1
|
Al-Haj-Taib R, Mejri A, Børsting C, Pereira V, Elkamel S, Herrera RJ, Benammar-Elgaaied A, Fadhlaoui-Zid K. Genetic analysis of sixteen autosomal STR loci in three Tunisian populations from Makthar, Nabeul and Sousse. Ann Hum Biol 2022; 48:590-597. [DOI: 10.1080/03014460.2022.2032338] [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)
- Rim Al-Haj-Taib
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Abir Mejri
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen.
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen.
| | - Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Rene J. Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| | - Amel Benammar-Elgaaied
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
- Department of Biology, College of Science, Taibah University, Al Madinah Al Monawarah, Saudi Arabia
- Higher Institute of Biotechnology of Beja, University of Jendouba, Beja, Tunisia
| |
Collapse
|
2
|
Adnan A, Anwar A, Simayijiang H, Farrukh N, Hadi S, Wang CC, Xuan JF. The Heart of Silk Road "Xinjiang," Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs. Front Genet 2021; 12:760760. [PMID: 34976009 PMCID: PMC8719170 DOI: 10.3389/fgene.2021.760760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors almost 50 ethnic groups including the Uyghur (UGR: 45.84%), Han (HAN: 40.48%), Kazakh (KZK: 6.50%), Hui (HUI: 4.51%), Kyrgyz (KGZ: 0.86%), Mongol (MGL: 0.81%), Manchu (MCH: 0.11%), and Uzbek (UZK: 0.066%), which make it one of the most colorful regions with abundant cultural and genetic diversities. In our previous study, we established allelic frequency databases for 14 autosomal short tandem repeats (STRs) for four minority populations from XUARC (MCH, KGZ, MGL, and UZK) using the AmpFlSTR® Identifiler PCR Amplification Kit. In this study, we genotyped 2,121 samples using the GoldenEye™ 20A Kit (Beijing PeopleSpot Inc., Beijing, China) amplifying 19 autosomal STR loci for four major ethnic groups (UGR, HAN, KZK, and HUI). These groups make up 97.33% of the total XUARC population. The total number of alleles for all the 19 STRs in these populations ranged from 232 (HAN) to 224 (KZK). We did not observe any departures from the Hardy-Weinberg equilibrium (HWE) in these populations after sequential Bonferroni correction. We did find minimal departure from linkage equilibrium (LE) for a small number of pairwise combinations of loci. The match probabilities for the different populations ranged from 1 in 1.66 × 1023 (HAN) to 6.05 × 1024 (HUI), the combined power of exclusion ranged from 0.999 999 988 (HUI) to 0.999 999 993 (UGR), and the combined power of discrimination ranged from 0.999 999 999 999 999 999 999 983 (HAN) to 0.999 999 999 999 999 999 999 997 (UGR). Genetic distances, principal component analysis (PCA), STRUCTURE analysis, and the phylogenetic tree showed that genetic affinity among studied populations is consistent with linguistic, ethnic, and geographical classifications.
Collapse
Affiliation(s)
- Atif Adnan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, China
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Kingdom of Saudi Arabia
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Adeel Anwar
- Department of Orthopedic Surgery, The 3rd Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Halimureti Simayijiang
- Department of Forensic Medicine, School of Basic Medical Sciences, Binzhou Medical University, Yantai, China
| | - Noor Farrukh
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jin-Feng Xuan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, China
| |
Collapse
|
3
|
Mateen RM, Sabar MF, Hussain S, Parveen R, Hussain M. Familial DNA analysis and criminal investigation: Usage, downsides and privacy concerns. Forensic Sci Int 2020; 318:110576. [PMID: 33234348 DOI: 10.1016/j.forsciint.2020.110576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/07/2020] [Accepted: 11/01/2020] [Indexed: 02/08/2023]
Abstract
Since the discovery of Deoxyribonucleic acid (DNA) capability in forensic investigation, it has been an important part of the criminal justice system. In most criminal cases DNA profile originating from evidence sample collected from the crime scene is compared with the DNA profile from the reference sample. However, when a reference sample is not available for comparison, familial DNA analysis can provide important investigation leads in a criminal investigation process by identifying an individual. Moreover, this analysis is also proving effective in the identification of ethnicity and ancestry of an individual. A number of different methodologies and software are being used for familial DNA analysis. This review describes the importance of familial DNA analysis, methodologies used for familial DNA searching and identification, and its advantages in forensic. Moreover, ethical, legal and social issues associated with familial DNA analysis have also been discussed along with future directions for the proper implementation of this technology.
