Report from the STRAND Working Group on the 2019 STR sequence nomenclature meeting

Gettings, Katherine B.; Ballard, David J.; Bodner, Martin; Borsuk, Lisa A.; King, Jonathan L.; Parson, Walther

doi:10.1016/j.fsigen.2019.102165

Cited by 32 publications

(20 citation statements)

References 37 publications

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“…A unified minimal nomenclature of the complex sequences obtained by MPS technologies was recommended by the International Society for Forensic Genetics (ISFG) in 2016 21,22 to facilitate communication between laboratories and to make this data backward compatible with LB data produced on CE platform. In early 2019, the STRAND Working Group was formalized to discuss the expanding and advancing topics of STR sequence nomenclature 23 . Quality control of string sequences and alleles has also been suggested by ISFG 24 .…”

mentioning

confidence: 99%

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Peng

Zhang

Ren

et al. 2020

Sci Rep

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Massively parallel sequencing (MPS) has rapidly become a promising method for forensic DNA typing, due to its ability to detect a large number of markers and samples simultaneously in a single reaction, and sequence information can be obtained directly. In the present study, two kinds of forensic genetic markers, short tandem repeat (STR) and identity-informative single nucleotide polymorphism (iiSNP) were analyzed simultaneously using ForenSeq DNA Signature Prep Kit, a commercially available kit on MPS platform. A total of 152 DNA markers, including 27 autosomal STR (A-STR) loci, 24 Y chromosomal STR (Y-STR) loci, 7 X chromosomal STR (X-STR) loci and 94 iiSNP loci were genotyped for 107 Tibetan individuals (53 males and 54 females). Compared with length-based STR typing methods, 112 more A-STR alleles, 41 more Y-STR alleles, and 24 more X-STR alleles were observed at 17 A-STRs, 9 Y-STRs, and 5 X-STRs using sequence-based approaches. Thirty-nine novel sequence variations were observed at 20 STR loci. When the flanking regions were also analyzed in addition to target SNPs at the 94 iiSNPs, 38 more alleles were identified. Our study provided an adequate genotype and frequencies data of the two types of genetic markers for forensic practice. Moreover, we also proved that this panel is highly polymorphic and informative in Tibetan population, and should be efficient in forensic kinship testing and personal identification cases. Several genetic markers have been introduced to forensic genetics to clarify the problems of kinship analysis and personal identification. Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are commonly used genetic markers in present forensic cases 1,2. STRs, usually 2-6 bp in length, are commonly typed with the amplified fragment length polymorphism (Amp-FLP) strategy combining fluorescently labelled multiplex PCR and capillary electrophoresis (CE) 3. Allele calling can thus be inferred from fragment length by comparison with a locus specific allelic ladder that has been previously sequenced, where the number of repeat units is distinct 2. Thus, each allele is regarded as a lengthbased (LB) allele using this approach. With the advancement of sequencing technologies over the last decade, the existence of sequence structure variations in alleles with the same length has been uncovered 4. SNPs, which could be amplified with smaller amplicons, are bi-allelic genetic markers with lower mutation rates compared with STRs 5. Several autosomal SNP marker sets and detection methods, such as single-base extension, chip-based microarrays, and allele-specific hybridization arrays, have been developed to compensate for the relatively weaker discrimination power of single loci caused by the bi-allelic nature of the human genome 5-7. However, these methods are not widely used in forensic practice due to the requirement of higher DNA inputs or the limited ability to detect a vast number of SNP loci in a single reaction 8. Different from detection methods mentioned above, massively paralle...

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mentioning

confidence: 99%

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Peng

Zhang

Ren

et al. 2020

Sci Rep

View full text Add to dashboard Cite

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“…The difficulty of retrieving MPS allele sequence data including sufficient FR information without advanced bioinformatics knowledge has in some cases hampered QC. FR output between unambiguous coordinates has been postulated [ 39 ]. STR sequence nomenclature was not assessed during QC; the highly desired forensic recommendation is currently under development [ 29 , 37 , 38 , 39 , 40 ].…”

Section: Results Of Strider Quality Controlmentioning

confidence: 99%

“…FR output between unambiguous coordinates has been postulated [ 39 ]. STR sequence nomenclature was not assessed during QC; the highly desired forensic recommendation is currently under development [ 29 , 37 , 38 , 39 , 40 ]. Further errors detected in CE-translated allele tables were similar to those described in the previous chapter, but not taken into account for a decision on the MPS datasets.…”

Section: Results Of Strider Quality Controlmentioning

confidence: 99%

The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets

Bodner

Parson

2020

Genes

Self Cite

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STRidER, the STRs for Identity ENFSI Reference Database, is a curated, freely publicly available online allele frequency database, quality control (QC) and software platform for autosomal Short Tandem Repeats (STRs) developed under the endorsement of the International Society for Forensic Genetics. Continuous updates comprise additional STR loci and populations in the frequency database and many further STR-related aspects. One significant innovation is the autosomal STR data QC provided prior to publication of datasets. Such scrutiny was lacking previously, leaving QC to authors, reviewers and editors, which led to an unacceptably high error rate in scientific papers. The results from scrutinizing 184 STR datasets containing >177,000 individual genotypes submitted in the first two years of STRidER QC since 2017 revealed that about two-thirds of the STR datasets were either being withdrawn by the authors after initial feedback or rejected based on a conservative error rate. Almost no error-free submissions were received, which clearly shows that centralized QC and data curation are essential to maintain the high-quality standard required in forensic genetics. While many errors had minor impact on the resulting allele frequencies, multiple error categories were commonly found within single datasets. Several datasets contained serious flaws. We discuss the factors that caused the errors to draw the attention to redundant pitfalls and thus contribute to better quality of autosomal STR datasets and allele frequency reports.

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“…Raw FASTQ data files were analyzed using MixtureAce™ (NicheVision Forensics, Akron, OH) with an analytical threshold of zero. Read sequences were bioinformatically trimmed to match the Verogen recommended analyzable regions [29] and exported to comma separated value (CSV) files along with their read count intensities (RCI). Stutter artifacts identified by MixtureAce were deleted from the CSV files.…”

Section: Methodsmentioning

confidence: 99%

Levenshtein Distance as a Measure of Accuracy and Precision in Forensic PCR-MPS Methods

Young¹,

Faris²,

Armogida³

2021

Preprint

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Accuracy and precision determinations are standard components of method validations where they help to describe the performance of methods. Despite their importance, a standard approach to calculating these parameters is not available for forensic PCR-MPS methods that detect sequence-based alleles. In this paper, we describe a method based on the Levenshtein distance metric which aptly summarizes method accuracy in terms of the closeness of read sequences to reference sequences, and method precision in terms of the agreement among read sequences. Inaccuracy or imprecision in forensic methods can lead to wrong allele calls. By expressing method performance in terms of a distance metric, this method places PCR-MPS on equal footing with distance-based measures in PCR-CE methods. Summary statistics based on the Levenshtein distance can be used to compare performance of different kits, markers, sequencers, or methods.

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Report from the STRAND Working Group on the 2019 STR sequence nomenclature meeting

Cited by 32 publications

References 37 publications

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets

Levenshtein Distance as a Measure of Accuracy and Precision in Forensic PCR-MPS Methods

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