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Brancato D, Coniglio E, Bruno F, Agostini V, Saccone S, Federico C. Forensic DNA Phenotyping: Genes and Genetic Variants for Eye Color Prediction. Genes (Basel) 2023; 14:1604. [PMID: 37628655 PMCID: PMC10454093 DOI: 10.3390/genes14081604] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
In recent decades, the use of genetic polymorphisms related to specific phenotypes, such as eye color, has greatly contributed to the development of the research field called forensic DNA phenotyping (FDP), enabling the investigators of crime cases to reduce the number of suspects, making their work faster and more precise. Eye color is a polygenic phenotype, and many genetic variants have been highlighted, with the major contributor being the HERC2-OCA2 locus, where many single nucleotide variations (SNPs) were identified. Interestingly, the HERC2-OCA2 locus, containing the intronic SNP rs12913832, the major eye color determinant, shows a high level of evolutionary conservation across many species of vertebrates. Currently, there are some genetic panels to predict eye color by genomic DNA analysis, even if the exact role of the SNP variants in the formation of eye color is still poorly understood, with a low level of predictivity in the so-called intermediate eye color. Many variants in OCA2, HERC2, and other genes lie in introns or correspond to synonymous variants, highlighting greater complexity in the mechanism of action of such genes than a simple missense variation. Here, we show the main genes involved in oculocutaneous pigmentation and their structural and functional features, as well as which genetic variants show the highest level of eye color predictivity in currently used FDP assays. Despite the great recent advances and impact of FDP in criminal cases, it is necessary to enhance scientific research to better understand the mechanism of action behind each genetic variant involved in eye color, with the goal of obtaining higher levels of prediction.
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Affiliation(s)
- Desiree Brancato
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Elvira Coniglio
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Francesca Bruno
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Vincenzo Agostini
- Department Science and Technical Innovation, University of Eastern Piedmont, Viale Teresa Michel 11, 15121 Alessandria, Italy;
| | - Salvatore Saccone
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Concetta Federico
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
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2
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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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3
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Bardan F, Higgins D, Austin JJ. A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage. Forensic Sci Int Genet 2023; 63:102822. [PMID: 36525814 DOI: 10.1016/j.fsigen.2022.102822] [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: 07/13/2022] [Revised: 11/02/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.
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Affiliation(s)
- Felicia Bardan
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Denice Higgins
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia; School of Dentistry, Health and Medical Sciences, The University of Adelaide, South Australia, Australia
| | - Jeremy J Austin
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia.
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4
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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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5
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Xu H, Fang Y, Zhao M, Lan Q, Mei S, Liu L, Bai X, Zhu B. Forensic Features and Genetic Structure Analyses of the Beijing Han Nationality Disclosed by a Self-Developed Panel Containing a Series of Ancestry Informative Deletion/Insertion Polymorphism Loci. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.890153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The utilization of the ancestry informative markers to disclose the ancestral composition of a certain population and explore the genetic affinities between diverse populations is beneficial to inferring the biogeographic ancestry of unknown individuals and assisting in case detection, as well as avoiding the impacts of population stratification during genome-wide association analysis studies. In the present study, we applied an in-house ancestry informative deletion/insertion polymorphic multiplex amplification system to investigate the ancestral compositions of the Beijing Han population and analyze the genetic relationships between the Beijing Han population and 31 global reference populations. The results demonstrated that 32 loci of this self-developed panel containing 39 loci significantly contributed to the inference of genetic information for the Beijing Han population. The results of multiple population genetics statistical analyses indicated that the ancestral component and genetic architecture of the Beijing Han population were analogous to the reference East Asian populations, and that the Beijing Han population was genetically close to the reference East Asian populations.
