Collaborative EDNAP exercise on the IrisPlex system for DNA-based prediction of human eye colour

Chaitanya, Lakshmi; Walsh, Susan; Andersen, Jeppe Dyrberg; Ansell, Ricky; Ballantyne, Kaye N.; Ballard, David J.; Banemann, R.; Bauer, Christiane Maria; Bento, A.M.; Brisighelli, Francesca; Capal, Tomas; Clarisse, Lindy; Gross, T.E.; Haas, Cordula; Hoff-Olsen, P.; Hollard, Clémence; Keyser, Christine; Kiesler, Kevin M.; Kohler, Priscila; Kupiec, Tomasz; Linacre, Adrian; Minawi, Anglika; Morling, Niels; Nilsson, Helena; Norén, L.; Ottens, Renée; Palo, Jukka U.; Parson, Walther; Pascali, Vincenzo Lorenzo; Phillips, C.; Porto, Maria João; Sajantila, Antti; Schneider, Peter M.; Sijen, Titia; Söchtig, Jens; Syndercombe‐Court, Denise; Tillmar, Andreas; Turanská, M.; Vallone, Peter M.; Zatkalíková, L.; Zidkova, Anastassiya; Branicki, Wojciech; Kayser, Manfred

doi:10.1016/j.fsigen.2014.04.006

Cited by 25 publications

(18 citation statements)

References 17 publications

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“…37–39 Variants in SLC45A2 and SLC24A4 influence pigmentation traits including iris color. 40 The particular SNP identified in this study gives rise to a synonymous codon that is highly conserved in zebrafish and among multiple mammalian species including rhesus monkeys, chimpanzees, cattle and dogs suggesting that this gene has a critical function in mammals. The only locus in the best VEGAS pathway result was C3orf58.…”

Section: Discussionmentioning

confidence: 74%

Genetic and Environmental Factors in Conjunctival UV Autofluorescence

et al. 2015

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IMPORTANCE Conjunctival UV autofluorescence (CUVAF) photography was developed to detect and characterize preclinical sunlight-induced ocular damage. Ocular sun exposure has been related to cases of pterygia and was recently negatively correlated with myopia. Hence, CUVAF has excellent potential as an objective biomarker of sun exposure. However, much variation in CUVAF has been observed, and the relative contributions of genes and environment to this variation have not yet been identified. OBJECTIVE To investigate sources of variation in CUVAF in relation to its potential clinical relevance. DESIGN, SETTING, AND PARTICIPANTS We performed a cross-sectional analysis of 3 population-based cohort studies in the general community, including the Twins Eye Study in Tasmania, the Brisbane Adolescent Twin Study, and the Western Australian Pregnancy Cohort (Raine) Study. The twin studies were conducted between 2001 and 2009, and the 20-year follow-up of the Raine Study was completed between March 2010 and February 2012. We included genotypic and phenotypic data from 295 Australian families in the Tasmanian and Brisbane twin studies and from 661 participants in the 20-year follow-up of the Raine Study.We compared CUVAF levels in the 3 cohorts and performed a classic twin study to partition variation in CUVAF. We also conducted a genome-wide association analysis to identify specific genetic variants associated with CUVAF. MAIN OUTCOMES AND MEASURESThe total area of CUVAF, heritability of CUVAF, and single-nucleotide polymorphisms (SNPs) associated with CUVAF from the genome-wide association study.RESULTS Within twin cohorts, individuals living closer to the equator (latitude, 27.47°S) had higher levels of CUVAF compared with individuals from southern regions (latitude, 42.88°S) (median [interquartile range], 45.4 [26.8-68.5] vs 28.7 [15.0-42.3] mm 2 ; P < .001). The variation in CUVAF explained by the additive genetic component was 0.37 (95% CI, 0.22-0.56), whereas the variation due to the common environment was 0.50 (95% CI; 0.29-0.71). The SNP rs1060043, located approximately 800 base pairs away from the SLC1A5 gene, a member of the solute carrier family 1, had a genome-wide significant association with a P value of 3.2 × 10 −8 . Gene-based analysis did not improve our power to detect association with other genes. CONCLUSIONS AND RELEVANCEOur findings confirm that, although a large environmental component to CUVAF (equivalent of sun exposure) exists, genes also play a significant role. We identified a SNP (rs1060043) as being significantly associated with CUVAF; replication of this finding in future studies is warranted.

