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Bukayev A, Gorin I, Aidarov B, Darmenov A, Balanovska E, Zhabagin M. Predictive accuracy of genetic variants for eye color in a Kazakh population using the IrisPlex system. BMC Res Notes 2024; 17:187. [PMID: 38970104 PMCID: PMC11227171 DOI: 10.1186/s13104-024-06856-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024] Open
Abstract
OBJECTIVE This study assesses the accuracy of the IrisPlex system, a genetic eye color prediction tool for forensic analysis, in the Kazakh population. The study compares previously published genotypes of 515 Kazakh individuals from varied geographical and ethnohistorical contexts with phenotypic data on their eye color, introduced for the first time in this research. RESULTS The IrisPlex panel's effectiveness in predicting eye color in the Kazakh population was validated. It exhibited slightly lower accuracy than in Western European populations but was higher than in Siberian populations. The sensitivity was notably high for brown-eyed individuals (0.99), but further research is needed for blue and intermediate eye colors. This study establishes IrisPlex as a useful predictive tool in the Kazakh population and provides a basis for future investigations into the genetic basis of phenotypic variations in this diverse population.
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Affiliation(s)
- Alizhan Bukayev
- National Center for Biotechnology, Astana, 010000, Kazakhstan
| | - Igor Gorin
- Research Centre for Medical Genetics, Moscow, 115522, Russia
| | - Baglan Aidarov
- National Center for Biotechnology, Astana, 010000, Kazakhstan
| | - Akynkali Darmenov
- Karaganda Academy of the Ministry of Internal Affairs of the Republic of Kazakhstan named after Barimbek Beisenov, Karaganda, 100000, Kazakhstan
| | | | - Maxat Zhabagin
- National Center for Biotechnology, Astana, 010000, Kazakhstan.
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Becher D, Jmel H, Kheriji N, Sarno S, Kefi R. Genetic landscape of forensic DNA phenotyping markers among Mediterranean populations. Forensic Sci Int 2024; 354:111906. [PMID: 38128201 DOI: 10.1016/j.forsciint.2023.111906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
Forensic DNA Phenotyping can reveal the appearance of an unknown individual by predicting the External Visible Characteristics (EVC) from DNA obtained at the crime scene. Our aim is to characterize the genetic landscape of Human identification markers responsible for EVC among Mediterranean populations compared to other worldwide groups. We conducted an exhaustive search for genes involved in EVC variation. Then, variants located on these genes were extracted from public genotypic data of Mediterranean, American, African and East Asiatic populations. The genetic landscape of these Human identification markers, their allelic distribution and admixture analyses, were determined using plink, R and ADMIXTURE softwares. Our results showed that the Mediterranean populations appear close to the Mexican populations and distinguished from sub Saharan African populations living in the USA and from East Asiatic populations. We highlighted a total of 103454 common variants shared between the studied populations and among them, 25 common variants associated with EVC. Interestingly, genotype frequencies results showed that the rs17646946, rs13016869, rs977588, rs1805008 and rs2240751 variants located respectively in the TCHH, PRKCE, OCA2, MC1R and MFSD12 genes are significantly different between the Mediterranean and Asiatic populations. The genotype frequencies of the variants rs977589 and rs7179994 located in the OCA2 gene, and of rs12913832 and rs2240751 located respectively in HERC2 and MFSD12 genes are significantly different between the Mediterranean and American populations. Our work generates a large number of EVC variants that could be a valuable resource for future studies in the forensic field.
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Affiliation(s)
- Dorra Becher
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; Directorate of Technical and Scientific Police, Sub-Directorate of Forensic and Scientific Laboratories, Tunis,Tunisia; University of Carthage, National Institute of Applied Science and Technology, Tunis, Tunisia
| | - Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; Genetic Typing Service, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; University of Tunis El Manar, 2092 El Manar I, Tunis, Tunisia
| | - Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; University of Tunis El Manar, 2092 El Manar I, Tunis, Tunisia
| | - Stefania Sarno
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; Genetic Typing Service, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; University of Tunis El Manar, 2092 El Manar I, Tunis, Tunisia.
