“New turns from old STaRs”: Enhancing the capabilities of forensic short tandem repeat analysis

Phillips, C.; Gelabert-Besada, Miguel; Fernandez-Formoso, L.; García-Magariños, Manuel; Santos, C.; Fondevila, M.; Ballard, David J.; Court, Denise Syndercombe; Carracedo, Ángel; Lareu, Marı́a Victoria

doi:10.1002/elps.201400095

Cited by 33 publications

(11 citation statements)

References 65 publications

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“…Ideally, it should be straightforward to use the genotypes to calculate a set of Bayes likelihoods for particular ancestries (or phenotypes) in comparison to reference populations whose patterns of genetic variation are already well defined. Although STRs can provide a degree of ancestry information [5,6] and Ychromosome/mtDNA variation is highly differentiated geographically, there are widely discussed reasons why stand-alone autosomal SNP tests provide more reliable indications of a person's ancestry [7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise

Santos

Fondevila

Ballard

et al. 2015

Forensic Science International: Genetics

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(C. Phillips).• Nineteen laboratories completed a collaborative EDNAP exercise to evaluate two forensic ancestry informative marker (AIM) assays and accompanying statistical tools to infer ancestry from the genotype data.• Laboratories were sent primers, reference data and five test DNAs of undisclosed origin plus an unmarked DNA mixture (but reported to be one of the samples).• Fourteen laboratories successfully genotyped the DNAs with a 34-plex SNP assay using SNaPshot, achieving 96.1% profile completeness and 93.5% genotype concordance.• All laboratories successfully genotyped the DNAs with a 46-plex Indel assay using dye-labelled PCR primers, achieving 99.8% profile completeness and genotype concordance.• All laboratories identified the mixed DNA sample, indicated by disrupted peak height ratios in the Indel profile and three-allele patterns in SNP rs5030240. 18/19 laboratories assigned the correct ancestry to each of the test DNAs of unknown origin, obtaining likelihood ratios from 80 markers in the range: 1.25E+07 to 1.78E+41. 25This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily 26 adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to 27 be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving 28 complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-29 generation sequencing analyses (each using different systems) and achieved high levels of genotyping 30 concordance using the exercise PCR primer mixes unmodified. 31 32

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Section: Introductionmentioning

confidence: 99%

Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise

Santos

Fondevila

Ballard

et al. 2015

Forensic Science International: Genetics

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“…was made by Zhu et al, in 2015 [16]. Although no analyses of the genomic and sequence characteristics of the AGCU STRs has been made, the original development by NIST of these loci as part of the 26 MiniSTR set included a quite comprehensive study of their sequences and they remain the best described of the supplementary autosomal STRs available to use (see also [17]).…”

Section: Nist Ministrsmentioning

confidence: 99%

A genomic audit of newly-adopted autosomal STRs for forensic identification

Phillips

2017

Forensic Science International: Genetics

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In preparation for the growing use of massively parallel sequencing (MPS) technology to genotype forensic STRs, a comprehensive genomic audit of 73 STRs was made in 2016 [Parson et al., Forensic Sci. Int. Genet. 22, 54-63]. The loci examined included miniSTRs that were not in widespread use, but had been incorporated into MPS kits or were under consideration for this purpose. The current study expands the genomic analysis of autosomal STRs that are not commonly used, to include the full set of developed miniSTRs and an additional 24 STRs, most of which have been recently included in several supplementary forensic multiplex kits for capillary electrophoresis. The genomic audit of these 47 newly-adopted STRs examined the linkage status of new loci on the same chromosome as established forensic STRs; analyzed world-wide population variation of the newly-adopted STRs using published data; assessed their forensic informativeness; and compiled the sequence characteristics, repeat structures and flanking regions of each STR. A further 44 autosomal STRs developed for forensic analyses but not incorporated into commercial kits, are also briefly described.

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“…Short tandem repeat (STR) loci are the most commonly used genetic markers in forensic applications because the multi‐allelic nature of STRs produce highly variable genotype combinations among individuals . Today, fluorescent‐labeled multiplex amplification combined with capillary electrophoresis (CE) has become the gold standard for STR genotyping and has been widely used in forensic personal identification and kinship testing.…”

Section: Introductionmentioning

confidence: 99%

Integrated massively parallel sequencing of 15 autosomal STRs and Amelogenin using a simplified library preparation approach

Xue

Pan³

et al. 2018

Electrophoresis

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Massively parallel sequencing (MPS) technologies, also termed as next-generation sequencing (NGS), are becoming increasingly popular in study of short tandem repeats (STR). However, current library preparation methods are usually based on ligation or two-round PCR that requires more steps, making it time-consuming (about 2 days), laborious and expensive. In this study, a 16-plex STR typing system was designed with fusion primer strategy based on the Ion Torrent S5 XL platform which could effectively resolve the above challenges for forensic DNA database-type samples (bloodstains, saliva stains, etc.). The efficiency of this system was tested in 253 Han Chinese participants. The libraries were prepared without DNA isolation and adapter ligation, and the whole process only required approximately 5 h. The proportion of thoroughly genotyped samples in which all the 16 loci were successfully genotyped was 86% (220/256). Of the samples, 99.7% showed 100% concordance between NGS-based STR typing and capillary electrophoresis (CE)-based STR typing. The inconsistency might have been caused by off-ladder alleles and mutations in primer binding sites. Overall, this panel enabled the large-scale genotyping of the DNA samples with controlled quality and quantity because it is a simple, operation-friendly process flow that saves labor, time and costs.

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“New turns from old STaRs”: Enhancing the capabilities of forensic short tandem repeat analysis

Cited by 33 publications

References 65 publications

Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise

Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise

A genomic audit of newly-adopted autosomal STRs for forensic identification

Integrated massively parallel sequencing of 15 autosomal STRs and Amelogenin using a simplified library preparation approach

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