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6
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Frégeau CJ. A multiple predictive tool approach for phenotypic and biogeographical ancestry inferences. CANADIAN SOCIETY OF FORENSIC SCIENCE JOURNAL 2021. [DOI: 10.1080/00085030.2021.2016206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Chantal J. Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Biology Policy & Program Support, Ottawa, ON, Canada
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7
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Further insight into the global variability of the OCA2-HERC2 locus for human pigmentation from multiallelic markers. Sci Rep 2021; 11:22530. [PMID: 34795370 PMCID: PMC8602267 DOI: 10.1038/s41598-021-01940-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
The OCA2-HERC2 locus is responsible for the greatest proportion of eye color variation in humans. Numerous studies extensively described both functional SNPs and associated patterns of variation over this region. The goal of our study is to examine how these haplotype structures and allelic associations vary when highly variable markers such as microsatellites are used. Eleven microsatellites spanning 357 Kb of OCA2-HERC2 genes are analyzed in 3029 individuals from worldwide populations. We found that several markers display large differences in allele frequency (10% to 35% difference) among Europeans, East Asians and Africans. In Europe, the alleles showing increased frequency can also discriminate individuals with (IrisPlex) predicted blue and brown eyes. Distinct haplotypes are identified around the variants C and T of the functional SNP rs12913832 (associated to blue eyes), with linkage disequilibrium r2 values significant up to 237 Kb. The haplotype carrying the allele rs12913832 C has high frequency (76%) in blue eye predicted individuals (30% in brown eye predicted individuals), while the haplotype associated to the allele rs12913832 T is restricted to brown eye predicted individuals. Finally, homozygosity values reach levels of 91% near rs12913832. Odds ratios show values of 4.2, 7.4 and 10.4 for four markers around rs12913832 and 7.1 for their core haplotype. Hence, this study provides an example on the informativeness of multiallelic markers that, despite their current limited potential contribution to forensic eye color prediction, supports the use of microsatellites for identifying causing variants showing similar genetic features and history.
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8
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Frégeau CJ. Validation of the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B for phenotypic and biogeographical ancestry predictions using the Micro MiSeq® Flow Cells. Forensic Sci Int Genet 2021; 53:102533. [PMID: 34058534 DOI: 10.1016/j.fsigen.2021.102533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
In anticipation of offering phenotypic and biogeographical ancestry predictions to help resolve cases, the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B was evaluated in the context of Micro MiSeq® Flow Cells. These flow cells were determined as the best format for a quick turnaround time response and cost effective approach compared to standard flow cells. The phenotype informative SNPs (piSNPs) and ancestry informative SNPs (aiSNPs) were thoroughly examined through sensitivity, reproducibility and repeatability, concordance, robustness (mock casework) and low level DNA mixture studies purposely selecting individuals with different phenotypes (hair and eye color) when possible and different biogeographical ancestry. SNP locus-specific interpretation thresholds were established for the Universal Analysis Software (UAS) based on surviving alleles and SNP predictor rank to minimize false homozygous genotypes and maximize the information that can be derived from an unknown sample. Dropin alleles' intensity determined an appropriate threshold to minimize false heterozygous SNP genotypes. The selection of inappropriate interpretation thresholds was shown to have major consequences on phenotypic predictions. A 3.2% and 4.8% minor DNA component contribution to a DNA mixture had no impact on ancestry predictions whereas a 9.1% contribution did. The multi-locus SNP genotypes generated using the ForenSeq™ DNA Signature Prep kit/Primer Mix B were shown to be reliable, reproducible, concordant and resulted in predictions that were also reliable, reproducible and concordant based on the limited number of donors (N = 19) used in this study.
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Affiliation(s)
- Chantal J Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Biology Policy & Program Support, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada.
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9
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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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Palmal S, Adhikari K, Mendoza-Revilla J, Fuentes-Guajardo M, Silva de Cerqueira CC, Bonfante B, Chacón-Duque JC, Sohail A, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Lozano RB, Everardo-Martínez P, Gómez-Valdés J, Villamil-Ramírez H, Hünemeier T, Ramallo V, Parolin ML, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Faux P, Ruiz-Linares A. Prediction of eye, hair and skin colour in Latin Americans. Forensic Sci Int Genet 2021; 53:102517. [PMID: 33865096 DOI: 10.1016/j.fsigen.2021.102517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the prediction of categorical pigmentation traits for forensic purposes in Latin America, while illustrating the impact of training datasets on its accuracy.