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Aguilar-Velázquez JA, Llamas-de-Dios BJ, Córdova-Mercado MF, Coronado-Ávila CE, Salas-Salas O, López-Quintero A, Ramos-González B, Rangel-Villalobos H. Accuracy of Eye and Hair Color Prediction in Mexican Mestizos from Monterrey City Based on ForenSeq TM DNA Signature Prep. Genes (Basel) 2023; 14:genes14051120. [PMID: 37239480 DOI: 10.3390/genes14051120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/14/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Forensic genomic systems allow simultaneously analyzing identity informative (iiSNPs), ancestry informative (aiSNPs), and phenotype informative (piSNPs) genetic markers. Among these kits, the ForenSeq DNA Signature prep (Verogen) analyzes identity STRs and SNPs as well as 24 piSNPs from the HIrisPlex system to predict the hair and eye color. We report herein these 24 piSNPs in 88 samples from Monterrey City (Northeast, Mexico) based on the ForenSeq DNA Signature prep. Phenotypes were predicted by genotype results with both Universal Analysis Software (UAS) and the web tool of the Erasmus Medical Center (EMC). We observed predominantly brown eyes (96.5%) and black hair (75%) phenotypes, whereas blue eyes, and blond and red hair were not observed. Both UAS and EMC showed high performance in eye color prediction (p ≥ 96.6%), but a lower accuracy was observed for hair color prediction. Overall, UAS hair color predictions showed better performance and robustness than those obtained with the EMC web tool (when hair shade is excluded). Although we employed a threshold (p > 70%), we suggest using the EMC enhanced approach to avoid the exclusion of a high number of samples. Finally, although our results are helpful to employ these genomic tools to predict eye color, caution is suggested for hair color prediction in Latin American (admixed) populations such as those studied herein, principally when no black color is predicted.
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Affiliation(s)
- José Alonso Aguilar-Velázquez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
- Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Blanca Jeannete Llamas-de-Dios
- Licenciatura en Ciencias Forenses, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Miranda Fabiola Córdova-Mercado
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Carolina Elena Coronado-Ávila
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Orlando Salas-Salas
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Andrés López-Quintero
- Instituto de Nutrigenética y Nutrigenómica Traslacional, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Benito Ramos-González
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCI-UdeG), Ocotlán 47820, Jalisco, Mexico
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Rahat MA, Akbar F, Rasool A, Ilyas M, Rakha A, Shams S, Jelani M, Bibi F, Shirah BH, Abdulkareem AA, Naseer MI, Israr M. Phenotypic Classification of Eye Colour and Developmental Validation of the Irisplex System on Population Living in Malakand Division, Pakistan. Biomedicines 2023; 11:biomedicines11041228. [PMID: 37189847 DOI: 10.3390/biomedicines11041228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
The core objective of forensic DNA typing is developing DNA profiles from biological evidence for personal identification. The present study was designed to check the validation of the IrisPlex system and the Prevalence of eye colour in the Pakhtoon population residing within the Malakand Division. METHODS Eye colour digital photographs and buccal swab samples of 893 individuals of different age groups were collected. Multiplexed SNaPshot single base extension chemistry was used, and the genotypic results were analysed. Snapshot data were used for eye colour prediction through the IrisPlex and FROG-kb tool. RESULTS The results of the present study found brown eye colour to be the most prevalent eye colour in comparison to intermediate and blue coloured. Overall, individuals with brown-coloured eyes possess CT (46.84%) and TT (53.16%) genotypes. Blue eye-coloured individuals are solely of the CC genotype, while individuals of intermediate eye colour carry CT (45.15%) and CC (53.85%) genotypes in rs12913832 SNP in the HERC2 gene. It was also revealed that brown-coloured eyes individuals were dominant among all age groups followed by intermediate and blue. Statistical analysis between particular variables and eye colour showed a significant p-value (<0.05) for rs16891982 SNP in SLC45A2 gene, rs12913832 SNP in HERC2 gene, rs1393350 SNP in SLC45A2, districts and gender. The rest of the SNPs were non-significant with eye colour, respectively. The rs12896399 SNP and SNP rs1800407 were found significant with rs16891982 SNP. The result also demonstrated that the study group differs from the world population based on eye colour. The two eye colour prediction results were compared, and it was discovered that IrisPlex and FROG-Kb had similar higher prediction ratios for Brown and Blue eye colour. CONCLUSIONS The results of the current study revealed brown eye colour to be the most prevalent amongst members of the local population of Pakhtoon ethnicity in the Malakand Division of northern Pakistan. A set of contemporary human DNA samples with known phenotypes are used in this research to evaluate the custom panel's prediction accuracy. With the aid of this forensic test, DNA typing can be supplemented with details about the appearance of the person from whom the sample was taken in cases involving missing persons, ancient human remains, and trace samples. This study may be helpful for future population genetics and forensics studies.
