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Feng Y, Chen L, Wang X, Zhang H, Wang Q, Liu Y, Jin X, Yang M, Huang J, Ren Z. Analysis of maternal genetic structure of mitochondrial DNA control region from Tai-Kadai-speaking Buyei population in southwestern China. BMC Genomics 2024; 25:50. [PMID: 38212691 PMCID: PMC10782584 DOI: 10.1186/s12864-023-09941-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Even though the Buyei are a recognised ethnic group in southwestern China, there hasn't been much work done on forensic population genetics, notably using mitochondrial DNA. The sequences and haplogroups of mitochondrial DNA control regions of the Buyei peoples were studied to provide support for the establishment of a reference database for forensic DNA analysis in East Asia. METHODS AND RESULTS The mitochondrial DNA control region sequences of 200 Buyei individuals in Guizhou were investigated. The haplotype frequencies and haplogroup distribution of the Buyei nationality in Guizhou were calculated. At the same time, the paired Fst values of the study population and other populations around the world were computed, to explore their genetic polymorphism and population relationship. A total of 179 haplotypes were detected in the Buyei population, with frequencies of 0.005-0.015. All haplotypes were assigned to 89 different haplogroups. The haplotype diversity and random matching probability were 0.999283 and 0.0063, respectively. The paired Fst genetic distances and correlation p-values among the 54 populations revealed that the Guizhou Buyei was most closely related to the Henan Han and the Guizhou Miao, and closer to the Hazara population in Pakistan and the Chiang Mai population. CONCLUSIONS The study of mitochondrial DNA based on the maternal genetic structure of the Buyei nationality in Guizhou will benefit the establishment of an East Asian forensic DNA reference database and provide a reference for anthropological research in the future.
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Grants
- KY No. [2021]065 Guizhou Province Education Department, Characteristic Region Project, Qian Education
- [2020] 4Y057 Guizhou Scientific Support Project, Qian Science Support
- No. 82160324 National Natural Science Foundation of China
- No. 82160324 National Natural Science Foundation of China
- [2020]6012 Guizhou "Hundred" High-level Innovative Talent Project, Qian Science Platform Talents
- KF202009 Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Open Project
- NO. [2016] 1345 Guizhou Engineering Technology Research Center Project, Qian High-Tech of Development and Reform Commission, NO. [2016] 1345
- [2020] 1Y353 Guizhou Science Project, Qian Science Foundation
- [2018] 5779-X Guizhou Scientific Cultivation Project, Qian Science Platform Talent
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Affiliation(s)
- Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Li Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaoxue Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China.
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China.
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Schurr TG, Shengelia R, Shamoon-Pour M, Chitanava D, Laliashvili S, Laliashvili I, Kibret R, Kume-Kangkolo Y, Akhvlediani I, Bitadze L, Mathieson I, Yardumian A. Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus). Genome Biol Evol 2023; 15:evad198. [PMID: 37935112 PMCID: PMC10665041 DOI: 10.1093/gbe/evad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/09/2023] Open
Abstract
To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.
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Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ramaz Shengelia
- Department of the History of Medicine, Tbilisi State Medical University, Tbilisi, Georgia
| | - Michel Shamoon-Pour
- First-year Research Immersion, Binghamton University, Binghamton, New York, USA
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Redate Kibret
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
| | - Yanu Kume-Kangkolo
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Aram Yardumian
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
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Uricoechea Patiño D, Collins A, García OJR, Santos Vecino G, Cuenca JVR, Bernal JE, Benavides Benítez E, Vergara Muñoz S, Briceño Balcázar I. High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia. Genes (Basel) 2023; 14:1853. [PMID: 37895202 PMCID: PMC10606881 DOI: 10.3390/genes14101853] [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: 08/09/2023] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.
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Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | - Jaime E. Bernal
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Escilda Benavides Benítez
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
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Rubin JD, Vogel NA, Gopalakrishnan S, Sackett PW, Renaud G. HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph human mtDNA haplogroup inference. PLoS Comput Biol 2023; 19:e1011148. [PMID: 37285390 DOI: 10.1371/journal.pcbi.1011148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 06/09/2023] Open
Abstract
Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the uncertainty in assignment. We present HaploCart, a probabilistic mtDNA haplogroup classifier which uses a pangenomic reference graph framework together with principles of Bayesian inference. We demonstrate that our approach significantly outperforms available tools by being more robust to lower coverage or incomplete consensus sequences and producing phylogenetically-aware confidence scores that are unbiased towards any haplogroup. HaploCart is available both as a command-line tool and through a user-friendly web interface. The C++ program accepts as input consensus FASTA, FASTQ, or GAM files, and outputs a text file with the haplogroup assignments of the samples along with the level of confidence in the assignments. Our work considerably reduces the amount of data required to obtain a confident mitochondrial haplogroup assignment.
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Affiliation(s)
- Joshua Daniel Rubin
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicola Alexandra Vogel
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Peter Wad Sackett
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gabriel Renaud
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
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5
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Ren Z, Feng Y, Zhang H, Wang Q, Yang M, Liu Y, Le C, Wang J, Huang J. Genetic analysis of the mitochondrial DNA control region in Tai-Kadai-speaking Dong population in southwest China. Ann Hum Biol 2022; 49:354-360. [PMID: 36190920 DOI: 10.1080/03014460.2022.2131334] [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] [Indexed: 11/01/2022]
Abstract
BACKGROUND Dong people in Southwest China are officially recognised as an ethnic group, but there has been a lack of population genetic research on this group, especially based on mitochondrial DNA data. AIM To study the sequences and haplogroups of the mitochondrial DNA control region in a typical Dong population, and to provide help for the construction of a forensic mitochondrial DNA analysis reference database in East Asia. SUBJECTS AND METHODS The sequences of the mitochondrial DNA control region were analysed in 200 individuals of Dong in Guizhou. The haplotype frequencies, haplogroup distribution and paired Fst values of Guizhou Dong and 51 other populations in the world were calculated and explained to explore the genetic polymorphism and population relationships. RESULTS A total of 180 haplotypes were detected, with frequencies of 0.005-0.02. All haplotypes were assigned to 97 different haplogroups. The haplotype diversity and random matching probability were 0.998643 and 0.00635, respectively. The paired Fst values and correlation p values of 52 populations showed that the Guizhou Dong had the closest genetic relationship with the Henan Han and the Guizhou Miao in China, and were closest to the Punjab population in Pakistan and the Kashmiri population when compared with the world populations. CONCLUSIONS Our study was based on the matrilineal genetic structure of Guizhou Dong to study mitochondrial DNA, which was helpful to promote the establishment of the forensic DNA reference database in East Asia and provide reference for anthropological research.
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Affiliation(s)
- Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Cuiyun Le
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Jie Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
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6
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Mitochondrial Control Region Variants Related to Breast Cancer. Genes (Basel) 2022; 13:genes13111962. [DOI: 10.3390/genes13111962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022] Open
Abstract
Breast cancer has an important incidence in the worldwide female population. Although alterations in the mitochondrial genome probably play an important role in carcinogenesis, the actual evidence is ambiguous and inconclusive. Our purpose was to explore differences in mitochondrial sequences of cases with breast cancer compared with control samples from different origins. We identified 124 mtDNA sequences associated with breast cancer cases, of which 86 were complete and 38 were partial sequences. Of these 86 complete sequences, 52 belonged to patients with a confirmed diagnosis of breast cancer, and 34 sequences were obtained from healthy mammary tissue of the same patients used as controls. From the mtDNA analysis, two polymorphisms with significant statistical differences were found: m.310del (rs869289246) in 34.6% (27/78) of breast cancer cases and 61.7% (21/34) in the controls; and m.315dup (rs369786048) in 60.2% (47/78) of breast cancer cases and 38.2% (13/34) in the controls. In addition, the variant m.16519T>C (rs3937033) was found in 59% of the control sequences and 52% of the breast cancer sequences with a significant statistical difference. Polymorphic changes are evolutionarily related to the haplogroup H of Indo-European and Euro-Asiatic origins; however, they were found in all non-European breast cancers.
