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Jawad M, Adnan A, Rehman RA, Nazir S, Adeyemo OA, Amer SAM, Hadi S, Liu F, Wang CC, Rakha A. Evaluation of facial hair-associated SNPs: a pilot study on male Pakistani Punjabi population. Forensic Sci Med Pathol 2023; 19:293-302. [PMID: 35994154 DOI: 10.1007/s12024-022-00515-z] [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] [Accepted: 08/03/2022] [Indexed: 10/15/2022]
Abstract
Variation in facial hair is one of the most conspicuous features of facial appearance, particularly in South Asia and Middle East countries. A genome-wide association study in Latin Americans has identified multiple genetic variants at distinct loci being associated with facial hair traits including eyebrow thickness, beard thickness, and monobrow. In this pilot study, we have evaluated 16 SNPs associated with facial hair traits in 58 male individuals from the Punjabi population of Pakistan. In our sample, rs365060 in EDAR and rs12597422 in FTO showed significant association with monobrow, rs6684877 in MACF1 showed significant association with eyebrow thickness, and two SNPs in LOC105379031 (rs9654415 and rs7702331) showed significant association with beard thickness. Our results also suggest that genetic association may vary between ethnic groups and geographic regions. Although more data are needed to validate our results, our findings are of value in forensic molecular photofitting research in Pakistan.
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Affiliation(s)
- Muhammad Jawad
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Atif Adnan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia.
| | - Rahat Abdul Rehman
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Oyenike A Adeyemo
- Department of Cell Biology and Genetics, Faculty of Science, University of Lagos, AkokaLagos, Yaba, Nigeria
| | - S A M Amer
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Fan Liu
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan.
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Inkret J, Zupanc T, Zupanič Pajnič I. A Multisample Approach in Forensic Phenotyping of Chronological Old Skeletal Remains Using Massive Parallel Sequencing (MPS) Technology. Genes (Basel) 2023; 14:1449. [PMID: 37510353 PMCID: PMC10379588 DOI: 10.3390/genes14071449] [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: 06/08/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
It is very important to generate phenotypic results that are reliable when processing chronological old skeletal remains for cases involving the identification of missing persons. To improve the success of pigmentation prediction in Second World War victims, three bones from each of the eight skeletons analyzed were included in the study, which makes it possible to generate a consensus profile. The PowerQuant System was used for quantification, the ESI 17 Fast System was used for STR typing, and a customized version of the HIrisPlex panel was used for PCR-MPS. The HID Ion Chef Instrument was used for library preparation and templating. Sequencing was performed with the Ion GeneStudio S5 System. Identical full profiles and identical hair and eye color predictions were achieved from three bones analyzed per skeleton. Blue eye color was predicted in five skeletons and brown in three skeletons. Blond hair color was predicted in one skeleton, blond to dark blond in three skeletons, brown to dark brown in two skeletons, and dark brown to black in two skeletons. The reproducibility and reliability of the results proved the multisample analysis method to be beneficial for phenotyping chronological old skeletons because differences in DNA yields in different bone types provide a greater possibility of obtaining a better-quality consensus profile.
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Affiliation(s)
- Jezerka Inkret
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
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Advancement in Human Face Prediction Using DNA. Genes (Basel) 2023; 14:genes14010136. [PMID: 36672878 PMCID: PMC9858985 DOI: 10.3390/genes14010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
The rapid improvements in identifying the genetic factors contributing to facial morphology have enabled the early identification of craniofacial syndromes. Similarly, this technology can be vital in forensic cases involving human identification from biological traces or human remains, especially when reference samples are not available in the deoxyribose nucleic acid (DNA) database. This review summarizes the currently used methods for predicting human phenotypes such as age, ancestry, pigmentation, and facial features based on genetic variations. To identify the facial features affected by DNA, various two-dimensional (2D)- and three-dimensional (3D)-scanning techniques and analysis tools are reviewed. A comparison between the scanning technologies is also presented in this review. Face-landmarking techniques and face-phenotyping algorithms are discussed in chronological order. Then, the latest approaches in genetic to 3D face shape analysis are emphasized. A systematic review of the current markers that passed the threshold of a genome-wide association (GWAS) of single nucleotide polymorphism (SNP)-face traits from the GWAS Catalog is also provided using the preferred reporting items for systematic reviews and meta-analyses (PRISMA), approach. Finally, the current challenges in forensic DNA phenotyping are analyzed and discussed.