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Affiliation(s)
- Murad Ali Rahat
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh 19120, Pakistan
- Department of Forensic Sciences, University of Swat, Charbagh 19120, Pakistan
| | - Fazal Akbar
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh 19120, Pakistan
| | - Akhtar Rasool
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh 19120, Pakistan
| | - Muhammad Ilyas
- Centre for Omic Sciences, Islamia College University Peshawar, Peshawar 25120, Pakistan
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Musharraf Jelani
- Centre for Omic Sciences, Islamia College University Peshawar, Peshawar 25120, Pakistan
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Bader H Shirah
- Department of Neuroscience, King Faisal Specialist Hospital & Research Centre, Jeddah 21589, Saudi Arabia
| | - Angham Abdulrhman Abdulkareem
- Faculty of Science, Department of Biochemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Muhammad Imran Naseer
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Muhammad Israr
- Department of Forensic Sciences, University of Swat, Charbagh 19120, Pakistan
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Sari O I, Simsek SZ, Filoglu G, Bulbul O. Predicting Eye and Hair Color in a Turkish Population Using the HIrisPlex System. Genes (Basel) 2022; 13:2094. [PMID: 36421769 PMCID: PMC9690125 DOI: 10.3390/genes13112094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 08/27/2023] Open
Abstract
Forensic DNA Phenotyping (FDP) can reveal the appearance of an unknown individual by predicting the ancestry, phenotype (i.e., hair, eye, skin color), and age from DNA obtained at the crime scene. The HIrisPlex system has been developed to simultaneously predict eye and hair color. However, the prediction accuracy of the system needs to be assessed for the tested population before implementing FDP in casework. In this study, we evaluated the performance of the HIrisPlex system on 149 individuals from the Turkish population. We applied the single-based extension (SNaPshot chemistry) method and used the HIrisPlex online tool to test the prediction of the eye and hair colors. The accuracy of the HIrisPlex system was assessed through the calculation of the area under the receiver characteristic operating curves (AUC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). The results showed that the proposed method successfully predicted the eye and hair color, especially for blue (100%) and brown (95.60%) eye and black (95.23) and brown (98.94) hair colors. As observed in previous studies, the system failed to predict intermediate eye color, representing 25% in our cohort. The majority of incorrect predictions were observed for blond hair color (40.7%). Previous HIrisPlex studies have also noted difficulties with these phenotypes. Our study shows that the HIrisPlex system can be applied to forensic casework in Turkey with careful interpretation of the data, particularly intermediate eye color and blond hair color.
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Affiliation(s)
- Ilksen Sari O
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, 34500 Istanbul, Turkey
- Department of Medical Services and Techniques, Vocational School of Health Services, Istanbul Gelisim University, 34310 Istanbul, Turkey
| | - Sumeyye Zulal Simsek
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, 34500 Istanbul, Turkey
| | - Gonul Filoglu
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, 34500 Istanbul, Turkey
| | - Ozlem Bulbul
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, 34500 Istanbul, Turkey
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Paparazzo E, Gozalishvili A, Lagani V, Geracitano S, Bauleo A, Falcone E, Passarino G, Montesanto A. A new approach to broaden the range of eye colour identifiable by IrisPlex in DNA phenotyping. Sci Rep 2022; 12:12803. [PMID: 35896692 PMCID: PMC9329466 DOI: 10.1038/s41598-022-17208-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
IrisPlex system represents the most popular model for eye colour prediction. Based on six polymorphisms this model provides very accurate predictions that strongly depend on the definition of eye colour phenotypes. The aim of the present study was to introduce a new approach to improve eye colour prediction using the well-validated IrisPlex system. A sample of 238 individuals from a Southern Italian population was collected and for each of them a high-resolution image of eye was obtained. By quantifying eye colour variation into CIELAB space several clustering algorithms were applied for eye colour classification. Predictions with the IrisPlex model were obtained using eye colour categories defined by both visual inspection and clustering algorithms. IrisPlex system predicted blue and brown eye colour with high accuracy while it was inefficient in the prediction of intermediate eye colour. Clustering-based eye colour resulted in a significantly increased accuracy of the model especially for brown eyes. Our results confirm the validity of the IrisPlex system for forensic purposes. Although the quantitative approach here proposed for eye colour definition slightly improves its prediction accuracy, further research is still required to improve the model particularly for the intermediate eye colour prediction.