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Affiliation(s)
- Sagnik Palmal
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú; Unit of Human Evolutionary Genetics, Institut Pasteur, Paris 75015, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | | | - Betty Bonfante
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France
| | - Juan Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Anood Sohail
- Department of Biotechnology, Kinnaird College for Women, 93 - Jail Road, Lahore 54000, Pakistan
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Claudia Jaramillo
- Department of Biotechnology, Kinnaird College for Women, 93 - Jail Road, Lahore 54000, Pakistan; GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera Lozano
- National Institute of Anthropology and History, Mexico City 6600, Mexico; Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena 07745, Germany
| | | | - Jorge Gómez-Valdés
- National Institute of Anthropology and History, Mexico City 6600, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil; Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Maria-Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | | | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Arica 1000000, Chile
| | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Pierre Faux
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France.
| | - Andrés Ruiz-Linares
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China.
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11
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Reis LB, Bakos RM, Vianna FSL, Macedo GS, Jacovas VC, Ribeiro-Dos-Santos AM, Santos S, Bakos L, Ashton-Prolla P. Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil. BMC Cancer 2020; 20:1069. [PMID: 33167923 PMCID: PMC7650158 DOI: 10.1186/s12885-020-07485-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Melanoma is the most aggressive type of skin cancer and is associated with environmental and genetic risk factors. It originates in melanocytes, the pigment-producing cells. Single nucleotide polymorphisms (SNPs) in pigmentation genes have been described in melanoma risk modulation, but knowledge in the field is still limited. METHODS In a case-control approach (107 cases and 119 controls), we investigated the effect of four pigmentation gene SNPs (TYR rs1126809, HERC2 rs1129038, SLC24A5 rs1426654, and SLC45A2 rs16891982) on melanoma risk in individuals from southern Brazil using a multivariate logistic regression model and multifactor dimensionality reduction (MDR) analysis. RESULTS Two SNPs were associated with an increased risk of melanoma in a dominant model: rs1129038AA and rs1426654AA [OR = 2.094 (95% CI: 1.106-3.966), P = 2.3 10- 2 and OR = 7.126 (95% CI: 1.873-27.110), P = 4.0 10- 3, respectively]. SNP rs16891982CC was associated with a lower risk to melanoma development in a log-additive model when the allele C was inherited [OR = 0.081 (95% CI: 0.008-0.782), P = 3 10- 2]. In addition, MDR analysis showed that the combination of the rs1426654AA and rs16891982GG genotypes was associated with a higher risk for melanoma (P = 3 10- 3), with a redundant effect. CONCLUSIONS These results contribute to the current knowledge and indicate that epistatic interaction of these SNPs, with an additive or correlational effect, may be involved in modulating the risk of melanoma in individuals from a geographic region with a high incidence of the disease.
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Affiliation(s)
- Larissa B Reis
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil.,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Renato M Bakos
- Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Serviço de Dermatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gabriel S Macedo
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil
| | - Vanessa C Jacovas
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Sidney Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Lúcio Bakos
- Serviço de Dermatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Patricia Ashton-Prolla
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil. .,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil. .,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
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12
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Al-Rashedi NA, Mandal AM, ALObaidi LAH. Eye color prediction using the IrisPlex system: a limited pilot study in the Iraqi population. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2020. [DOI: 10.1186/s41935-020-00200-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Abstract
Background
Forensic DNA phenotyping has gained momentum in the recent past due to the prediction of externally visible characters (EVCs) from the biological sample. The most common phenotypes like eye, hair, and skin color are predicted from the biological samples using a web-based system called IrisPlex. Based on six genetic SNPs, the IrisPlex system is developed and validated for its prediction accuracy in diverse ethnic groups worldwide. In previous studies, this system proved to have significant prediction accuracy. The EVCs vary substantially based on different geographical locations. Hence, the objective of this study was to validate the accuracy of the IrisPlex system in predicting the eye colors in the Iraqi population.