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Section: Discussionmentioning

confidence: 74%

Genetic and Environmental Factors in Conjunctival UV Autofluorescence

et al. 2015

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“…All participants achieved good quality profiles that reached the high level of genotyping concordance of 99.8% and then efficiently detected mixed sample F. In contrast, SNaPshot typing was both more challenging and for many participants less reliable, despite most laboratories having successfully genotyped six SNPs for the preceding IrisPlex EDNAP exercise [21]. Miscalled genotypes with SNaPshot produced an overall genotyping concordance rate of 97.3% when a single participant's results were excluded (13/14 laboratories).…”

Section: Discussionmentioning

confidence: 99%

“…As well as the 15 European laboratories including USC, two participants were from Australia, one from New Zealand and one from the USA. All but three laboratories had participated in the preceding EDNAP IrisPlex exercise that applied SNaPshot analysis to the genotyping of six FDP SNPs [21]. Five EDNAP laboratories, were part of the EUROFORGEN-NoE pilot ancestry exercise.…”

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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“…Over the last 10 years, candidate gene association studies and genome-wide association studies (GWASs), as well as subsequent prediction analyses, have established various EVC-predictive SNPs and prediction models, most notably for human pigmentation traits . In particular, the prediction of broad (i.e., categorical) eye and hair colour phenotypes from SNP genotypes is now achievable with practically useful accuracies, for instance by applying the IrisPlex and HIrisPlex DNA test systems that have been forensically validated [31][32][33][34], as well as tested and applied [35,36]. Similar tools for eye and hair colour DNA prediction that largely overlap in SNP predictors with the Iris/HIrisPlex systems have also been generated and used [21,[37][38][39][40][41][42].…”

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confidence: 99%

“…Therefore, the predictability of skin colour from DNA [37][38][39] lagged behind that of eye and hair colour [30][31][32][33][34][35][36][37][38][39][40][41][42]. Valenzuela et al [21] obtained a low R 2 value for skin reflectance of 45.7% based on three SNPs.…”

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confidence: 99%

The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation

Chaitanya

Breslin

Zuñiga

et al. 2018

Forensic Science International: Genetics

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Forensic DNA Phenotyping (FDP), i.e. the prediction of human externally visible traits from DNA, has become a fast growing subfield within forensic genetics due to the intelligence information it can provide from DNA traces. FDP outcomes can help focus police investigations in search of unknown perpetrators, who are generally unidentifiable with standard DNA profiling. Therefore, we previously developed and forensically validated the IrisPlex DNA test system for eye colour prediction and the HIrisPlex system for combined eye and hair colour prediction from DNA traces. Here we introduce and forensically validate the HIrisPlex-S DNA test system (S for skin) for the simultaneous prediction of eye, hair, and skin colour from trace DNA. This FDP system consists of two SNaPshot-based multiplex assays targeting a total of 41 SNPs via a novel multiplex assay for 17 skin colour predictive SNPs and the previous HIrisPlex assay for 24 eye and hair colour predictive SNPs, 19 of which also contribute to skin colour prediction. The HIrisPlex-S system further comprises three statistical prediction models, the previously developed IrisPlex model for eye colour prediction based on 6 SNPs, the previous HIrisPlex model for hair colour prediction based on 22 SNPs, and the recently introduced HIrisPlex-S model for skin colour prediction based on 36 SNPs. In the forensic developmental validation testing, the novel 17-plex assay performed in full agreement with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, as previously shown for the 24-plex assay. Sensitivity testing of the 17-plex assay revealed complete SNP profiles from as little as 63 pg of input DNA, equalling the previously demonstrated sensitivity threshold of the 24-plex HIrisPlex assay. Testing of simulated forensic casework samples such as blood, semen, saliva stains, of inhibited DNA samples, of low quantity touch (trace) DNA samples, and of artificially degraded DNA samples as well as concordance testing, demonstrated the robustness, efficiency, and forensic suitability of the new 17-plex assay, as previously shown for the 24-plex assay. Finally, we provide an update to the publically available HIrisPlex website https://hirisplex.erasmusmc.nl/, now allowing the estimation of individual probabilities for 3 eye, 4 hair, and 5 skin colour categories from HIrisPlex-S input genotypes. The HIrisPlex-S DNA test represents the first forensically validated tool for skin colour prediction, and reflects the first forensically validated tool for simultaneous eye, hair and skin colour prediction from DNA.

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Collaborative EDNAP exercise on the IrisPlex system for DNA-based prediction of human eye colour

Cited by 25 publications

References 17 publications

Genetic and Environmental Factors in Conjunctival UV Autofluorescence

Genetic and Environmental Factors in Conjunctival UV Autofluorescence

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

The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation

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