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Affiliation(s)
- Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Anzor Gozalishvili
- Toptal, LLC, 2810 N. Church St. #36879, Wilmington, DE, 19802-4447, USA.,Ivane Javakhishvili Tbilisi State University, 0162, Tbilisi, Georgia
| | - Vincenzo Lagani
- Institute of Chemical Biology, Ilia State University, 0162, Tbilisi, Georgia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, 23952, Saudi Arabia
| | - Silvana Geracitano
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Alessia Bauleo
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100, Cosenza, ASP, Italy
| | - Elena Falcone
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100, Cosenza, ASP, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy.
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Predicting eye and hair colour in a Norwegian population using Verogen's ForenSeq™ DNA signature prep kit. Forensic Sci Int Genet 2021; 56:102620. [PMID: 34735941 DOI: 10.1016/j.fsigen.2021.102620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/24/2021] [Accepted: 10/21/2021] [Indexed: 01/01/2023]
Abstract
Prediction of eye and hair colour from DNA can be an important investigative tool in forensic cases if conventional DNA profiling fails to match DNA from any known suspects or cannot obtain a hit in a DNA database. The HIrisPlex model for simultaneous eye and hair colour predictions was developed for forensic usage. To genotype a DNA sample, massively parallel sequencing (MPS) has brought new possibilities to the analysis of forensic DNA samples. As part of an in-house validation, this study presents the genotyping and predictive performance of the HIrisPlex SNPs in a Norwegian study population, using Verogen's ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx system and the HIrisPlex webtool. DNA-profiles were successfully typed with DNA input down to 125 pg. In samples with DNA input < 125 pg, false homozygotes were observed with as many as 92 reads. Prediction accuracies in terms of AUC were high for red (0.97) and black (0.93) hair colours, as well as blue (0.85) and brown (0.94) eye colours. The AUCs for blond (0.72) and brown (0.70) hair colour were considerably lower. None of the individuals was predicted to have intermediate eye colour. Therefore, the error rates of the overall eye colour predictions were 37% with no predictive probability threshold (pmax) and 26% with a probability threshold of 0.7. We also observed that more than half of the incorrect predictions were for individuals carrying the rs12913832 GG genotype. For hair colour, 65% of the individuals were correctly predicted when using the highest probability category approach. The main error was observed for individuals with brown hair colour that were predicted to have blond hair. Utilising the prediction guide approach increased the correct predictions to 75%. Assessment of phenotype-genotype associations of eye colours using a quantitative eye colour score (PIE-score), revealed that rs12913832 AA individuals of Norwegian descent had statistically significantly higher PIE-score (less brown eye colour) than individuals of non-northern European descent. To our knowledge, this has not been reported in other studies. Our study suggests that careful assessment of the target population prior to the implementation of forensic DNA phenotyping to case work is beneficial.
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Meyer OS, Salvo NM, Kjærbye A, Kjersem M, Andersen MM, Sørensen E, Ullum H, Janssen K, Morling N, Børsting C, Olsen GH, Andersen JD. Prediction of Eye Colour in Scandinavians Using the EyeColour 11 (EC11) SNP Set. Genes (Basel) 2021; 12:821. [PMID: 34071952 PMCID: PMC8227851 DOI: 10.3390/genes12060821] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
Description of a perpetrator's eye colour can be an important investigative lead in a forensic case with no apparent suspects. Herein, we present 11 SNPs (Eye Colour 11-EC11) that are important for eye colour prediction and eye colour prediction models for a two-category reporting system (blue and brown) and a three-category system (blue, intermediate, and brown). The EC11 SNPs were carefully selected from 44 pigmentary variants in seven genes previously found to be associated with eye colours in 757 Europeans (Danes, Swedes, and Italians). Mathematical models using three different reporting systems: a quantitative system (PIE-score), a two-category system (blue and brown), and a three-category system (blue, intermediate, brown) were used to rank the variants. SNPs with a sufficient mean variable importance (above 0.3%) were selected for EC11. Eye colour prediction models using the EC11 SNPs were developed using leave-one-out cross-validation (LOOCV) in an independent data set of 523 Norwegian individuals. Performance of the EC11 models for the two- and three-category system was compared with models based on the IrisPlex SNPs and the most important eye colour locus, rs12913832. We also compared model performances with the IrisPlex online tool (IrisPlex Web). The EC11 eye colour prediction models performed slightly better than the IrisPlex and rs12913832 models in all reporting systems and better than the IrisPlex Web in the three-category system. Three important points to consider prior to the implementation of eye colour prediction in a forensic genetic setting are discussed: (1) the reference population, (2) the SNP set, and (3) the reporting strategy.