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7
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Font-Porterias N, García-Fernández C, Aizpurua-Iraola J, Comas D, Torrents D, de Cid R, Calafell F. Sequence diversity of the uniparentally transmitted portions of the genome in the resident population of Catalonia. Forensic Sci Int Genet 2022; 61:102783. [DOI: 10.1016/j.fsigen.2022.102783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022]
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8
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Post hoc deconvolution of human mitochondrial DNA mixtures by EMMA 2 using fine-tuned Phylotree nomenclature. Comput Struct Biotechnol J 2022; 20:3630-3638. [PMID: 35860401 PMCID: PMC9283771 DOI: 10.1016/j.csbj.2022.06.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 11/23/2022] Open
Abstract
MtDNA mixtures are observed frequently and difficult to deconvolute. Most previous methods require raw data or quantitative information. EMMA 2 produces valid splittings from consensus sequences of any sequencing technology. EMMA 2 can deconvolute 2 and 3 person mixtures in a fast and traceable way.
In this paper we present a new algorithm for splitting (partial) human mitogenomes into components with high similarity to haplogroup motifs of Phylotree. The algorithm reads a (partial) mitogenome coded by the differences to the reference (rCRS) and outputs the estimated haplogroups of the putative components. The algorithm requires no special information on the raw data of the sequencing process and is therefore suited for the post hoc analysis of mixtures of any sequencing technology. The software EMMA 2 implementing the algorithm will be made available via the EMPOP (https://empop.online) database and extends the nine years old software EMMA for haplogrouping single mitogenomes to mixtures with at most three components.
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Kristjansson D, Bohlin J, Nguyen TT, Jugessur A, Schurr TG. Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography. BMC Genomics 2022; 23:354. [PMID: 35525961 PMCID: PMC9080151 DOI: 10.1186/s12864-022-08572-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/20/2022] [Indexed: 12/28/2022] Open
Abstract
Background We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondrial DNA (mtDNA) haplogroup U5, which appears at high frequencies in northern Europe. Methods Haplogroup U5 mitogenome sequences were gathered from GenBank. The hierarchal Bayesian Analysis of Population Structure (hierBAPS) method was used to generate groups of sequences that were then projected onto a rooted maximum likelihood (ML) phylogenetic tree to visualize the pattern of clustering. The haplogroup statuses of the individual sequences were assessed using Haplogrep2. Results A total of 23 hierBAPS groups were identified, all of which corresponded to subclades defined in Phylotree, v.17. The hierBAPS groups projected onto the ML phylogeny accurately clustered all haplotypes belonging to a specific haplogroup in accordance with Haplogrep2. By incorporating the geographic source of each sequence and subclade age estimates into this framework, inferences about the diversification of U5 mtDNAs were made. Haplogroup U5 has been present in northern Europe since the Mesolithic, and spread in both eastern and western directions, undergoing significant diversification within Scandinavia. A review of historical and archeological evidence attests to some of the population interactions contributing to this pattern. Conclusions The hierBAPS algorithm accurately grouped mitogenome sequences into subclades in a phylogenetically robust manner. This analysis provided new insights into the phylogeographic structure of haplogroup U5 diversity in northern Europe, revealing a detailed perspective on the diversity of subclades in this region and their distribution in Scandinavian populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08572-y.
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Affiliation(s)
- Dana Kristjansson
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Jon Bohlin
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Truc Trung Nguyen
- IT Systems Bergen, Norwegian Institute of Public Health, Bergen, Norway
| | - Astanand Jugessur
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA
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Huszar TI, Bodmer WF, Hutnik K, Wetton JH, Jobling MA. Sequencing of autosomal, mitochondrial and Y-chromosomal forensic markers in the People of the British Isles cohort detects population structure dominated by patrilineages. Forensic Sci Int Genet 2022; 59:102725. [DOI: 10.1016/j.fsigen.2022.102725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/08/2022] [Accepted: 05/13/2022] [Indexed: 11/27/2022]
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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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Xin Y, Jia R, Zhang S, Guo F. Mitochondrial genome sequencing with short overlapping amplicons on MiSeq FGx system. Forensic Sci Res 2021; 7:142-153. [PMID: 35784421 PMCID: PMC9246037 DOI: 10.1080/20961790.2021.1963514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/03/2022] Open
Abstract
With the development and maturation of massively parallel sequencing (MPS) technology, the mitochondrial genome (mitogenome) sequencing is increasingly applied in the forensic field. In this study, we employed the strategy of short overlapping amplicons for the whole mitogenome, library preparation with tagmentation using the Nextera® XT DNA Library Preparation Kit, sequencing on the MiSeq FGxTM Forensic Genomics System and analyzing data using the mitochondrial(mtDNA) MSR Plug-in and the mtDNA Variant Analyzer. A total of 27 libraries and 56 libraries were sequenced in a run using MiSeq Reagent Kit v2 and v3, respectively. Results showed more than 1800 × of averaged depth of coverage (DoC) at each position. Concordant haplotypes of 9947 A and 2800 M were obtained at 32 variants. Cross-reactivity was observed with 1 ng primate DNA and 10 ng non-primate DNA but could be easily distinguished. Full and accurate variants were obtained from at least 50 pg input DNA and from minor contributors between 19:1 and 1:19 mixed ratios with known reference profiles. More than 86% variants were detected from ≥200-bp degraded samples but its haplotype was assigned to more ancestral haplogroup. Further, a total of 3 962 variants were observed at 613 nucleotide positions from 103 Xibe mitogenomes with 25:1 ratio of transitions to transversions. Two new transversions (C13735A and A14755C) and two tri-alleles at nps 9824 and 16092 were identified. There were 103 unique mitogenome haplotypes from 103 Chinese Xibe that were assigned to 79 haplogroups. Haplogroup D was the preponderant top-level haplogroup in Xibe followed by F, B, M, A, N, G, C, Z, Y, HV and J. Random match probability (RMP) and haplotype diversity (HD) of the whole mitogenome was calculated as 0.0097 and 1.0000, respectively. Compared with HVS-I only, RMP decreased 33.56%, while the number of haplotypes and HD increased 15.73% and 0.49%, respectively. Principal component analysis (PCA) showed that Xibe was clustered to East and Southeast Asian. As a whole, this MPS strategy is suitable for the whole mitogenome sequencing especially for degraded samples and can facilitate generating mitogenome data to support the routine application in forensic sciences. EMP00726 is the first whole mitogenome dataset from Xibe contributed to the EMPOP. Supplemental data for this article are available online at.