Methods
Six genetic single-nucleotide polymorphisms SNPs (HERC2-rs12913832, OCA2- rs1800407, SLC24A4-rs12896399, SLC45A2- rs16891982, TYR-rs1393350, and IRF4- rs12203592) in 58 Iraqi subjects were performed using Sequenom MassARRAY Genotyping. According to Liu et al., a predicted probability of 0.7 was considered as the threshold.
Results
Participants in this study of brown color were observed in 44.83%, intermediate in 43.1%, and blue in 12.07%. Completely predictive accuracy is obtained in 1; we observed the AUC at threshold 0.7 was 0.91 for brown, 0.79 for blue, and 0.60 for intermediate eye color. The sensitivity was 42.85% for blue, 0% for intermediate eye color, and 100% for brown-colored eye. Specificity was 100% for blue, 100% for intermediate, and 78.13% for brown eye color.
Conclusion
Hence, it was concluded that the prediction accuracy of the IrisPlex system for blue and brown color eye in the Iraqi population is significant in the studied population size. However, a pivotal study with larger sample size is required to represent the prediction accuracy of the IrisPlex system in the whole Iraqi population.
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Carratto TMT, Marcorin L, Debortoli G, Hünemeier T, Norton H, Parra EJ, Castelli EC, Mendes-Junior CT. Insights on hair, skin and eye color of ancient and contemporary Native Americans. Forensic Sci Int Genet 2020; 48:102335. [PMID: 32593164 DOI: 10.1016/j.fsigen.2020.102335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/20/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022]
Abstract
Over the past few years, tools capable of predicting pigmentation phenotypes have been developed aiming to contribute for criminal and anthropological investigations. In this study, we used eight genetic systems to infer eye, hair, and skin color of ancient and contemporary Native Americans. To achieve this goal, we retrieved 61 SNPs from 42 samples available in free online repositories of DNA sequences. We performed pigmentation predictions using two freely available tools, HIrisPlex-S and Snipper, in addition to two other published models. This workflow made possible to predict all three phenotypes with at least one tool for 29 out of the 42 samples. Considering these 29 individuals, predictions for eye, hair, and skin color were obtained with HIrisPlex-S for 27, 28 and 27 individuals, respectively, while 24, 25 and 25 individuals had such predictions with Snipper. In general, ancient and contemporary Native Americans were predicted to have intermediate/brown eyes, black hair, and intermediate/darker skin pigmentation.
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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, 14040-901, Ribeirão Preto, SP, Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900, Ribeirão Preto, SP, Brazil
| | - Guilherme Debortoli
- Department of Anthropology, University of Toronto at Mississauga, L5L 1C6, Mississauga, ON, Canada
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Heather Norton
- Department of Anthropology, University of Cincinnati, 45221, Cincinnati, OH, United States
| | - Esteban Juan Parra
- Department of Anthropology, University of Toronto at Mississauga, L5L 1C6, Mississauga, ON, Canada
| | - Erick C Castelli
- São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, SP, 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, 14040-901, Ribeirão Preto, SP, Brazil.
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Differentiation of Hispanic biogeographic ancestry with 80 ancestry informative markers. Sci Rep 2020; 10:7745. [PMID: 32385290 PMCID: PMC7210943 DOI: 10.1038/s41598-020-64245-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 04/03/2020] [Indexed: 11/09/2022] Open
Abstract
Ancestry informative single nucleotide polymorphisms (SNPs) can identify biogeographic ancestry (BGA); however, population substructure and relatively recent admixture can make differentiation difficult in heterogeneous Hispanic populations. Utilizing unrelated individuals from the Genomic Origins and Admixture in Latinos dataset (GOAL, n = 160), we designed an 80 SNP panel (Setser80) that accurately depicts BGA through STRUCTURE and PCA. We compared our Setser80 to the Seldin and Kidd panels via resampling simulations, which models data based on allele frequencies. We incorporated Admixed American 1000 Genomes populations (1000 G, n = 347), into a combined populations dataset to determine robustness. Using multinomial logistic regression (MLR), we compared the 3 panels on the combined dataset and found overall MLR classification accuracies: 93.2% Setser80, 87.9% Seldin panel, 71.4% Kidd panel. Naïve Bayesian classification had similar results on the combined dataset: 91.5% Setser80, 84.7% Seldin panel, 71.1% Kidd panel. Although Peru and Mexico were absent from panel design, we achieved high classification accuracy on the combined populations for Peru (MLR = 100%, naïve Bayes = 98%), and Mexico (MLR = 90%, naïve Bayes = 83.4%) as evidence of the portability of the Setser80. Our results indicate the Setser80 SNP panel can reliably classify BGA for individuals of presumed Hispanic origin.
