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Connell JR, Benton MC, Lea RA, Sutherland HG, Haupt LM, Wright KM, Griffiths LR. Evaluating the suitability of current mitochondrial DNA interpretation guidelines for multigenerational whole mitochondrial genome comparisons. J Forensic Sci 2022; 67:1766-1775. [PMID: 35855536 PMCID: PMC9543078 DOI: 10.1111/1556-4029.15097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/06/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022]
Abstract
Sanger sequencing of the mitochondrial DNA (mtDNA) control region was previously the only method available for forensic casework involving degraded samples from skeletal remains. The introduction of Next Generation Sequencing (NGS) has transformed genetic data generation and human identification using mtDNA. Whole mitochondrial genome (mtGenome) analysis is now being introduced into forensic laboratories around the world to analyze historical remains. Research into large pedigrees using the mtGenome is critical to evaluate currently available interpretation guidelines for mtDNA analysis, which were developed for comparisons using the control region. This study included mtGenomes from 225 individuals from the last four generations of the Norfolk Island (NI) genetic isolate pedigree consisting of 49 distinct maternal lineages. The data from these individuals were arranged into 2339 maternally related pairs separated by up to 18 meioses. Our results show that 97.3% of maternally related pairs were concordant at all nucleotide positions, resulting in the correct interpretation of “Cannot Exclude”; 2.7% of pairs produced an “Inconclusive” result, and there were no instances of false exclusion. While these results indicate that existing guidelines are suitable for multigenerational whole mtGenome analysis, we recommend caution be taken when classifying heteroplasmic changes as differences for human identification. Our data showed the classification of heteroplasmic changes as differences increases the prevalence of inconclusive identification by 6%, with false exclusions observed in 0.34% of pairs examined. Further studies of multigenerational pedigrees, however, are needed to validate mtGenome interpretation guidelines for historical case work to more fully utilize emerging advancements.
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Affiliation(s)
- Jasmine R Connell
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Miles C Benton
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia.,Human Genomics, Kenepuru Science Centre, Institute of Environmental Science and Research, Wellington, New Zealand
| | - Rodney A Lea
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Heidi G Sutherland
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Kirsty M Wright
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia.,Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, ACT, Australia.,Royal Australian Air Force (RAAF), Headquarters History and Heritage, Unrecovered War Casualties-Air Force, Russell, ACT, Australia
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
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Mitochondrial Haplogroup Classification of Ancient DNA Samples Using Haplotracker. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5344418. [PMID: 35342764 PMCID: PMC8956381 DOI: 10.1155/2022/5344418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/17/2022] [Accepted: 02/26/2022] [Indexed: 11/17/2022]
Abstract
Mitochondrial DNA haplogroup classification is used to study maternal lineage of ancient human populations. The haplogrouping of ancient DNA is not easy because the DNA is usually found in small pieces in limited quantities. We have developed Haplotracker, a straightforward and efficient high-resolution haplogroup classification tool optimized specifically for ancient DNA samples. Haplotracker offers a user-friendly input interface for multiple mitochondrial DNA sequence fragments in a sample. It provides accurate haplogroup classification with full-length mitochondrial genome sequences and provides high-resolution haplogroup predictions for some fragmented control region sequences using a novel algorithm built on Phylotree mtDNA Build 17 (Phylotree) and our haplotype database (n = 118,869). Its performance for accuracy was demonstrated to be high through haplogroup classification using 8,216 Phylotree full-length and control region mitochondrial DNA sequences compared with HaploGrep 2, one of the most accurate current haplogroup classifiers. Haplotracker provides a novel haplogroup tracking solution for fragmented sequences to track subhaplogroups or verify the haplogroups efficiently. Using Haplotracker, we classified mitochondrial haplogroups to the final subhaplogroup level in nine ancient DNA samples extracted from human skeletal remains found in 2,000-year-old elite Xiongnu cemetery in Northeast Mongolia. Haplotracker can be freely accessed at https://haplotracker.cau.ac.kr.