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Dash HR, Arora M. CRISPR-CasB technology in forensic DNA analysis: challenges and solutions. Appl Microbiol Biotechnol 2022; 106:4367-4374. [PMID: 35704073 DOI: 10.1007/s00253-022-12016-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 01/23/2023]
Abstract
CRISPR-Cas technology has revolutionized the field of biotechnology with its precise therapeutic use from genetic as well as infectious diseases point of view. This technology is rapidly evolving to single tool enabling site-directed cut in the genome and highly specific activation or inhibition of gene expression or the exchange of single bases. Besides clinical applications, CRISPR-Cas technology has also shown promising use in the field of forensic DNA analysis. Enrichment of targeted genetic marker for identification followed by sequencing and non-PCR-dependent technique ensures the use of CRISPR-Cas technology in challenging forensic biological samples. The use of this advanced technology is also deemed helpful in mixed profile attribution, mostly in LCN contributors and the generation of a useful DNA profile in degraded samples. Besides its useful applications in forensic DNA analysis, CRISPR-Cas technology poses a huge threat from the generation of ghost DNA profiles by modification/alteration of target genetic markers. Forensic DNA analysts should carry out analysis of additional markers such as non-CODIS markers, Y-, X-chromosome markers, and mitochondrial DNA sequencing in a suspected ghost DNA profile case. KEY POINTS: • CRISPR-Cas9 technique is useful in analyzing LCN, mixed and degraded samples • Alteration of DNA using this technique can lead to generation of ghost DNA profiles • Alternative genetic markers and methylation pattern may detect a ghost DNA profile.
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Affiliation(s)
- Hirak Ranjan Dash
- School of Forensic Sciences, National Forensic Sciences University, Delhi Campus, Sector-3, Rohini, New Delhi, 110085, India.
| | - Mansi Arora
- School of Forensic Sciences, National Forensic Sciences University, Delhi Campus, Sector-3, Rohini, New Delhi, 110085, India
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Evaluation of the VISAGE basic tool for appearance and ancestry inference using ForenSeq® chemistry on the MiSeq FGx® system. Forensic Sci Int Genet 2022; 58:102675. [DOI: 10.1016/j.fsigen.2022.102675] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/13/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
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Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System. Genes (Basel) 2020; 11:genes11060708. [PMID: 32604780 PMCID: PMC7349024 DOI: 10.3390/genes11060708] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/23/2023] Open
Abstract
The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful Forensic DNA Phenotyping (FDP). The EU-funded VISAGE (VISible Attributes through GEnomics) Consortium has developed various targeted MPS-based lab tools to apply FDP in routine forensic analyses. Here, we present an evaluation of the VISAGE Basic tool for appearance and ancestry prediction based on PowerSeq chemistry (Promega) on a MiSeq FGx System (Illumina). The panel consists of 153 single nucleotide polymorphisms (SNPs) that provide information about EVCs (41 SNPs for eye, hair and skin color from HIrisPlex-S) and continental BGA (115 SNPs; three overlap with the EVCs SNP set). The assay was evaluated for sensitivity, repeatability and genotyping concordance, as well as its performance with casework-type samples. This targeted MPS assay provided complete genotypes at all 153 SNPs down to 125 pg of input DNA and 99.67% correct genotypes at 50 pg. It was robust in terms of repeatability and concordance and provided useful results with casework-type samples. The results suggest that this MPS assay is a useful tool for basic appearance and ancestry prediction in forensic genetics for users interested in applying PowerSeq chemistry and MiSeq for this purpose.
