Open source software EuroForMix can be used to analyse complex SNP mixtures

Bleka, Øyvind; Eduardoff, Mayra; Santos, C.; Parson, Walther; Gill, Peter

doi:10.1016/j.fsigen.2017.08.001

Cited by 41 publications

(37 citation statements)

References 10 publications

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“…Only under rare scenarios is it possible to derive EVC and BGA information reliably from mixed DNA samples. However, for the sake of completeness and because mixture detection in SNP panels, and particularly in EVC and BGA panels, has been previously described and published [20,21,25,41], this study was included in the validation. It is based on the fluctuation of allele frequencies and increase of heterozygosity values that indicate the presence of additional contributors.…”

Section: Concordance and Mixturesmentioning

confidence: 99%

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Development and validation of the VISAGE AmpliSeq basic tool to predict appearance and ancestry from DNA

Xavier

Puente

Mosquera-Miguel

et al. 2020

Forensic Science International: Genetics

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Forensic DNA phenotyping is gaining interest as the number of applications increases within the forensic genetics community. The possibility of providing investigative leads in addition to conventional DNA profiling for human identification provides new insights into otherwise "cold" police investigations. The ability of reporting on the bio-geographical ancestry (BGA), appearance characteristics and age based on DNA obtained from a crime scene sample of an unknown donor makes the exploration of such markers and the development of new methods meaningful for criminal investigations. The VISible Attributes through GEnomics (VISAGE) Consortium aims to disseminate and broaden the use of predictive markers and develop fully optimized and validated prototypes for forensic casework implementation. Here, the first VISAGE appearance and ancestry tool development, performance and validation is reported. A total of 153 SNPs (96.84 % assay conversion rate) were successfully incorporated into a single multiplex reaction using the AmpliSeq™ design pipeline, and applied for massively parallel sequencing with the Ion S5 platform. A collaborative effort involving six VISAGE laboratory partners was devised to perform all validation tests. An extensive validation plan was carefully organized to explore the assay's overall performance with optimum and low-input samples, as well as with challenging and casework mock samples. In addition, forensic validation studies such as concordance and mixture tests recurring to the Coriell sample set with known genotypes were performed. Finally, inhibitor tolerance and specificity were also evaluated. Results showed a robust, highly sensitive assay with good overall concordance between laboratories. genetics community to start the development of tools to infer information about the donor of biological traces found at the crime-scene to be used in police investigations to help find unknown perpetrators of crime. These investigative DNA analyses have been termed Forensic DNA Phenotyping (FDP), which includes three components: the inference of bio-geographical ancestry (BGA), the prediction of externally visible characteristics (EVC), and the estimation of chronological age.

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Section: Concordance and Mixturesmentioning

confidence: 99%

“…Mixture detection using binary markers is challenging, but has been successfully achieved in previous forensic MPS studies [20,21,25,41,43]. The basis for mixture detection with such markers is the ratio of allele read frequencies observed when more than one contributor is present.…”

Section: Mixturesmentioning

confidence: 99%

Development and validation of the VISAGE AmpliSeq basic tool to predict appearance and ancestry from DNA

Xavier

Puente

Mosquera-Miguel

et al. 2020

Forensic Science International: Genetics

Self Cite

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“…With Nitz, betting on the wrong number of contributors does not necessarily result in lower LRs. So the rule of three invoked by Bleka et al [36] has limited application with NITZ.…”

Section: Discussionmentioning

confidence: 99%

“…The importance of the whole issue is directly proportional to the impact the value of n may have over the LR values. Bleka et al 2017 [36] have explored this issue by simulating 100 mixtures with two to up to six virtual contributors and calculated likelihoods at various quantitative POI proportions to the POI. They found that, when the POI is not quantitatively predominant, their two-person mixture model of analysis would return them higher LRs compared to the three-or more-person .…”

