their nominal allele lengths, which have traditionally been detected by CE instruments. Recently, Thermo Fisher Scientific has updated the MPS-STR panel, named the Precision ID GlobalFiler next-generation sequencing (NGS) STR Panel version 2, with primers redesigned to add two pentanucleotide tandem repeat loci and profile interpretation supported by the Converge software. Using the Ion Chef System, the Ion S5XL System, and the Converge software, genetic variations were characterized within STR repeat and flanking regions of 30 autosomal STR markers in 115 unrelated individuals from two Chinese population groups (58 Tibetans and 57 Hans). Nineteen STRs demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. In total, 390 alleles were identified by their sequences compared with 258 alleles that were identified by length. Of these 92 sequence variants found within the STR repeat regions, 40 variants were located in STR flanking regions. Additionally, the agreement of the results with CE data was evaluated, as was the ability of this new MPS panel to analyze case-type (11 samples) and artificially degraded samples (seven samples in triplicate). The results generated from this study illustrate that extensive sequence variation exists in commonly used STR markers in the selected population samples and indicate that this NGS STR panel has the potential to be used as an effective tool for human forensics.

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“…More precise inference of the geographic background of an unknown DNA sample has been achieved with the analysis of ancestry-informative SNP markers whose bi- or tri-allelic distributions across populations are indicative of continental-scale geographic backgrounds. With the emergence of MPS techniques, larger ancestry-informative SNP marker PCR multiplexes were developed that can, for example, be used to differentiate between 5 major sub-continental populations (Africa, Europe, East Asia, Native America and Oceania) using 128 markers [6]. …”

Section: Limitations Of Confirmatory Forensic Dna Testing and New Avementioning

confidence: 99%

Age Estimation with DNA: From Forensic DNA Fingerprinting to Forensic (Epi)Genomics: A Mini-Review

Parson

2018

Gerontology

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Forensic genetics developed from protein-based techniques a quarter of a century ago and became famous as “DNA fingerprinting,” this being based on restriction fragment length polymorphisms (RFLPs) of high-molecular-weight DNA. The amplification of much smaller short tandem repeat (STR) sequences using the polymerase chain reaction soon replaced RFLP analysis and advanced to become the gold standard in genetic identification. Meanwhile, STR multiplexes have been developed and made commercially available which simultaneously amplify up to 30 STR loci from as little as 15 cells or fewer. The enormous information content that comes with the large variety of observed STR genotypes allows for genetic individualisation (with the exception of identical twins). Carefully selected core STR loci form the basis of intelligence-led DNA databases that provide investigative leads by linking unsolved crime scenes and criminals through their matched STR profiles. Nevertheless, the success of modern DNA fingerprinting depends on the availability of reference material from suspects. In order to provide new investigative leads in cases where such reference samples are absent, forensic scientists started to explore the prediction of phenotypic traits from the DNA of the evidentiary sample. This paradigm change now uses DNA and epigenetic markers to forecast characteristics that are useful to triage further investigative work. So far, the best investigated externally visible characteristics are eye, hair and skin colour, as well as geographic ancestry and age. Information on the chronological age of a stain donor (or any sample donor) is elemental for forensic investigations in a number of aspects and has, therefore, been explored by researchers in some detail. Among different methodological approaches tested to date, the methylation-sensitive analysis of carefully selected DNA markers (CpG sites) has brought the most promising results by providing prediction accuracies of ±3–4 years, which can be comparable to, or even surpass those from, eyewitness reports. This mini-review puts recent developments in age estimation via (epi)genetic methods in the context of the requirements and goals of forensic genetics and highlights paths to follow in the future of forensic genomics.

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Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

Cited by 55 publications

References 42 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

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Age Estimation with DNA: From Forensic DNA Fingerprinting to Forensic (Epi)Genomics: A Mini-Review

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