A nomenclature for sequence-based forensic DNA analysis

Young, Brian; Faris, Tom; Armogida, Luigi

doi:10.1016/j.fsigen.2019.06.001

Cited by 20 publications

(12 citation statements)

References 17 publications

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“…It is urgent to know how the MPS data should be analysed and reported, what connections do these data have with LB alleles, and how to record and search such datasets in a database 4 . Some researchers have tried to answer these questions 19,20 but a perfect nomenclature is still under development. 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.…”

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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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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“…There are a number of barriers to widespread adoption of MPS for forensic applications, including variable performance of some markers in terms of coverage and locus imbalance [11], and susceptibility to PCR inhibitors when compared with standard STR typing kits [25,26], but these are rapidly being overcome. Development of a standardised nomenclature system, which captures sequence variation in MPS-generated STR alleles whilst maintaining compatibility with existing CE-based STR data in national DNA databases, is a particular challenge, but recommendations are now in place to address this [27][28][29][30]. The availability of frequency data for alleles detected using MPS is also increasing with the publication of datasets from populations worldwide [31][32][33][34][35].…”

Section: Massively Parallel Sequencingmentioning

confidence: 99%

Developments in forensic DNA analysis

Haddrill

2021

Emerging Topics in Life Sciences

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The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.

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“…This study identified several novel identity SNPS were identified. The novel variants were compared to the human genome reference sequence (GRCh38) (Supplementary Materials Table 1) (8,10). The repeat pattern variants were compared to the existing database published literature and the database STRBase (strbase.nist.gov) [Accessed Date: 13-09-2019].…”

Section: Softwarementioning

confidence: 99%

The study of 95 identity SNPs for Qatari population using massively parallel sequencing (MPS)

Almohammed

Hadi

2019

Forensic Science International: Genetics Supplement Series

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For the last three decades, Short Tandem Repeat (STR) markers and capillary electrophoresis-based DNA sequencers have been the gold standard technology for human identification testing in the forensic field. However, Massively Parallel Sequencing (MPS) has the potential to replace the current CE-based technology. All laboratories globally, including the Qatar Forensic Laboratory, have stringent strategies and regulations in improving and processing high numbers of reference and casework samples, using instrumentation and technologies to maximize output using new STR kits consisting of larger number of loci. MPS technology has enabled sequencing of several types of genetic loci in one multiplex including single nucleotide polymorphisms (SNPs) and STRs. One hundred and fifty (150) reference samples were profiled using the ForenSeq TM DNA Signature kit. The average read depth was 20,000 reads for all sequencing runs. The data generated through MPS were analysed using ForenSeq TM Universal software and STRait Razor V3 for the primary, secondary and tertiary analyses. The analyses of the sequence of alleles in STRait Razor software were able to determine novel alleles in the Identntiy SNPs loci. The Qatari population has been a melting pot of various populations and this forensic study was the first of its kind to generate new data on the genetics of Qatari population. The 95 identity SNPS allele frequency data for 150 samples were analysed. In conclusion, the results have clearly demonstrated the potential use of MPS methods to study the genetics of Qatari population.

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A nomenclature for sequence-based forensic DNA analysis

Cited by 20 publications

References 17 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

Developments in forensic DNA analysis

The study of 95 identity SNPs for Qatari population using massively parallel sequencing (MPS)

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