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Salvoro C, Faccinetto C, Zucchelli L, Porto M, Marino A, Occhi G, de Los Campos G, Vazza G. Performance of four models for eye color prediction in an Italian population sample. Forensic Sci Int Genet 2019; 40:192-200. [PMID: 30884346 DOI: 10.1016/j.fsigen.2019.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/27/2019] [Accepted: 03/10/2019] [Indexed: 11/29/2022]
Abstract
Forensic DNA phenotyping (FDP) has recently provided important advancements in forensic investigations, by predicting the physical appearance of a subject from a biological sample, using SNP markers. The majority of operable prediction models have been developed for iris color; however, replication studies to understand their applicability on a worldwide scale are still limited for many of them. In this work, 4 models for eye color prediction (IrisPlex, Ruiz, Allwood and Hart models) were systematically evaluated in a sample of 296 subjects of Italian origin. Genotypes were determined by a custom NGS-based panel targeting all the predictive SNPs included in the 4 tested models. Overall, 60-69% of the Italian sample could be correctly predicted with the IrisPlex, Ruiz and Allwood models, applying the recommended threshold. The IrisPlex model showed the lowest frequency of errors (17%), but also the highest number of inconclusive results (18%). In the absence of the threshold, the highest proportion of correct predictions was again obtained with the IrisPlex model (76%), followed by the Allwood (73%) and the Ruiz (65%) models. Lastly, the Hart predictive algorithm had the lowest error rate (2%), but the majority of predictions (87%) were restricted to the less informative categories of "not-blue" and "not-brown", and correct color predictions were obtained only for 11% of the sample. As observed in previous studies, the majority of incorrect and undefined predictions were ascribable to the intermediate category, which represented 25% of the Italian sample. An adjustment of the IrisPlex (multinomial logistic regression) and Ruiz models (Snipper Bayesian classifier) with Italian allele frequencies gave only minor improvements in predicting intermediate eye color and no remarkable overall changes in performance. This suggests an incomplete knowledge underlying the intermediate colors. Considering the impact of this phenotype in the Italian sample as well as in other admixed populations, future improvements of eye color prediction methods should include a better genetic and phenotypic characterization of this category.
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Affiliation(s)
| | - Christian Faccinetto
- Reparto Carabinieri Investigazioni Scientifiche di Parma, Sezione Biologia, Parma, Italy.
| | - Luca Zucchelli
- Department of Biology, University of Padova, Padova, Italy
| | - Marika Porto
- Department of Biology, University of Padova, Padova, Italy
| | - Alberto Marino
- Reparto Carabinieri Investigazioni Scientifiche di Parma, Sezione Biologia, Parma, Italy
| | - Gianluca Occhi
- Department of Biology, University of Padova, Padova, Italy
| | - Gustavo de Los Campos
- Departments of Epidemiology & Biostatistics and Statistics & Probability, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan United States
| | - Giovanni Vazza
- Department of Biology, University of Padova, Padova, Italy.