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Affiliation(s)
- Olivia Strunge Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; (A.K.); (N.M.); (C.B.); (J.D.A.)
| | - Nina Mjølsnes Salvo
- Centre for Forensic Genetics, Department of Medical Biology, UiT–The Arctic University of Norway, 9037 Tromsø, Norway; (N.M.S.); (M.K.); (K.J.); (G.-H.O.)
| | - Anne Kjærbye
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; (A.K.); (N.M.); (C.B.); (J.D.A.)
| | - Marianne Kjersem
- Centre for Forensic Genetics, Department of Medical Biology, UiT–The Arctic University of Norway, 9037 Tromsø, Norway; (N.M.S.); (M.K.); (K.J.); (G.-H.O.)
| | | | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Henrik Ullum
- Statens Serum Institut, 2300 Copenhagen, Denmark;
| | - Kirstin Janssen
- Centre for Forensic Genetics, Department of Medical Biology, UiT–The Arctic University of Norway, 9037 Tromsø, Norway; (N.M.S.); (M.K.); (K.J.); (G.-H.O.)
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; (A.K.); (N.M.); (C.B.); (J.D.A.)
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; (A.K.); (N.M.); (C.B.); (J.D.A.)
| | - Gunn-Hege Olsen
- Centre for Forensic Genetics, Department of Medical Biology, UiT–The Arctic University of Norway, 9037 Tromsø, Norway; (N.M.S.); (M.K.); (K.J.); (G.-H.O.)
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; (A.K.); (N.M.); (C.B.); (J.D.A.)
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Carratto TMT, Marcorin L, do Valle-Silva G, de Oliveira MLG, Donadi EA, Simões AL, Castelli EC, Mendes-Junior CT. Prediction of eye and hair pigmentation phenotypes using the HIrisPlex system in a Brazilian admixed population sample. Int J Legal Med 2021; 135:1329-1339. [PMID: 33884487 DOI: 10.1007/s00414-021-02554-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/26/2021] [Indexed: 01/23/2023]
Abstract
Human pigmentation is a complex trait, probably involving more than 100 genes. Predicting phenotypes using SNPs present in those genes is important for forensic purpose. For this, the HIrisPlex tool was developed for eye and hair color prediction, with both models achieving high accuracy among Europeans. Its evaluation in admixed populations is important, since they present a higher frequency of intermediate phenotypes, and HIrisPlex has demonstrated limitations in such predictions; therefore, the performance of this tool may be impaired in such populations. Here, we evaluate the set of 24 markers from the HIrisPlex system in 328 individuals from Ribeirão Preto (SP) region, predicting eye and hair color and comparing the predictions with their real phenotypes. We used the HaloPlex Target Enrichment System and MiSeq Personal Sequencer platform for massively parallel sequencing. The prediction of eye and hair color was accomplished by the HIrisPlex online tool, using the default prediction settings. Ancestry was estimated using the SNPforID 34-plex to observe if and how an individual's ancestry background would affect predictions in this admixed sample. Our sample presented major European ancestry (70.5%), followed by African (21.1%) and Native American/East Asian (8.4%). HIrisPlex presented an overall sensitivity of 0.691 for hair color prediction, with sensitivities ranging from 0.547 to 0.782. The lowest sensitivity was observed for individuals with black hair, who present a reduced European contribution (48.4%). For eye color prediction, the overall sensitivity was 0.741, with sensitivities higher than 0.85 for blue and brown eyes, although it failed in predicting intermediate eye color. Such struggle in predicting this phenotype category is in accordance with what has been seen in previous studies involving HIrisPlex. Individuals with brown eye color are more admixed, with European ancestry decreasing to 62.6%; notwithstanding that, sensitivity for brown eyes was almost 100%. Overall sensitivity increases to 0.791 when a 0.7 threshold is set, though 12.5% of the individuals become undefined. When combining eye and hair prediction, hit rates between 51.3 and 68.9% were achieved. Despite the difficulties with intermediate phenotypes, we have shown that HIrisPlex results can be very helpful when interpreted with caution.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, SP, 14040-901, Ribeirão Preto, Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Guilherme do Valle-Silva
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, SP, 14040-901, Ribeirão Preto, Brazil
| | | | - Eduardo Antônio Donadi
- Divisão de Imunologia Clínica, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14048-900, Brazil
| | - Aguinaldo Luiz Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Erick C Castelli
- Departamento de Patologia, Faculdade de Medicina de Botucatu, Unesp - Universidade Estadual Paulista, Botucatu, SP, 18618-970, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, SP, 14040-901, Ribeirão Preto, Brazil.