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Affiliation(s)
- Yang Xin
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
| | - Rulin Jia
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Fei Guo
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
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13
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Feng Y, Zhang H, Wang Q, Yang M, Liu Y, Wang Jie, Huang J, Ren Z. The mitochondrial DNA control region sequences from the Chinese Sui population of southwestern China. Ann Hum Biol 2021; 48:635-640. [PMID: 34663140 DOI: 10.1080/03014460.2021.1994649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Sui people are officially recognised people living in southwest China, but there has been a lack of genetic research, especially based on mitochondrial DNA data. AIM To study the sequences and haplogroups of the mitochondrial DNA control region in a typical Sui population, with the aim of helping to promote the establishment of a forensic DNA analysis reference database in East Asia. SUBJECTS AND METHODS We analysed 201 Sui individuals and observed the sequences of the mitochondrial DNA control region. We calculated and explained the haplotype frequencies, haplogroup distribution and pairwise Fst values between the Sui and 47 other populations in the world, in order to explore genetic polymorphisms and population relationships. RESULTS 161 haplotypes were found in the Sui population, with frequencies of 0.0049-0.0199. All samples were assigned to 80 different haplogroups. The haplotype diversity and random matching probability were 0.999938 and 0.024729, respectively. The pairwise Fst values and correlation p-values of 48 populations showed that the Sui population was most closely related to the Miao population in Guizhou and the Han population in Henan, and closer to the Punjab population and Pukhtunkhwa population in Pakistan, and was significantly different from the other 43 groups. Compared with the other 43 groups, it is relatively isolated. CONCLUSION Our results show that the study of mitochondrial DNA based on the analysis of matrilineal genetic structure of the Sui population can help to promote the establishment of a forensic DNA reference database in East Asia and provide reference for future anthropological research.
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Affiliation(s)
- Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Wang Jie
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
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14
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García-Olivares V, Muñoz-Barrera A, Lorenzo-Salazar JM, Zaragoza-Trello C, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Iñigo-Campos A, González-Montelongo R, Flores C. A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data. Sci Rep 2021; 11:20510. [PMID: 34654896 PMCID: PMC8519921 DOI: 10.1038/s41598-021-99895-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships. Because of this and the advent of high-throughput sequencing (HTS) technology, there is a diversity of bioinformatic tools for haplogroup classification. We present a benchmarking of the 11 most salient tools for human mtDNA classification using empirical whole-genome (WGS) and whole-exome (WES) short-read sequencing data from 36 unrelated donors. We also assessed the best performing tool in third-generation long noisy read WGS data obtained with nanopore technology for a subset of the donors. We found that, for short-read WGS, most of the tools exhibit high accuracy for haplogroup classification irrespective of the input file used for the analysis. However, for short-read WES, Haplocheck and MixEmt were the most accurate tools. Based on the performance shown for WGS and WES, and the accompanying qualitative assessment, Haplocheck stands out as the most complete tool. For third-generation HTS data, we also showed that Haplocheck was able to accurately retrieve mtDNA haplogroups for all samples assessed, although only after following assembly-based approaches (either based on a referenced-based assembly or a hybrid de novo assembly). Taken together, our results provide guidance for researchers to select the most suitable tool to conduct the mtDNA analyses from HTS data.
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Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - José M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - Luis A Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
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15
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Genetic characterization of a collection of Tsantsas from Ecuadorian museums. Forensic Sci Int 2021; 325:110879. [PMID: 34174769 DOI: 10.1016/j.forsciint.2021.110879] [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: 02/13/2021] [Revised: 05/17/2021] [Accepted: 06/11/2021] [Indexed: 11/22/2022]
Abstract
Tsantsas are shrunken human heads originally made for ceremonial purposes by Amazonian indigenous groups of the Shuar and Achuar family, previously called Jivaroan tribes. A significant demand of these objects during the first half of the 20th century led to the manufacture of counterfeit shrunken heads for commercial purposes. For museums where these collections are held, as well as for the indigenous groups who claim their ownership, it is important to identify the origin and authenticity of these tsantsas. We hypothesized that a collection of 14 tsantsas from 3 different museum collections in Ecuador are human and aimed to characterize their sex and potential origin. We amplified the amelogenin gene and performed a high resolution melting analysis to determine their human origin and characterize their sex. We also analyzed a fragment (16209-16402) from the HVR-1 region to identify the mtDNA haplogroups present in the tsantsa collection. Our exploratory results show that all the tsantsas are human and that the collection is comprised of 13 males and 1 female. A total of seven mtDNA haplogroups were found among the tsantsa collection using the mtDNA EMPOP database. These results show a predominance of the Amerindian mtDNA haplogroups B, C and D. Additional principal component analysis, genetic distance tree and haplotype network analyses suggest a relationship between the tsantsa specimens and Native American groups.
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16
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Chierto E, Cena G, Mann RW, Mattutino G, Nuzzolese E, Robino C. Sweet tooth: DNA profiling of a cranium from an isolated retained root fragment. J Forensic Sci 2021; 66:1973-1979. [PMID: 34106477 PMCID: PMC8453871 DOI: 10.1111/1556-4029.14748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/21/2021] [Indexed: 11/29/2022]
Abstract
Sampling of healthy multi‐rooted teeth is recommended for the genetic identification of human skeletal remains. However, this may not always be possible, as in the reported case consisting of an isolated human cranium found in an aggregate crushing and processing plant in Piedmont, Northwest Italy. The cranium displayed significant weathering, suggesting a post‐mortem interval of several years, and was edentulous with the exception of the apical root fragment of the upper left canine, consequence of an antemortem horizontal fracture. Prolonged decalcification of the root fragment followed by powder‐free DNA extraction from ~10 mg of root tip tissue led to the recovery of >10 ng of high molecular weight human DNA, in comparison with ~0.01 ng of DNA per mg of bone powder obtained from the petrous portion of the temporal bone. Quantity and quality of DNA isolated from apical tooth tissue enabled multiple genotyping, including a reportable female STR profile, mitochondrial DNA analysis, and ancestry‐informative insertion/deletion polymorphisms. Although the cranium remained unidentified after DNA comparisons, our findings confirm that apical tooth tissue is a promising source of DNA, easily obtained through a powder‐free extraction protocol. Results also indicate that root tips should not be overlooked in challenging identification cases, even in the presence of compromised tooth specimens.
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Affiliation(s)
- Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Greta Cena
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Robert W Mann
- John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Grazia Mattutino
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Emilio Nuzzolese
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
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17
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Jagadeesan A, Ebenesersdóttir SS, Guðmundsdóttir VB, Thordardottir EL, Moore KHS, Helgason A. HaploGrouper: a generalized approach to haplogroup classification. Bioinformatics 2021; 37:570-572. [PMID: 32805011 DOI: 10.1093/bioinformatics/btaa729] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans. RESULTS HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species-given an extant annotated phylogenetic tree defined by sequence variants. AVAILABILITY AND IMPLEMENTATION The software is available at the following URL https://gitlab.com/bio_anth_decode/haploGrouper. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anuradha Jagadeesan
- deCODE Genetics/Amgen, Reykjavik 101, Iceland.,Department of Anthropology, University of Iceland, Reykjavik 101, Iceland
| | - S Sunna Ebenesersdóttir
- deCODE Genetics/Amgen, Reykjavik 101, Iceland.,Department of Anthropology, University of Iceland, Reykjavik 101, Iceland
| | - Valdis B Guðmundsdóttir
- deCODE Genetics/Amgen, Reykjavik 101, Iceland.,Department of Anthropology, University of Iceland, Reykjavik 101, Iceland
| | | | | | - Agnar Helgason
- deCODE Genetics/Amgen, Reykjavik 101, Iceland.,Department of Anthropology, University of Iceland, Reykjavik 101, Iceland
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18
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Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences. Int J Mol Sci 2021; 22:ijms22115747. [PMID: 34072215 PMCID: PMC8198973 DOI: 10.3390/ijms22115747] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/21/2022] Open
Abstract
In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible.