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Lan Q, Shen C, Jin X, Guo Y, Xie T, Chen C, Cui W, Fang Y, Yang G, Zhu B. Distinguishing three distinct biogeographic regions with an in‐house developed 39‐AIM‐InDel panel and further admixture proportion estimation for Uyghurs. Electrophoresis 2019; 40:1525-1534. [DOI: 10.1002/elps.201800448] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/27/2019] [Accepted: 02/03/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Qiong Lan
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
| | - Chunmei Shen
- Institute of Brain and Behavioral SciencesCollege of Life SciencesShaanxi Normal University Xi'an P. R. China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Tong Xie
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
| | - Yating Fang
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
| | - Guang Yang
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota USA
| | - Bofeng Zhu
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical University Guangzhou P. R. China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi'an Jiaotong University Xi'an P. R. China
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Socio-technical disagreements as ethical fora: Parabon NanoLab’s forensic DNA Snapshot™ service at the intersection of discourses around robust science, technology validation, and commerce. BIOSOCIETIES 2018. [DOI: 10.1057/s41292-018-0138-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bradbury C, Köttgen A, Staubach F. Off-target phenotypes in forensic DNA phenotyping and biogeographic ancestry inference: A resource. Forensic Sci Int Genet 2018; 38:93-104. [PMID: 30391626 DOI: 10.1016/j.fsigen.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/27/2018] [Accepted: 10/13/2018] [Indexed: 01/04/2023]
Abstract
With recent advances in DNA sequencing technologies it has become feasible and cost effective to genotype larger marker sets for forensic purposes. Two technologies that make use of the larger marker sets have come into focus in forensic research and applications; inference of biogeographic ancestry (BGA) and forensic DNA phenotyping (FDP). These methods hold the promise to reveal information about a yet unknown perpetrator from a DNA sample. In contrast, DNA-profiling, that is a standard practice in case work, relies on matching DNA-profiles between crime scene material and suspects on a database of DNA-profiles. Markers for DNA-profiling were developed under the premise to reveal as little additional information about the human source of the profile as possible, the rationale being that personal privacy rights have to be balanced against the public interest in solving a crime. The same argument holds for markers used in BGA and FDP; these markers might also reveal information on off-target phenotypes (OTPs), that go beyond BGA and the phenotypes targeted in FDP. In particular, health related OTPs might shift the balance between privacy protection and public interest. However, to our knowledge, there is currently no convenient resource available to incorporate knowledge on OTPs in BGA and FDP assay design and application. In order to provide such a resource, we performed a systematic search for OTPs associated with a comprehensive set of markers (1766 SNPs) used or suggested to be used for BGA inference and FDP. In this set, we identified a relatively small number of 27 SNPs (1.53%) that convey information on diverse health related OTPs such as cancer risk, induced asthma, or risk of alcoholism. Some of these SNPs are commonly used for FDP and BGA across different marker sets. We conclude that the effects of SNP markers used in FDP and BGA on OTPs are currently limited, with few exceptions that should be considered in a balanced decision on assay design and application.
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Affiliation(s)
- Cedric Bradbury
- University College Freiburg, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Dept. of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Fabian Staubach
- Institute of Biology I, Dept. of Evolutionary Biology and Ecology, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
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Eye color prediction using single nucleotide polymorphisms in Saudi population. Saudi J Biol Sci 2018; 26:1607-1612. [PMID: 31762634 PMCID: PMC6864217 DOI: 10.1016/j.sjbs.2018.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 01/18/2023] Open
Abstract
Background DNA prediction of eye color represent one application of the externally visible characteristics (EVC), which attained growing interest in the field of DNA forensic phenotyping. This is mainly due to its ability to narrow the pool of suspects without the need to compare any retrieved DNA material from the crime scene to a reference DNA. Several methods and multiplex genetic panel were proposed with variable prediction accuracy between different populations. However, such panel was not previously tested in the Saudi population, nor any populations of the Middle East and North Africa origin. Method A panel of eleven single nucleotide polymorphisms (SNPs) was tested for their association with three eye colors (brown, hazel, and intermediate) in 80 volunteer Saudi individuals. SNPs and haplotype association test with eye colors were performed to identify the top significant SNPs with the three eye colors. Also, multinomial logistic regression was used to construct the prediction model using a training set of 60 subjects, and a validation set of 20 subjects. The goodness of fit parameter of the model to correctly predicts each eye color as compared to the other was performed. Results Eye color was significantly associated with rs12913832, rs7170852, and rs916977 that are located within HERC2. SNP rs12913832 was the top significant SNP (p-value = 1.78E−15) that accounted for the association in this region, as the other SNPs were not significant after adjusting for rs12913832. A prediction model containing five SNPs showed high prediction accuracy with Area Under the receiver operating characteristic Curves (AUC) equals to 0.95 and 0.83 for brown and intermediate eye colors, respectively. However, the model’s performance was very low for predicting the hazel eye color with AUC equals 0.75. Discussion Despite the small sample size of our study, we reported very significant SNP associations with eye color. Our model to predict eye colors based on DNA material showed high accuracy for brown and intermediate eye colors. The eye color prediction-model underperformed for the hazel eye colors, suggesting that larger sample size, as well as more comprehensive set of SNPs, could improve the model-prediction accuracy.