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10
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Ragazzo M, Carboni S, Caputo V, Buttini C, Manzo L, Errichiello V, Puleri G, Giardina E. Interpreting Mixture Profiles: Comparison between Precision ID GlobalFiler™ NGS STR Panel v2 and Traditional Methods. Genes (Basel) 2020; 11:E591. [PMID: 32466613 PMCID: PMC7349666 DOI: 10.3390/genes11060591] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 04/28/2020] [Accepted: 05/22/2020] [Indexed: 12/11/2022] Open
Abstract
Forensic investigation for the identification of offenders, recognition of human remains, and verification of family relationships requires the analysis of particular types of highly informative DNA markers, which have high discriminatory power and are efficient for typing degraded samples. These markers, called STRs (Short Tandem Repeats), can be amplified by multiplex-PCR (Polymerase Chain Reaction) allowing attainment of a unique profile through which it is possible to distinguish one individual from another with a high statistical significance. The rapid and progressive evolution of analytical techniques and the advent of Next-Generation Sequencing (NGS) have completely revolutionized the DNA sequencing approach. This technology, widely used today in the diagnostic field, has the advantage of being able to process several samples in parallel, producing a huge volume of data in a short time. At this time, although default parameters of interpretation software are available, there is no general agreement on the interpretation rules of forensic data produced via NGS technology. Here we report a pilot study aimed for a comparison between NGS (Precision ID GlobalFiler™ NGS STR Panel v2, Thermo Fisher Scientific, Waltham, MA, USA) and traditional methods in their ability to identify major and minor contributors in DNA mixtures from saliva and urine samples. A quantity of six mixed samples were prepared for both saliva and urine samples from donors. A total of 12 mixtures were obtained in the ratios of 1:2; 1:4; 1:6; 1:8; 1:10; and 1:20 between minor and major contributors. Although the number of analyzed mixtures is limited, our results confirm that NGS technology offers a huge range of additional information on samples, but cannot ensure a higher sensitivity in respect to traditional methods. Finally, the Precision ID GlobalFiler™ NGS STR Panel v2 is a powerful method for kinship analyses and typing reference samples, but its use in biological evidence should be carefully considered on the basis of the characteristics of the evidence.
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Affiliation(s)
- Michele Ragazzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Stefania Carboni
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation IRCCS, 00142 Rome, Italy;
| | - Valerio Caputo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Carlotta Buttini
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Laura Manzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Valeria Errichiello
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Giulio Puleri
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Emiliano Giardina
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation IRCCS, 00142 Rome, Italy;
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11
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Butler JM, Willis S. Interpol review of forensic biology and forensic DNA typing 2016-2019. Forensic Sci Int Synerg 2020; 2:352-367. [PMID: 33385135 PMCID: PMC7770417 DOI: 10.1016/j.fsisyn.2019.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 12/23/2022]
Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2016 to 2019 as a part of the 19th Interpol International Forensic Science Managers Symposium. The review papers are also available at the Interpol website at: https://www.interpol.int/content/download/14458/file/Interpol%20Review%20Papers%202019.pdf.
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12
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Development of a forensic DNA phenotyping panel using massive parallel sequencing. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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