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19
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The analysis of ancestry with small-scale forensic panels of genetic markers. Emerg Top Life Sci 2021; 5:443-453. [PMID: 33949669 DOI: 10.1042/etls20200327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/07/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022]
Abstract
In the last 10 years, forensic genetic analysis has been extended beyond identification tests that link a suspect to crime scene evidence using standard DNA profiling, to new supplementary tests that can provide information to investigators about a suspect in the absence of a database hit or eyewitness testimony. These tests now encompass the prediction of physical appearance, ancestry and age. In this review, we give a comprehensive overview of the full range of DNA-based ancestry inference tests designed to work with forensic contact traces, when the level of DNA is often very low or highly degraded. We outline recent developments in the design of ancestry-informative marker sets, forensic assays that use capillary electrophoresis or massively parallel sequencing, and the statistical analysis frameworks that examine the test profile and compares it to reference population variation. Three casework ancestry analysis examples are described which were successfully accomplished in the authors' laboratory, where the ancestry information obtained was critical to the outcome of the DNA analyses made.
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20
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Melchionda F, Stanciu F, Buscemi L, Pesaresi M, Tagliabracci A, Turchi C. Searching the undetected mtDNA variants in forensic MPS data. Forensic Sci Int Genet 2020; 49:102399. [PMID: 33038616 DOI: 10.1016/j.fsigen.2020.102399] [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: 06/12/2020] [Revised: 08/27/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
The efficiency of MPS in forensic mtDNA analysis has been thoroughly proven, although a reliable and well established data evaluation still remains a critical point. Numerous bioinformatics tools have been developed, but most of them require specific operating systems and high costs, while free open-source programs with user-friendly interfaces are few. In this study, 43 full mtGenomes were sequenced using the Ion Personal Genome Machine™ (PGM™) System and analyzed utilizing the plug-in Variant Caller (TVC) of the Ion Torrent Software Suite and the mtDNA-Server (mDS), a free web-based mitochondrial analysis tool for MPS data. The outcomes of these two different analysis tools were compared to variants noted after manual inspection of the aligned reads performed using Integrative Genomics Viewer (IGV). The comparison highlighted the presence of thirty-nine discordant variant calls, which were resolved by Sanger sequencing that confirmed the presence of all variants, except for 7 deletions. The combined adoption of IGV and Sanger type sequencing confirmatory steps, in addition of TVC and mDS analysis, resulted in a more accurate variants assignment with the detection of 32 additional true polymorphisms, which were noted in the final dataset. Regarding the heteroplasmy issue, out of a total of thirty heteroplasmic variants, twenty-eight were detected by the TVC, while the mDS detected twenty-two. Overall, none of the used bioinformatics tools were the perfect choice and a secondary analysis with an expert's opinion in complete mtGenome MPS data evaluation is still required in forensic genetic analysis.
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Affiliation(s)
- Filomena Melchionda
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Florin Stanciu
- Romanian National DNA Database, National Forensic Science Institute, General Inspectorate of Romanian Police, Bucharest, Romania.
| | - Loredana Buscemi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Mauro Pesaresi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Adriano Tagliabracci
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Chiara Turchi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
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21
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Le C, Ren Z, Zhang H, Wang Q, Yang M, Liu Y, Huang J, Wang J. The mitochondrial DNA control region sequences from the Chinese Miao population of southeastern China. Ann Hum Biol 2019; 46:606-609. [PMID: 31775532 DOI: 10.1080/03014460.2019.1694701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: Miao people are an officially recognised ethnic group living in southwest China, but have seldom been studied genetically, especially with respect to mtDNA data.Aim: To investigate the sequences and haplogroups of the mtDNA control region in a typical Miao population, with the aim of providing a good start for the expansion of the East Asian mtDNA reference database for forensic DNA analysis.Subjects and methods: We analysed 203 Miao individuals, looking at mtDNA control region sequences. We calculated and illustrated the haplotype frequencies, haplogroup distribution and pairwise Fst values between the Miao and six other worldwide populations to explore genetic polymorphisms and population relationships.Results: We observed 121 haplotypes with corresponding frequencies ranging from 0.0049 to 0.0690 in the Miao population. All the samples were assigned to 71 different haplogroups. The haplotype diversity and the random match probability were estimated to be 0.9844 and 0.0204, respectively. The pairwise Fst values and associated p values among seven populations suggest that the Miao population has significant differences to the other six populations, and is relatively isolated compared with them.Conclusions: Our results suggest that frequency estimates for mtDNA haplotypes in Miao ethnic groups should be determined independently rather than being pooled with other populations.
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Affiliation(s)
- Cuiyun Le
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Jie Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
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22
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Resolving mitochondrial haplogroups B2 and B4 with next-generation mitogenome sequencing to distinguish Native American from Asian haplotypes. Forensic Sci Int Genet 2019; 43:102143. [DOI: 10.1016/j.fsigen.2019.102143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
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23
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Desmyter S, Dognaux S, Noel F, Prieto L. Base specific variation rates at mtDNA positions 16093 and 16183 in human hairs. Forensic Sci Int Genet 2019; 43:102142. [PMID: 31437782 DOI: 10.1016/j.fsigen.2019.102142] [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: 04/23/2019] [Revised: 07/25/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
Abstract
Small variations between haplotypes detected in different tissues from the same individual have been previously described. These differences complicate the interpretation of mtDNA results in real forensic casework. mtDNA haplotypes detected in hair strands collected at the crime scene have to be frequently compared with haplotypes of reference samples (buccal swabs) from victims or suspects. Nucleotide position 16093 is a well-known hot spot where differences can accumulate between different tissues of the same individual. Intra individual variation was also detected at positions 16182 and 16183 in haplotypes showing an uninterrupted HV1 poly-C stretch (with 16189C). In order to better characterize the type of variation in these positions between buccal cells and hair strands from the same individual, we have performed Sanger sequencing in 25-28 hair strands (411 in total) from 15 individuals showing either an uninterrupted HV1 polyC-stretch (16189C) or 16093C/Y in their buccal cells. The results have been evaluated by also taking into account our previous results published in [19]. We have found that no variation among hair strands was detected in individuals showing T16093 in buccal cells, while variation in hair strands (T16093, 16093C and 16093Y) were detected in individuals showing 16093C or 16093Y in buccal cells. Regarding nucleotide positions 16182 and 16183 in combination with an uninterrupted polyC-stretch, no variation was detected in hairs from individuals showing A16182 16183C in their buccal cells. In contrast, individuals A16182 A16183 showed hair strands with A16182 16183 M and A16182 16183C. And finally, individuals with 16182C 16183C showed some variation in a small amount of their hair strands (some hairs with 16182 M 16183C). These results can be relevant for forensic practitioners when comparing reference samples with hair strands, which is the type of sample most tested by using mtDNA analysis in forensic casework.