Section: Number Of Contributorsmentioning

confidence: 99%

“…Nearly at the same time, Gill et al (2015) [ 35] have explored the feasibility of the semi-continuous (or qualitative) calculations to the case of 2-person and 3-person mixtures. More recently, Bleka et al [36] have readapted the open-source EUROFORMIX software to the biallelic scheme and performed quantitative calculations starting from the 'reads' produced by a massive parallel sequencing (MPS) equipment.…”

Section: Introductionmentioning

confidence: 99%

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Calculating likelihoods and likelihood ratios at SNPs-based mixtures. A reappraisal of the binomial inference, as applied to forensic identity tests

2021

Preprint

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Single nucleotide polymorphisms (SNPs) are useful forensic markers. When a SNPs-based forensic protocol targets a body fluid stain, it returns elementary evidence regardless of the number of individuals that might have contributed to the stain deposition. Therefore, drawing inference from a mixed stain with SNPs is different than drawing it while using multinomial polymorphisms. We here revisit this subject, with a view to contribute to a fresher insight into it. First, we manage to model conditional semi-continuous likelihoods in terms of matrices of genotype permutations vs number of contributors (NTZsc). Secondly, we redefine some algebraic formulas to approach the semi-continuous calculation. To address allelic dropouts, we introduce a peak height ratio index (‘h’, or: the minor read divided by the major read at any NGS-based typing result) into the semi-continuous formulas, for they to act as an acceptable proxy of the ‘split drop’ (Haned et al, 2012) model of calculation. Secondly, we introduce a new, empirical method to deduct the expected quantitative ratio at which the contributors of a mixture have originally mixed and the observed ratio generated by each genotype combination at each locus. Compliance between observed and expected quantity ratios is measured in terms of (1-χ2 ) values at each state of a locus deconvolution. These probability values are multiplied, along with the h index, to the relevant population probabilities to weigh the overall plausibility of each combination according to the quantitative perspective. We compare calculation performances of our empirical procedure (NITZq) with those of the EUROFORMIX software ver. 3.0.3. NITZq generates LR values a few orders of magnitude lower than EUROFORMIX when true contributors are used as POIs, but much lower LR values when false contributors are used as POIs. NITZ calculation routines may be useful, especially in combination with mass genomics typing protocols.

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Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing

Bülbül

Filoğlu

2018

Electrophoresis

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Inferring ancestry and physical characteristics of an unknown individual can contribute to the direction of the investigation and to clarify the event for unknown contributors, cold cases or identification of missing persons and disaster victims. The objective of this study is to develop a custom SNP panel on massively parallel sequencing devices for predicting the biogeographic ancestry and phenotype of an individual. We focused on a two-tier approach to enhance ancestry. Our MPS panel contains two ancestry informative SNP (AISNPs) panels (i.e., Kidd 55 and SWA panel) to differentiate Southwest Asia from Europe and other continental regions. Then we integrated the set of phenotype informative SNPs into a set of AISNPs. The final set of 156 SNPs was evaluated on the following: sensitivity, genotype concordance, mixtures, ancestry assignment, and phenotype prediction. SNP rs6599400 had consistently poor performance and was removed from further analyses. The extreme mixture (1:10) was difficult to interpret for minor contributor. Ancestry assignment and phenotype predictions (for eye, hair and skin) were accurate for samples' population origin. The results show that the developed panel provides high coverage data that can be used for inferring ancestry and predicting eye, hair, and skin color from the intermediate population regions.

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Open source software EuroForMix can be used to analyse complex SNP mixtures

Cited by 41 publications

References 10 publications

Development and validation of the VISAGE AmpliSeq basic tool to predict appearance and ancestry from DNA

Development and validation of the VISAGE AmpliSeq basic tool to predict appearance and ancestry from DNA

Calculating likelihoods and likelihood ratios at SNPs-based mixtures. A reappraisal of the binomial inference, as applied to forensic identity tests

Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing

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