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Siddiqi MH, Rakha A, Khan K, Akhtar T. Current pool of ultimate collection of mitochondrial DNA from remnants of Kalash. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2410-2414. [PMID: 34345711 PMCID: PMC8284132 DOI: 10.1080/23802359.2021.1952119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The mitochondrial DNA (mtDNA) complete control region coverage of 111 individuals from Kalash population of Pakistan has been presented for forensic applications and to infer their genetic parameters. We detected in total 14 different haplotypes with only five unique and nine shared by more than one individual. This population has come up with quite lower haplotype diversity (0.8393) and very higher random match probability (0.1682), and ultimately lower power of discrimination (0.832). Additionally, haplogroup distribution reveals the genetic ancestry of Kalash, mainly from West Eurasia (98.8%) and very little from South Asia (0.9%). Neither African lineages nor East Asian genetic segments were detected among these Kalash. This study will contribute to the database development for forensic applications as well as to track the evolutionary highlights of this ethnic group.
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Affiliation(s)
- Muhammad Hassan Siddiqi
- Department of Zoology, University of the Punjab, Lahore, Pakistan.,Department of Zoology, Government College Women University, Sialkot, Pakistan
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Khushbukhat Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Tanveer Akhtar
- Department of Zoology, University of the Punjab, Lahore, Pakistan
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Hanif F, Amir QUA, Washdev W, Bilwani F, Simjee SU, Haque Z. A Novel Variant in Dopamine Receptor Type 2 Gene is Associated with Schizophrenia. Arch Med Res 2020; 52:348-353. [PMID: 33187731 DOI: 10.1016/j.arcmed.2020.10.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/10/2020] [Accepted: 10/29/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND Being the primary target of antipsychotic therapy, dopamine receptor type 2 (DRD2) remains a point of interest in schizophrenia pathology. Polymorphisms in DRD2 have been shown to alter patients' response to antipsychotics. DRD2 SNP rs6275 (C>T) have found to be associated with schizophrenia in different populations; however, data remains inconsistent. AIM OF THE STUDY Keeping in view the genetic diversity the present study was aimed to explore association of rs6275 with schizophrenia in population from Pakistan. METHOD Using Diagnostic and statistical Manual 5 (DSM 5) criteria, 100 schizophrenia cases and 100 controls (individuals without any psychiatric illness) were enrolled in the study. Severity of illness was determined using PANSS score. Genotyping was done via Sanger sequencing. MEGA-X was used to align the sequences, Expasy translate tool was used to translate nucleotide sequences. Difference in genotype and allele frequencies between cases and controls was determined using χ2 test. RESULT No significant difference in genotype or allele frequencies of rs6275 (p >0.0.5) was found between cases and controls. Interestingly, a novel SNP (C>A, Pro297Thr) was spotted during electropherogram analysis at position chr11:113412805. Significant difference was found in genotype and allele frequency of this novel SNP among schizophrenia cases and controls (p = 0.003). CONCLUSION No association of rs6275 was observed with schizophrenia in Pakistani population. However, the study found significant association of a novel missense SNP of DRD2 at chr11:113412805 (C>T) with schizophrenia in Pakistani population. A large-scale multicenter study will be required to confirm the association of this novel SNP with schizophrenia.
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Affiliation(s)
- Farina Hanif
- Institute of Biomedical Sciences, Dow University of Health Sciences, OJHA Campus, SUPARCO Road, Karachi, Pakistan.