Collapse
Affiliation(s)
- Rana Muhammad Mateen
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | | | - Safdar Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Rukhsana Parveen
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Manzoor Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| |
Collapse
|
4
|
Rubab A, Shafique M, Javed F, Saleem S, Zahra FT, McNevin D, Shahid AA. Population genetic portrait of Pakistani Lahore-Christians based on 32 STR loci. Sci Rep 2020; 10:18960. [PMID: 33144642 PMCID: PMC7609739 DOI: 10.1038/s41598-020-76016-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/22/2020] [Indexed: 11/30/2022] Open
Abstract
Phylogenetic relationship and the population structure of 500 individuals from the Christian community of Lahore, Pakistan, were examined based on 15 autosomal short tandem repeats (STRs) using the AmpFℓSTR Identifiler Plus PCR Amplification Kit and our previously published Y-filer kit data (17 Y-STRs) of same samples. A total of 147 alleles were observed in 15 loci and allele 11 at the TPOX locus was the most frequent with frequency value (0.464). The data revealed that the Christian population has unique genetic characteristics with respect to a few unusual alleles and their frequencies relative to the other Pakistani population. Significant deviations from Hardy–Weinberg equilibrium were found at two loci (D13S317, D18S51) after Boneferroni’s correction (p ≤ 0.003). The combined power of discrimination, combined power of exclusion and cumulative probability of matching were 0.999999999999999978430815060354, 0.999995039393942 and 2.15692 × 10−17, respectively. On the bases of genetic distances, PCA, phylogenetic and structure analysis Lahore-Christians appeared genetically more associated to south Asian particularly Indian populations like Tamil, Karnataka, Kerala and Andhra Pradesh than rest of global populations.
Collapse
Affiliation(s)
- Aqsa Rubab
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Muhammad Shafique
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan.
| | - Faqeeha Javed
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Samia Saleem
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Fatima Tuz Zahra
- School of Biomedical Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Dennis McNevin
- Centre for Forensic Science, University of Technology Sydney, Ultimo, Australia
| | - Ahmad Ali Shahid
- Forensic DNA Typing Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| |
Collapse
|
5
|
Adnan A, Rakha A, Nazir S, Rehman Z, Lu J, Xuan JF. Genetic characterization of 15 autosomal STRs in the interior Sindhi population of Pakistan and their phylogenetic relationship with other populations. Int J Immunogenet 2019; 47:149-157. [PMID: 31657139 DOI: 10.1111/iji.12458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 09/02/2019] [Accepted: 09/18/2019] [Indexed: 11/28/2022]
Abstract
Genetic structure of a population can be influenced by evolutionary processes and cultural histories which can alter the frequencies of different variants at particular genetic markers. These characteristics make DNA evidence suitable for forensic applications. Little relevant data are available from the interior Sindhi population; thus, in the current study, we have investigated 15 autosomal STRs in 181 unrelated individuals belonging to the interior parts of Sindh Pakistan, to establish its lineage and parameters of forensic interest. These STRs revealed a high power of discrimination (CPD), power of exclusion (CPE) and matching probability (CMP) are 0.9999999999999999968997, 0.99998612 and 3.1003 × 10-18 respectively. The genetic distances, neighbour-joining (NJ) tree, interactivity test and principal component analysis (PCA) based on 15 autosomal STR loci showed that the interior Sindhi population had a closer genetic relationship with Pakistani populations and distant relationships with regional (India and Afghanistan) populations. The present findings exhibited that STRs included in AmpFLSTR Identifiler kit (Applied Biosystems) are genetically polymorphic in the interior Sindhi population of Pakistan. This study provides valuable population genetic data for the genetic information study, forensic human individual identification and paternity testing.
Collapse
Affiliation(s)
- Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, China
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Ziaur Rehman
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Jie Lu
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, China
| | - Jin-Feng Xuan
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, Shenyang, China
| |
Collapse
|
6
|
Zhan X, Adnan A, Zhou Y, Khan A, Kasim K, McNevin D. Forensic characterization of 15 autosomal STRs in four populations from Xinjiang, China, and genetic relationships with neighboring populations. Sci Rep 2018; 8:4673. [PMID: 29549272 PMCID: PMC5856808 DOI: 10.1038/s41598-018-22975-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/05/2018] [Indexed: 11/29/2022] Open
Abstract
The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors 47 ethnic groups including the Manchu (MCH: 0.11%), Mongols (MGL: 0.81%), Kyrgyz (KGZ: 0.86%) and Uzbek (UZK: 0.066%). To establish DNA databases for these populations, allele frequency distributions for 15 autosomal short tandem repeat (STR) loci were determined using the AmpFlSTR Identifiler PCR amplification kit. There was no evidence of departures from Hardy-Weinberg equilibrium (HWE) in any of the four populations and minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The probabilities of identity for the different populations ranged from 1 in 1.51 × 1017 (MCH) to 1 in 9.94 × 1018 (MGL), the combined powers of discrimination ranged from 0.99999999999999999824 (UZK) to 0.9999999999999999848 (MCH) and the combined probabilities of paternal exclusion ranged from 0.9999979323 (UZK) to 0.9999994839 (MCH). Genetic distances, a phylogenetic tree and principal component analysis (PCA) revealed that the MCH, KGZ and UZK are genetically closer to the Han population of Liaoning and the Mongol population of Mongolia while the MGL are closer to Han, Japanese, Korean, Malaysian, Hong Kong Han and Russians living in China.
Collapse
Affiliation(s)
- Xiaoni Zhan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China
| | - Atif Adnan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China.
| | - Yuzhang Zhou
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China
| | - Amjad Khan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China
| | - Kadirya Kasim
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China
| | - Dennis McNevin
- National Centre for Forensic Studies, Faculty of Science & Technology, University of Canberra, Canberra, Australia
| |
Collapse
|
7
|
Genetic distribution of 15 autosomal STR markers in the Punjabi population of Pakistan. Int J Legal Med 2016; 130:1487-1488. [DOI: 10.1007/s00414-016-1351-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/25/2016] [Indexed: 11/25/2022]
|