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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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Mehta B, Daniel R, Phillips C, Doyle S, Elvidge G, McNevin D. Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq. Electrophoresis 2017; 37:2832-2840. [PMID: 27605155 DOI: 10.1002/elps.201600190] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/20/2016] [Accepted: 08/23/2016] [Indexed: 02/04/2023]
Abstract
Forensic DNA-based intelligence, or forensic DNA phenotyping, utilises SNPs to infer the biogeographical ancestry and externally visible characteristics of the donor of evidential material. SNaPshot® is a commonly employed forensic SNP genotyping technique, which is limited to multiplexes of 30-40 SNPs in a single reaction and prone to PCR contamination. Massively parallel sequencing has the ability to genotype hundreds of SNPs in multiple samples simultaneously by employing an oligonucleotide sample barcoding strategy. This study of the Illumina MiSeq massively parallel sequencing platform analysed 136 unique SNPs in 48 samples from SNaPshot PCR amplicons generated by five established forensic DNA phenotyping assays comprising the SNPforID 52-plex, SNPforID 34-plex, Eurasiaplex, Pacifiplex and IrisPlex. Approximately 3 GB of sequence data were generated from two MiSeq flow cells and profiles were obtained from just 0.25 ng of DNA. Compared with SNaPshot, an average 98% genotyping concordance was achieved. Our customised approach was successful in attaining SNP profiles from extremely degraded, inhibited, and compromised casework samples. Heterozygote imbalance and sequence coverage in negative controls highlight the need to establish baseline sequence coverage thresholds and refine allele frequency thresholds. This study demonstrates the potential of the MiSeq for forensic SNP analysis.
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Affiliation(s)
- Bhavik Mehta
- National Centre for Forensic Studies, Faculty of ESTeM, University of Canberra, Canberra, Australia.
| | - Runa Daniel
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Melbourne, Australia
| | - Chris Phillips
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Stephen Doyle
- Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, Australia
| | | | - Dennis McNevin
- National Centre for Forensic Studies, Faculty of ESTeM, University of Canberra, Canberra, Australia
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Population and performance analyses of four major populations with Illumina's FGx Forensic Genomics System. Forensic Sci Int Genet 2017. [PMID: 28651097 DOI: 10.1016/j.fsigen.2017.06.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The MiSeq FGx Forensic Genomics System (Illumina) enables amplification and massively parallel sequencing of 59 STRs, 94 identity informative SNPs, 54 ancestry informative SNPs, and 24 phenotypic informative SNPs. Allele frequency and population statistics data were generated for the 172 SNP loci included in this panel on four major population groups (Chinese, African Americans, US Caucasians, and Southwest Hispanics). Single-locus and combined random match probability values were generated for the identity informative SNPs. The average combined STR and identity informative SNP random match probabilities (assuming independence) across all four populations were 1.75E-67 and 2.30E-71 with length-based and sequence-based STR alleles, respectively. Ancestry and phenotype predictions were obtained using the ForenSeq™ Universal Analysis System (UAS; Illumina) based on the ancestry informative and phenotype informative SNP profiles generated for each sample. Additionally, performance metrics, including profile completeness, read depth, relative locus performance, and allele coverage ratios, were evaluated and detailed for the 725 samples included in this study. While some genetic markers included in this panel performed notably better than others, performance across populations was generally consistent. The performance and population data included in this study support that accurate and reliable profiles were generated and provide valuable background information for laboratories considering internal validation studies and implementation.