| | - Qurat-Ul-Ain Amir
- Institute of Biomedical Sciences, Dow University of Health Sciences, OJHA Campus, SUPARCO Road, Karachi, Pakistan
| | - Washdev Washdev
- Institute of Behavioral Sciences, Dow University of Health Sciences, OJHA Campus SUPARCO Road, Karachi, Pakistan
| | - Fareena Bilwani
- Department of Biological and Biomedical Sciences, Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Shabana Usman Simjee
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zeba Haque
- Institute of Biomedical Sciences, Dow University of Health Sciences, OJHA Campus, SUPARCO Road, Karachi, Pakistan
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Systematic sequence analysis of the FUT3 gene identifies 11 novel alleles in the Sindhi and Punjabi populations from Pakistan. Sci Rep 2020; 10:5543. [PMID: 32218479 PMCID: PMC7099025 DOI: 10.1038/s41598-020-62524-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/16/2020] [Indexed: 11/16/2022] Open
Abstract
The FUT3 (Lewis) gene is responsible for the expression of Lewis fucosyltransferase, which is required for the synthesis of the structural determinants of both Lewisa and Lewisb specificity. These factors play an important role not only in clinical but also in medico-legal investigations. The gene sequence is highly polymorphic and ethnically specific. In the current study, we performed systematic sequence analysis of the coding region of FUT3 by DNA sequencing to investigate the genetic variations of FUT3 and the molecular basis of the Lewis phenotype in the Sindhi and Punjabi populations of Pakistan. Twenty-three point mutations were observed, including 7 unreported mutations, among which two missense mutations (490 G > A and 959 T > C) were predicted to be deleterious to enzyme activity by software assessment. In total, we observed 24 Lewis alleles, including 11 novel ones. However, all unreported missense mutations were present in Lewis-negative alleles confirmed previously. According to genotypic data, the Lewis-negative phenotypic frequencies were 11.5% and 22.93% in the Sindhi and Punjabi ethnic groups, respectively. Moreover, we found that le202,314 and le59,1067 were predominant among Lewis-negative alleles, while the frequency of le59,1067 in the Punjabi population was significantly higher than that in the Sindhi population. In summary, our study revealed that there is a relatively high degree of sequence variation of the Lewis gene in Pakistani populations and provided the first genetic data on FUT3 in these two ethnic groups from Pakistan. The allele types and their frequencies showed that these ethnic groups exhibit more Caucasian components.
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Mitochondrial DNA control region variants analysis in Balti population of Gilgit-Baltistan, Pakistan. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Wei YY, Ren ZP, Jin XY, Cui W, Chen C, Guo YX, Meng HT, Zhu BF. Haplogroup Structure and Genetic Variation Analyses of 60 Mitochondrial DNA Markers in Southern Shaanxi Han Population. Biochem Genet 2019; 58:279-293. [PMID: 31696339 DOI: 10.1007/s10528-019-09942-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 10/24/2019] [Indexed: 12/30/2022]
Abstract
Mitochondrial DNA (mtDNA) has been widely employed as one tool for the studies of human migration and phylogenetic evolution owing to the characteristics of its lack of recombination and matrilineal inheritance. In this study, we analyze genetic distributions of 60 mtDNA markers in 126 unrelated individuals of Southern Shaanxi Han population and classify their haplogroups. Genetic distribution comparisons between Southern Shaanxi Han and other populations from different continents are conducted based on the same mtDNA markers. The majority of 60 mtDNA markers are polymorphic in Southern Shaanxi Han population. The most common haplogroups observed in Southern Shaanxi Han population are B5, followed by D5, A, D4e, and N9a1'3. Obtained matching probability for these 60 mtDNA markers indicates that the panel could be used as a valuable tool in forensic caseworks. Results of genetic distances (Fst) and multidimensional scaling analysis show that Southern Shaanxi Han population has relatively close genetic relationships with other Han populations in different regions. In conclusion, the panel comprising 60 mtDNA markers could be utilized for forensic applications in Southern Shaanxi Han population.
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Affiliation(s)
- Yuan-Yuan Wei
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Zhan-Ping Ren
- Department of Cranio-Maxillofacial Trauma Plastic Surgery, Stomatology Hospital of Xi'an Jiaotong University College of Medicine, Xi'an, China
| | - Xiao-Ye Jin
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wei Cui
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chong Chen
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yu-Xin Guo
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Hao-Tian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Bo-Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China. .,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China. .,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China.