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Affiliation(s)
- Stijn Desmyter
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium.
| | - Sophie Dognaux
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
| | - Fabrice Noel
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
| | - Lourdes Prieto
- Instituto de Ciencias Forenses. Grupo de Medicina Xenómica. Universidade de Santiago de Compostela, Spain; Laboratorio ADN. Comisaría General de Policía Científica, Madrid, Spain
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24
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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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25
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Levinstein Hallak K, Tzur S, Rosset S. Big data analysis of human mitochondrial DNA substitution models: a regression approach. BMC Genomics 2018; 19:759. [PMID: 30340456 PMCID: PMC6195736 DOI: 10.1186/s12864-018-5123-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We study Phylotree, a comprehensive representation of the phylogeny of global human mitochondrial DNA (mtDNA) variations, to better understand the mtDNA substitution mechanism and its most influential factors. We consider a substitution model, where a set of genetic features may predict the rate at which mtDNA substitutions occur. To find an appropriate model, an exhaustive analysis on the effect of multiple factors on the substitution rate is performed through Negative Binomial and Poisson regressions. We examine three different inclusion options for each categorical factor: omission, inclusion as an explanatory variable, and by-value partitioning. The examined factors include genes, codon position, a CpG indicator, directionality, nucleotide, amino acid, codon, and context (neighboring nucleotides), in addition to other site based factors. Partitioning a model by a factor's value results in several sub-models (one for each value), where the likelihoods of the sub-models can be combined to form a score for the entire model. Eventually, the leading models are considered as viable candidates for explaining mtDNA substitution rates. RESULTS Initially, we introduce a novel clustering technique on genes, based on three similarity tests between pairs of genes, supporting previous results regarding gene functionalities in the mtDNA. These clusters are then used as a factor in our models. We present leading models for the protein coding genes, rRNA and tRNA genes and the control region, showing it is disadvantageous to separate the models of transitions/transversions, or synonymous/non-synonymous substitutions. We identify a context effect that cannot be attributed solely to protein level constraints or CpG pairs. For protein-coding genes, we show that the substitution model should be partitioned into sub-models according to the codon position and input codon; additionally we confirm that gene identity and cluster have no significant effect once the above factors are accounted for. CONCLUSIONS We leverage the large, high-confidence Phylotree mtDNA phylogeny to develop a new statistical approach. We model the substitution rates using regressions, allowing consideration of many factors simultaneously. This admits the use of model selection tools helping to identify the set of factors best explaining the mutational dynamics when considered in tandem.
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Affiliation(s)
- Keren Levinstein Hallak
- Department of Statistics and Operations Research, School of Mathematical Sciences, Tel-Aviv University, 6997801, Tel-Aviv, Israel
| | - Shay Tzur
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Saharon Rosset
- Department of Statistics and Operations Research, School of Mathematical Sciences, Tel-Aviv University, 6997801, Tel-Aviv, Israel.
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26
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Huber N, Parson W, Dür A. Next generation database search algorithm for forensic mitogenome analyses. Forensic Sci Int Genet 2018; 37:204-214. [PMID: 30241075 DOI: 10.1016/j.fsigen.2018.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA) variation is being reported relative to the corrected version of the first sequenced human mitochondrial genome. A review of the existing literature across disciplines that employ mtDNA demonstrates that insertions and deletions are not reported in a standardized way. This may lead to false exclusions of identical sequences, unidentified matches in missing persons mtDNA databases, biased mtDNA database frequency estimates and overestimation of the genetic evidence. Seven years ago we introduced alignment-free database search software (SAM) and implemented it into the mtDNA database EMPOP (https://empop.online) to produce reliable and conservative frequency estimates that are required in the forensic context. However, ambiguity remained in how laboratories have been reporting mitotypes, as often more than one single alignment of a given mtDNA sequence was feasible. In order to overcome this limitation we here describe a concept and provide software for producing stable, harmonized phylogenetic alignment of mtDNA sequences for database searches. The new software SAM 2 will be made available via EMPOP and provide the user with the already established conservative frequency estimates. In addition, SAM 2 offers the rCRS-coded haplotype of a given mtDNA sequence following the established and widely accepted phylogenetic alignment. This provides the user with feedback on how mitotypes are stored in EMPOP and how they should be reported in order to harmonize nomenclature. Finally, this approach does not only permit reliable mtDNA nomenclature in forensics but invites related disciplines to take advantage of a standardized way of reporting mtDNA variation, thus closing the ranks between different genetic fields and supporting dialogue and collaboration between mtDNA scholars from various disciplines.
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Affiliation(s)
- Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
| | - Arne Dür
- Institute of Mathematics, University of Innsbruck, Austria
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Juras A, Chyleński M, Ehler E, Malmström H, Żurkiewicz D, Włodarczak P, Wilk S, Peška J, Fojtík P, Králík M, Libera J, Bagińska J, Tunia K, Klochko VI, Dabert M, Jakobsson M, Kośko A. Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations. Sci Rep 2018; 8:11603. [PMID: 30072694 PMCID: PMC6072757 DOI: 10.1038/s41598-018-29914-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/19/2018] [Indexed: 11/22/2022] Open
Abstract
From around 4,000 to 2,000 BC the forest-steppe north-western Pontic region was occupied by people who shared a nomadic lifestyle, pastoral economy and barrow burial rituals. It has been shown that these groups, especially those associated with the Yamnaya culture, played an important role in shaping the gene pool of Bronze Age Europeans, which extends into present-day patterns of genetic variation in Europe. Although the genetic impact of these migrations from the forest-steppe Pontic region into central Europe have previously been addressed in several studies, the contribution of mitochondrial lineages to the people associated with the Corded Ware culture in the eastern part of the North European Plain remains contentious. In this study, we present mitochondrial genomes from 23 Late Eneolithic and Bronze Age individuals, including representatives of the north-western Pontic region and the Corded Ware culture from the eastern part of the North European Plain. We identified, for the first time in ancient populations, the rare mitochondrial haplogroup X4 in two Bronze Age Catacomb culture-associated individuals. Genetic similarity analyses show close maternal genetic affinities between populations associated with both eastern and Baltic Corded Ware culture, and the Yamnaya horizon, in contrast to larger genetic differentiation between populations associated with western Corded Ware culture and the Yamnaya horizon. This indicates that females with steppe ancestry contributed to the formation of populations associated with the eastern Corded Ware culture while more local people, likely of Neolithic farmer ancestry, contributed to the formation of populations associated with western Corded Ware culture.
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Affiliation(s)
- Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznań, Poland.
| | - Maciej Chyleński
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614, Poznań, Poland
| | - Edvard Ehler
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznań, Poland
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
| | - Danuta Żurkiewicz
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614, Poznań, Poland
| | - Piotr Włodarczak
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Sławkowska str. 17, 31-016, Kraków, Poland
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, Gołębia 11, 31-007, Kraków, Poland
| | - Jaroslav Peška
- Archaeological Centre Olomouc, U Hradiska 42/6, 779 00, Olomouc, Czech Republic
- Department of History - Section of Archaeology, Philosophical faculty, Palacký University Olomouc, Na Hradě 5, 771 80, Olomouc, Czech Republic
| | - Pavel Fojtík
- Institute of Archaeological Heritage Brno, v.v.i., Kaloudova 30, 614 00, Brno, Czech Republic
| | - Miroslav Králík
- Laboratory of Morphology and Forensic Anthropology (LaMorFA), Department of Anthropology, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37, Brno, Czech Republic
| | - Jerzy Libera
- Institute of Archaeology, Maria Curie-Skłodowska University, Maria Curie-Skłodowska Square 4, 20-031, Lublin, Poland
| | - Jolanta Bagińska
- Muzeum Regionalne im. Janusza Petera, ul. Zamojska 2, 22-600, Tomaszów Lubelski, Poland
| | - Krzysztof Tunia
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Sławkowska str. 17, 31-016, Kraków, Poland
| | - Viktor I Klochko
- National University of "Kyiv-Mohyla Academy", Institute of Archaeology, Hryhoriya Skovorody St. 2, 04655, Kyiv, Ukraine
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznań, Poland
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
| | - Aleksander Kośko
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614, Poznań, Poland
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Mitochondrial DNA control region diversity in a population from Parana state-increasing the Brazilian forensic database. Int J Legal Med 2018; 133:347-351. [PMID: 29959556 DOI: 10.1007/s00414-018-1886-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
Abstract
The entire mitochondrial DNA (mtDNA) control region (nucleotide position 16024-576) sequences were obtained through Sanger sequencing method for 122 individuals from Parana state, South of Brazil. We observed a total of 108 different haplotypes of which 97 were unique and 11 were shared by more than one individual. The haplogroups were classified according to the updated mtDNA phylogeny, by EMMA (estimating mitochondrial haplogroups using a maximum likelihood approach). Our results revealed the predominance of Amerindian haplogroups with a frequency of 49.2% of the population sample, followed by European lineages with 38.5% and 12.3% of African lineages. Parana population sample set presented a high haplotype diversity (0.9976) and the random match probability was 0.0106. The phylogenetical findings and the diversity indices confirm the high genetic heterogeneity of this population and suggest a high informativeness of mtDNA analyses in forensic cases. The population data will contribute to increase the Brazilian mtDNA database for forensic purposes and it is available through EMPOP (European DNA Profiling Group mitochondrial DNA population database) under the accession number EMP00714.