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Gontijo CC, Mendes FM, Santos CA, Klautau-Guimarães MDN, Lareu MV, Carracedo Á, Phillips C, Oliveira SF. Ancestry analysis in rural Brazilian populations of African descent. Forensic Sci Int Genet 2018; 36:160-166. [DOI: 10.1016/j.fsigen.2018.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
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Bulbul O, Filoglu G. Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing. Electrophoresis 2018; 39:2743-2751. [DOI: 10.1002/elps.201800243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Ozlem Bulbul
- Institute of Forensic Science; Istanbul University; Istanbul Turkey
| | - Gonul Filoglu
- Institute of Forensic Science; Istanbul University; Istanbul Turkey
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22
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Bulbul O, Zorlu T, Filoglu G. Prediction of human eye colour using highly informative phenotype SNPs (PISNPs). AUST J FORENSIC SCI 2018. [DOI: 10.1080/00450618.2018.1484161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ozlem Bulbul
- Institute of Forensic Science, Istanbul University, Istanbul, Turkey
| | - Tolga Zorlu
- Institute of Forensic Science, Istanbul University, Istanbul, Turkey
| | - Gonul Filoglu
- Institute of Forensic Science, Istanbul University, Istanbul, Turkey
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Bardan F, Higgins D, Austin JJ. A mini-multiplex SNaPshot assay for the triage of degraded human DNA. Forensic Sci Int Genet 2018; 34:62-70. [DOI: 10.1016/j.fsigen.2018.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/03/2018] [Accepted: 02/05/2018] [Indexed: 12/01/2022]
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Costa BSR, Freitas EPS, Cruz MS, Duarte VHR, Silva AMGD, Santos ICCD, Santos JCD, Rezende AA, Sena-Evangelista KCM, Silbiger VN. Association between kidney function and Framingham risk score in an admixed population of Brazil. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902017000317185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Andrade ES, Fracasso NC, Strazza Júnior PS, Simões AL, Mendes-Junior CT. Associations of OCA2 - HERC2 SNPs and haplotypes with human pigmentation characteristics in the Brazilian population. Leg Med (Tokyo) 2017; 24:78-83. [DOI: 10.1016/j.legalmed.2016.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 11/24/2016] [Accepted: 12/14/2016] [Indexed: 10/20/2022]
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26
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Forensic genetic analysis of bio-geographical ancestry. Forensic Sci Int Genet 2015; 18:49-65. [DOI: 10.1016/j.fsigen.2015.05.012] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 05/02/2015] [Accepted: 05/14/2015] [Indexed: 01/20/2023]
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27
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Forensic DNA Phenotyping: Predicting human appearance from crime scene material for investigative purposes. Forensic Sci Int Genet 2015; 18:33-48. [DOI: 10.1016/j.fsigen.2015.02.003] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/29/2015] [Accepted: 02/11/2015] [Indexed: 01/17/2023]
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