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Khidri FF, Waryah YM, Ali FK, Shaikh H, Ujjan ID, Waryah AM. MTHFR and F5 genetic variations have association with preeclampsia in Pakistani patients: a case control study. BMC MEDICAL GENETICS 2019; 20:163. [PMID: 31646966 PMCID: PMC6813118 DOI: 10.1186/s12881-019-0905-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 10/02/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND To study the role of single nucleotide variants (SNVs) of genes related to preeclampsia in Pakistani pregnant women. METHODS After ethical approval and getting informed consent; 250 pregnant women were enrolled and equally divided into two groups (125 preeclamptic cases and 125 normotensive pregnant women). Demographic details and medical history were recorded, and 10 ml blood sample was obtained for DNA extraction. The tetra-primer amplification refractory mutation system (ARMS) assays were developed for assessing the variants of three preeclampsia related genes; F5, MTHFR and VEGFA. An association of six SNVs; F5:c.1601G > A (rs6025), F5:c.6665A > G (rs6027), MTHFR: c.665C > T (rs1801133), MTHFR: c.1286A > C (rs1801131), VEGFA: c.-2055A > C (rs699947) and VEGFA: c.*237C > T (rs3025039) with preeclampsia was determined by using different genetic models. RESULTS Genotyping of the SNVs revealed that patients with MTHFR:c.665C > T, have increased susceptibility to preeclampsia (CT versus CC/TT: OR = 2.79, 95% CI = 1.18-6.59; P* = 0.046 and CT/TT vs CC: OR = 2.91, 95% CI = 1.29-6.57; P* = 0.0497, in overdominant and dominant models, respectively), whereas F5:c.6665A > G, (A/G vs AA/GG: OR = 0.42, 95% CI = 0.21-0.84; P* = 0.038 in overdominant model) and MTHFR:c.1286A > C, (CC versus AA: OR = 0.36, 95% CI = 0.18-0.72; P* = 0.0392 in codominant model) have significantly decreased risk for preeclampsia. F5:c.1601G > A, VEGFA: c.-2055A > C and VEGFA: c.*237C > T variants revealed no relationship with the disease. CONCLUSION This is the first case control study describing the protective role of F5:c.6665A > G against preeclampsia in any world population. In addition, the present study confirmed the association and role of MTHFR gene variations in the development of preeclampsia in Pakistani patients. Further genetic studies may be required to better understand the complex genetic mechanism of SNVs in preeclampsia related genes in pregnant women.
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Affiliation(s)
- Feriha Fatima Khidri
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
- Department of Biochemistry, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Yar Muhammad Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
- Department of Chemistry, Shaheed Benazir Bhutto University, Shaheed Benazir Abad, Pakistan
| | - Faiza Kamran Ali
- Department of Gynaecology and Obstetrics, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Hina Shaikh
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ikram Din Ujjan
- Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ali Muhammad Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan.
- Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan.
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Amorim A, Fernandes T, Taveira N. Mitochondrial DNA in human identification: a review. PeerJ 2019; 7:e7314. [PMID: 31428537 PMCID: PMC6697116 DOI: 10.7717/peerj.7314] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/18/2019] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial DNA (mtDNA) presents several characteristics useful for forensic studies, especially related to the lack of recombination, to a high copy number, and to matrilineal inheritance. mtDNA typing based on sequences of the control region or full genomic sequences analysis is used to analyze a variety of forensic samples such as old bones, teeth and hair, as well as other biological samples where the DNA content is low. Evaluation and reporting of the results requires careful consideration of biological issues as well as other issues such as nomenclature and reference population databases. In this work we review mitochondrial DNA profiling methods used for human identification and present their use in the main cases of humanidentification focusing on the most relevant issues for forensics.
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Affiliation(s)
- António Amorim
- Instituto Nacional de Medicina Legal e Ciências Forenses, Lisboa, Portugal
- Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Teresa Fernandes
- Escola de Ciências e Tecnologias, Universidade de Évora, Évora, Portugal
- Research Center for Anthropology and Health (CIAS), Universidade de Coimbra, Coimbra, Portugal
| | - Nuno Taveira
- Instituto Universitário Egas Moniz (IUEM), Almada, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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