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Zander J, Otremba P, Nagy M. Validation of haplotype-specific extraction for separating a mitochondrial DNA model mixture and application to simulated casework. Forensic Sci Int Genet 2018; 35:57-64. [PMID: 29665468 DOI: 10.1016/j.fsigen.2018.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 01/14/2023]
Abstract
Haplotype-specific extraction (HSE) is a new field of application for the separation of mitochondrial DNA (mtDNA) mixtures and is developed to identify the mtDNA haplotypes of the contributors subsequently by sequencing. Here we show the validation of HSE with an exemplary mitochondrial DNA mixture into its individual haplotypes according to our laboratory standards. These specify several critical areas of assay performance to be tested, such as sensitivity, robustness and mixture studies comprising varying proportions of their components,degraded samples and samples of different qualities and material. Wereport the successful and unambiguous analysis of the exemplary separated mitochondrial DNA mixture under various conditions as well as simulated casework samples, which manifest as mixed nucleotide calls at single base positions previously. Here we demonstrate that the HSE assay is high sensitive, stable against degradation and applicable in a wide range of sample qualities. Based on our findings from the validation study, we believe that this assay has great potential power and may be useful for distinguishing among the mtDNA of individuals and their geographical origin in mixed DNA samples.
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Affiliation(s)
- Judith Zander
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
| | - Petra Otremba
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
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30
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Yao L, Xu Z, Zhao H, Tu Z, Liu Z, Li W, Hu L, Wan L. Concordance of mitochondrial DNA sequencing methods on bloodstains using Ion PGM™. Leg Med (Tokyo) 2018; 32:27-30. [PMID: 29499472 DOI: 10.1016/j.legalmed.2018.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 12/03/2017] [Accepted: 02/23/2018] [Indexed: 11/28/2022]
Abstract
In this study, the complete mitochondrial genome (mtGenome) of six samples from three forensic cases was sequenced using the Ion Torrent Personal Genome Machine (PGM). The analyzed samples from forensic cases included bloodstains from several materials, such as gauze, Flinder's Technology Associates (FTA) cards and swabs. The age of the samples ranged from two months to twelve years. The complete mtGenomes were amplified using the tiling sequencing strategy which divided the whole mtGenome into 162 amplicons. All amplicons were successfully recovered. A phylogenetic analysis was performed to determine the accuracy of the PGM data, and which were compared to partial Sanger-based sequencing data. The average coverage of the PGM data were above 4000× in all case samples, and 99.86% concordance was observed using both sequencing methods. In conclusion, we demonstrate the ability to recover the complete mtGenome from bloodstains with relatively poor DNA quality by PGM. Moreover, the results are concordant with Sanger sequencing data. This new method has potential use in forensic practice.
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Affiliation(s)
- Lan Yao
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Zhen Xu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Hemiao Zhao
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Zheng Tu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Zhifang Liu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Wanshui Li
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Lan Hu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Lihua Wan
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China.
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31
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Peck MA, Sturk-Andreaggi K, Thomas JT, Oliver RS, Barritt-Ross S, Marshall C. Developmental validation of a Nextera XT mitogenome Illumina MiSeq sequencing method for high-quality samples. Forensic Sci Int Genet 2018; 34:25-36. [PMID: 29413633 DOI: 10.1016/j.fsigen.2018.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/21/2017] [Accepted: 01/12/2018] [Indexed: 12/15/2022]
Abstract
Generating mitochondrial genome (mitogenome) data from reference samples in a rapid and efficient manner is critical to harnessing the greater power of discrimination of the entire mitochondrial DNA (mtDNA) marker. The method of long-range target enrichment, Nextera XT library preparation, and Illumina sequencing on the MiSeq is a well-established technique for generating mitogenome data from high-quality samples. To this end, a validation was conducted for this mitogenome method processing up to 24 samples simultaneously along with analysis in the CLC Genomics Workbench and utilizing the AQME (AFDIL-QIAGEN mtDNA Expert) tool to generate forensic profiles. This validation followed the Federal Bureau of Investigation's Quality Assurance Standards (QAS) for forensic DNA testing laboratories and the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines. The evaluation of control DNA, non-probative samples, blank controls, mixtures, and nonhuman samples demonstrated the validity of this method. Specifically, the sensitivity was established at ≥25 pg of nuclear DNA input for accurate mitogenome profile generation. Unreproducible low-level variants were observed in samples with low amplicon yields. Further, variant quality was shown to be a useful metric for identifying sequencing error and crosstalk. Success of this method was demonstrated with a variety of reference sample substrates and extract types. These studies further demonstrate the advantages of using NGS techniques by highlighting the quantitative nature of heteroplasmy detection. The results presented herein from more than 175 samples processed in ten sequencing runs, show this mitogenome sequencing method and analysis strategy to be valid for the generation of reference data.
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Affiliation(s)
- Michelle A Peck
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States
| | - Jacqueline T Thomas
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States
| | - Robert S Oliver
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States
| | - Suzanne Barritt-Ross
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States
| | - Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States.
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32
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Massive parallel sequencing of mitochondrial DNA genomes from mother-child pairs using the ion torrent personal genome machine (PGM). Forensic Sci Int Genet 2018; 32:88-93. [DOI: 10.1016/j.fsigen.2017.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/26/2017] [Accepted: 11/05/2017] [Indexed: 11/15/2022]
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33
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A review of bioinformatic methods for forensic DNA analyses. Forensic Sci Int Genet 2017; 33:117-128. [PMID: 29247928 DOI: 10.1016/j.fsigen.2017.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/30/2017] [Accepted: 12/10/2017] [Indexed: 12/20/2022]
Abstract
Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used.
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34
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An unexpected case in the prehistory of the Iberian Peninsula: Biogeographical origin analysis through mitochondrial DNA. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Sturk-Andreaggi K, Peck MA, Boysen C, Dekker P, McMahon TP, Marshall CK. AQME: A forensic mitochondrial DNA analysis tool for next-generation sequencing data. Forensic Sci Int Genet 2017; 31:189-197. [DOI: 10.1016/j.fsigen.2017.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/21/2017] [Accepted: 09/16/2017] [Indexed: 12/20/2022]
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36
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Eduardoff M, Xavier C, Strobl C, Casas-Vargas A, Parson W. Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin. Genes (Basel) 2017; 8:genes8100237. [PMID: 28934125 PMCID: PMC5664087 DOI: 10.3390/genes8100237] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/06/2017] [Accepted: 09/18/2017] [Indexed: 11/24/2022] Open
Abstract
The analysis of mitochondrial DNA (mtDNA) has proven useful in forensic genetics and ancient DNA (aDNA) studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR) is commonly sequenced using established Sanger-type Sequencing (STS) protocols involving fragment sizes down to approximately 150 base pairs (bp). Recent developments include Massively Parallel Sequencing (MPS) of (multiplex) PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC) methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less), and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples), and tested challenging forensic samples (n = 2) as well as compromised solid tissue samples (n = 15) up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS method for final implementation in forensic genetic laboratories.