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Mehta B, Venables S, Roffey P. Comparison between magnetic bead and qPCR library normalisation methods for forensic MPS genotyping. Int J Legal Med 2017; 132:125-132. [PMID: 28417259 DOI: 10.1007/s00414-017-1591-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/06/2017] [Indexed: 11/27/2022]
Abstract
Massively parallel sequencing (MPS) is fast approaching operational use in forensic science, with the capability to analyse hundreds of DNA identity and DNA intelligence markers in multiple samples simultaneously. The ForenSeq™ DNA Signature Kit on MiSeq FGx™ (Illumina) workflow can provide profiles for autosomal short tandem repeats (STRs), X chromosome and Y chromosome STRs, identity single nucleotide polymorphisms (SNPs), biogeographical ancestry SNPs and phenotype (eye and hair colour) SNPs from a sample. The library preparation procedure involves a series of steps including target amplification, library purification and library normalisation. This study highlights the comparison between the manufacturer recommended magnetic bead normalisation and quantitative polymerase chain reaction (qPCR) methods. Furthermore, two qPCR chemistries, KAPA® (KAPA Biosystems) and NEBNext® (New England Bio Inc.), have also been compared. The qPCR outperformed the bead normalisation method, while the NEBNext® kit obtained higher genotype concordance than KAPA®. The study also established an MPS workflow that can be utilised in any operational forensic laboratory.
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Affiliation(s)
- Bhavik Mehta
- National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics (ESTeM), University of Canberra, Canberra, Bruce, ACT 2617, Australia. .,Specialist Operations - Forensics, Australian Federal Police, Tambreet Street, Majura, ACT 2609, Australia.
| | - Samantha Venables
- National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics (ESTeM), University of Canberra, Canberra, Bruce, ACT 2617, Australia.,Specialist Operations - Forensics, Australian Federal Police, Tambreet Street, Majura, ACT 2609, Australia
| | - Paul Roffey
- National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics (ESTeM), University of Canberra, Canberra, Bruce, ACT 2617, Australia.,Specialist Operations - Forensics, Australian Federal Police, Tambreet Street, Majura, ACT 2609, Australia
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Forensically relevant SNaPshot® assays for human DNA SNP analysis: a review. Int J Legal Med 2016; 131:21-37. [DOI: 10.1007/s00414-016-1490-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/31/2016] [Indexed: 10/20/2022]
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Yun L, Gu Y, Rajeevan H, Kidd KK. Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations. Int J Legal Med 2014; 128:447-53. [DOI: 10.1007/s00414-013-0953-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/28/2013] [Indexed: 10/25/2022]
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Gettings KB, Lai R, Johnson JL, Peck MA, Hart JA, Gordish-Dressman H, Schanfield MS, Podini DS. A 50-SNP assay for biogeographic ancestry and phenotype prediction in the U.S. population. Forensic Sci Int Genet 2013; 8:101-8. [PMID: 24315596 DOI: 10.1016/j.fsigen.2013.07.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 06/28/2013] [Accepted: 07/23/2013] [Indexed: 11/17/2022]
Abstract
When an STR DNA profile obtained from crime scene evidence does not match identified suspects or profiles from available databases, further DNA analyses targeted at inferring the possible ancestral origin and phenotypic characteristics of the perpetrator could yield valuable information. Single Nucleotide Polymorphisms (SNPs), the most common form of genetic polymorphisms, have alleles associated with specific populations and/or correlated to physical characteristics. We have used single base primer extension (SBE) technology to develop a 50 SNP assay (composed of three multiplexes) designed to predict ancestry among the primary U.S. populations (African American, East Asian, European American, and Hispanic American/Native American), as well as pigmentation phenotype (eye, hair, and skin color) among European American. We have optimized this assay to a sensitivity level comparable to current forensic DNA analyses, and shown robust performance on forensic-type samples. In addition, we developed a prediction model for ancestry in the U.S. population, based on the random match probability and likelihood ratio formulas already used in forensic laboratories. Lastly, we evaluated the biogeographic ancestry prediction model using a test set, and we evaluated an existing model for eye color with our U.S. sample set. Using these models with recommended thresholds, the 50 SNP assay provided accurate ancestry information in 98.6% of the test set samples, and provided accurate eye color information in 61% of the European samples tested (25% were inconclusive and 14% were incorrect). This method, which uses equipment already available in forensic DNA laboratories, is recommended for use in U.S. forensic casework to provide additional information about the donor of a DNA sample when the STR profile has not been linked to an individual.
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