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Affiliation(s)
- Mayra Eduardoff
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
| | - Andrea Casas-Vargas
- Grupo de Genética de Poblaciones e Identificación, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia.
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA.
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Malyarchuk B, Litvinov A, Derenko M, Skonieczna K, Grzybowski T, Grosheva A, Shneider Y, Rychkov S, Zhukova O. Mitogenomic diversity in Russians and Poles. Forensic Sci Int Genet 2017. [PMID: 28633069 DOI: 10.1016/j.fsigen.2017.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Complete mtDNA genome sequencing improves molecular resolution for distinguishing variation between individuals and populations, but there is still deficiency of mitogenomic population data. To overcome this limitation, we used Sanger-based protocol to generate complete mtDNA sequences of 376 Russian individuals from six populations of European part of Russia and 100 Polish individuals from northern Poland. Nearly complete resolution of mtDNA haplotypes was achieved - about 97% of haplotypes were unique both in Russians and Poles, and no haplotypes overlapped between them when indels were considered. While European populations showed a low, but statistically significant level of between-population differentiation (Fst=0.66%, p=0), Russians demonstrate lack of between-population differences (Fst=0.22%, p=0.15). Results of the Bayesian skyline analysis of Russian mitogenomes demonstrate not only post-Last Glacial Maximum expansion, but also rapid population growth starting from about 4.3kya (95% CI: 2.9-5.8kya), i.e. in the Bronze Age. This expansion strongly correlates with the Kurgan model established by archaeologists and confirmed by paleogeneticists.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia.
| | - Andrey Litvinov
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - Katarzyna Skonieczna
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University,Sklodowskiej-Curie Street 9, Bydgoszcz 85-094, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University,Sklodowskiej-Curie Street 9, Bydgoszcz 85-094, Poland
| | - Aleksandra Grosheva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
| | - Yuri Shneider
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
| | - Sergei Rychkov
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
| | - Olga Zhukova
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
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38
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Vohr SH, Gordon R, Eizenga JM, Erlich HA, Calloway CD, Green RE. A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixtures. Forensic Sci Int Genet 2017; 30:93-105. [PMID: 28667863 DOI: 10.1016/j.fsigen.2017.05.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/05/2017] [Accepted: 05/26/2017] [Indexed: 12/11/2022]
Abstract
Massively parallel (next-generation) sequencing provides a powerful method to analyze DNA from many different sources, including degraded and trace samples. A common challenge, however, is that many forensic samples are often known or suspected mixtures of DNA from multiple individuals. Haploid lineage markers, such as mitochondrial (mt) DNA, are useful for analysis of mixtures because, unlike nuclear genetic markers, each individual contributes a single sequence to the mixture. Deconvolution of these mixtures into the constituent mitochondrial haplotypes is challenging as typical sequence read lengths are too short to reconstruct the distinct haplotypes completely. We present a powerful computational approach for determining the constituent haplotypes in massively parallel sequencing data from potentially mixed samples. At the heart of our approach is an expectation maximization based algorithm that co-estimates the overall mixture proportions and the source haplogroup for each read individually. This approach, implemented in the software package mixemt, correctly identifies haplogroups from mixed samples across a range of mixture proportions. Furthermore, our method can separate fragments in a mixed sample by the most likely originating contributor and generate reconstructions of the constituent haplotypes based on known patterns of mtDNA diversity.
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Affiliation(s)
- Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA.
| | - Rachel Gordon
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
| | - Jordan M Eizenga
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Henry A Erlich
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
| | - Cassandra D Calloway
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA; Forensic Science Graduate Program, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
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39
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Kapoor V, Elk M, Toledo-Hernandez C, Santo Domingo JW. Analysis of human mitochondrial DNA sequences from fecally polluted environmental waters as a tool to study population diversity. AIMS ENVIRONMENTAL SCIENCE 2017; 4:443-455. [PMID: 32802939 PMCID: PMC7425658 DOI: 10.3934/environsci.2017.3.443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mitochondrial signature sequences have frequently been used to study human population diversity around the world. Traditionally, this requires obtaining samples directly from individuals which is cumbersome, time consuming and limited to the number of individuals that participated in these types of surveys. Here, we used environmental DNA extracts to determine the presence and sequence variability of human mitochondrial sequences as a means to study the diversity of populations inhabiting in areas nearby a tropical watershed impacted with human fecal pollution. We used high-throughput sequencing (Illumina) and barcoding to obtain thousands of sequences from the mitochondrial hypervariable region 2 (HVR2) and determined the different haplotypes present in 10 different water samples. Sequence analyses indicated a total of 19 distinct variants with frequency greater than 5%. The HVR2 sequences were associated with haplogroups of West Eurasian (57.6%), Sub-Saharan African (23.9%), and American Indian (11%) ancestry. This was in relative accordance with population census data from the watershed sites. The results from this study demonstrates the potential value of mitochondrial sequence data retrieved from fecally impacted environmental waters to study the population diversity of local municipalities. This environmental DNA approach may also have other public health implications such as tracking background levels of human mitochondrial genes associated with diseases. It may be possible to expand this approach to other animal species inhabiting or using natural water systems.
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Affiliation(s)
- Vikram Kapoor
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Michael Elk
- Pegasus Technical Services, Inc., Cincinnati, OH 45268, USA
| | | | - Jorge W Santo Domingo
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
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40
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Weiler N, Baca K, Ballard D, Balsa F, Bogus M, Børsting C, Brisighelli F, Červenáková J, Chaitanya L, Coble M, Decroyer V, Desmyter S, van der Gaag K, Gettings K, Haas C, Heinrich J, João Porto M, Kal A, Kayser M, Kúdelová A, Morling N, Mosquera-Miguel A, Noel F, Parson W, Pereira V, Phillips C, Schneider P, Syndercombe Court D, Turanska M, Vidaki A, Woliński P, Zatkalíková L, Sijen T. A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing. Forensic Sci Int Genet 2017; 26:77-84. [DOI: 10.1016/j.fsigen.2016.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/04/2016] [Accepted: 10/23/2016] [Indexed: 01/27/2023]
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41
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Heinz T, Pala M, Gómez-Carballa A, Richards MB, Salas A. Updating the African human mitochondrial DNA tree: Relevance to forensic and population genetics. Forensic Sci Int Genet 2016; 27:156-159. [PMID: 28086175 DOI: 10.1016/j.fsigen.2016.12.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 12/14/2016] [Accepted: 12/30/2016] [Indexed: 11/24/2022]
Abstract
Analysis of human mitochondrial DNA (mtDNA) variation plays an important role in forensic genetic investigations, especially in degraded biological samples and hair shafts. There are many issues of the mtDNA phylogeny that are of special interest to the forensic community, such as haplogroup classification or the post hoc investigation of potential errors in mtDNA datasets. We have analyzed >2200 mitogenomes of African ancestry with the aim of improving the known worldwide phylogeny. More than 300 new minor subclades were identified, and the Time to the Most Recent Common Ancestor (TMRCA) was estimated for each node of the phylogeny. Phylogeographic details are provided which might also be relevant to forensic genetics. The present study has special interest for forensic investigations because current analysis and interpretation of mtDNA casework rest on a solid worldwide phylogeny, as is evident from the role that phylogeny plays in popular resources in the field (e.g. PhyloTree), software (e.g. Haplogrep 2), and databases (e.g. EMPOP). Apart from this forensic genetic interest, we also highlight the impact of this research in anthropological studies, such as those related to the reconstruction of the transatlantic slave trade.
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Affiliation(s)
- Tanja Heinz
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.
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Rathbun MM, McElhoe JA, Parson W, Holland MM. Considering DNA damage when interpreting mtDNA heteroplasmy in deep sequencing data. Forensic Sci Int Genet 2016; 26:1-11. [PMID: 27718383 DOI: 10.1016/j.fsigen.2016.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/15/2016] [Accepted: 09/27/2016] [Indexed: 10/20/2022]
Abstract
Resolution of mitochondrial (mt) DNA heteroplasmy is now possible when applying a massively parallel sequencing (MPS) approach, including minor components down to 1%. However, reporting thresholds and interpretation criteria will need to be established for calling heteroplasmic variants that address a number of important topics, one of which is DNA damage. We assessed the impact of increasing amounts of DNA damage on the interpretation of minor component sequence variants in the mtDNA control region, including low-level mixed sites. A passive approach was used to evaluate the impact of storage conditions, and an active approach was employed to accelerate the process of hydrolytic damage (for example, replication errors associated with depurination events). The patterns of damage were compared and assessed in relation to damage typically encountered in poor quality samples. As expected, the number of miscoding lesions increased as conditions worsened. Single nucleotide polymorphisms (SNPs) associated with miscoding lesions were indistinguishable from innate heteroplasmy and were most often observed as 1-2% of the total sequencing reads. Numerous examples of miscoding lesions above 2% were identified, including two complete changes in the nucleotide sequence, presenting a challenge when assessing the placement of reporting thresholds for heteroplasmy. To mitigate the impact, replication of miscoding lesions was not observed in stored samples, and was rarely seen in data associated with accelerated hydrolysis. In addition, a significant decrease in the expected transition:transversion ratio was observed, providing a useful tool for predicting the presence of damage-induced lesions. The results of this study directly impact MPS analysis of minor sequence variants from poorly preserved DNA extracts, and when biological samples have been exposed to agents that induce DNA damage. These findings are particularly relevant to clinical and forensic investigations.
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Affiliation(s)
- Molly M Rathbun
- Forensic Science Program, Biochemistry and Molecular Biology Department, The Pennsylvania State University, 014 Thomas Building, University Park, PA 16802, United States
| | - Jennifer A McElhoe
- Forensic Science Program, Biochemistry and Molecular Biology Department, The Pennsylvania State University, 014 Thomas Building, University Park, PA 16802, United States
| | - Walther Parson
- Forensic Science Program, Biochemistry and Molecular Biology Department, The Pennsylvania State University, 014 Thomas Building, University Park, PA 16802, United States; The Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria
| | - Mitchell M Holland
- Forensic Science Program, Biochemistry and Molecular Biology Department, The Pennsylvania State University, 014 Thomas Building, University Park, PA 16802, United States.
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43
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Serin A, Canan H, Alper B, Korkut Gulmen M, Zimmermann B, Parson W. Mitochondrial DNA control region haplotype and haplogroup diversity in South Eastern Turkey. Forensic Sci Int Genet 2016; 24:176-179. [DOI: 10.1016/j.fsigen.2016.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/12/2016] [Accepted: 07/23/2016] [Indexed: 10/21/2022]
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44
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Turchi C, Stanciu F, Paselli G, Buscemi L, Parson W, Tagliabracci A. The mitochondrial DNA makeup of Romanians: A forensic mtDNA control region database and phylogenetic characterization. Forensic Sci Int Genet 2016; 24:136-142. [DOI: 10.1016/j.fsigen.2016.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/26/2016] [Accepted: 06/18/2016] [Indexed: 01/13/2023]
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EMPOP-quality mtDNA control region sequences from Kashmiri of Azad Jammu & Kashmir, Pakistan. Forensic Sci Int Genet 2016; 25:125-131. [PMID: 27591488 DOI: 10.1016/j.fsigen.2016.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 01/13/2023]
Abstract
The mitochondrial DNA (mtDNA) control region (nucleotide position 16024-576) sequences were generated through Sanger sequencing method for 317 self-identified Kashmiris from all districts of Azad Jammu & Kashmir Pakistan. The population sample set showed a total of 251 haplotypes, with a relatively high haplotype diversity (0.9977) and a low random match probability (0.54%). The containing matrilineal lineages belonging to three different phylogeographic origins of Western Eurasian (48.9%), South Asian (47.0%) and East Asian (4.1%). The present study was compared to previous data from Pakistan and other worldwide populations (Central Asia, Western Asia, and East & Southeast Asia). The dataset is made available through EMPOP under accession number EMP00679 and will serve as an mtDNA reference database in forensic casework in Pakistan.
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46
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Hairy matters: MtDNA quantity and sequence variation along and among human head hairs. Forensic Sci Int Genet 2016; 25:1-9. [PMID: 27484846 DOI: 10.1016/j.fsigen.2016.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/20/2016] [Accepted: 07/23/2016] [Indexed: 01/31/2023]
Abstract
Hairs from the same donor have been found to differ in mtDNA sequence within and among themselves and from other tissues, which impacts interpretation of results obtained in a forensic setting. However, little is known on the magnitude of this phenomenon and published data on systematic studies are scarce. We addressed this issue by generating mtDNA control region (CR) profiles of >450 hair fragments from 21 donors by Sanger-type sequencing (STS). To mirror forensic scenarios, we compared hair haplotypes from the same donors to each other, to the corresponding buccal swab reference haplotypes and analyzed several fragments of individual hairs. We also investigated the effects of hair color, donor sex and age, mtDNA haplogroup and chemical treatment on mtDNA quantity, amplification success and variation. We observed a wide range of individual CR sequence variation. The reference haplotype was the only or most common (≥75%) hair haplotype for most donors. However, in two individuals, the reference haplotype was only found in about a third of the investigated hairs, mainly due to differences at highly variable positions. Similarly, most hairs revealed the reference haplotype along their entire length, however, about a fifth of the hairs contained up to 71% of segments with deviant haplotypes, independent of the longitudinal position. Variation affected numerous positions, typically restricted to the individual hair and in most cases heteroplasmic, but also fixed (i.e. homoplasmic) substitutions were observed. While existing forensic mtDNA interpretation guidelines were found still sufficient for all comparisons to reference haplotypes, some comparisons between hairs from the same donor could yield false exclusions when those guidelines are strictly followed. This study pinpoints the special care required when interpreting mtDNA results from hair in forensic casework.
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Ma K, Li H, Cao Y, Zhao X, Liu W, Zhao X. Haplotype diversity in mitochondrial genome in a Chinese Han population. J Hum Genet 2016; 61:903-906. [PMID: 27305984 DOI: 10.1038/jhg.2016.74] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/08/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022]
Abstract
Investigations into the use of mitochondrial genome (mtGenome) typing by massively parallel sequencing technologies are well underway in many areas, including forensic genetics. Previous studies have demonstrated that mtGenome sequencing data generated from Ion torrent personal genome machine (PGM) system were highly viable and reliable in forensic research. In this study, 145 whole mtGenomes from unrelated Chinese Han population were sequenced using the Ion PGM system. Results showed that 145 distinct haplotypes were obtained at a relatively high coverage with limited strand bias. The distribution of variants across the entire mtGenomes was illustrated and 70.74% of the variants were observed outside of the control region. An overall increase in the number of unique haplotypes as well as haplotype diversity were observed by detection of mtGenome compared with hypervariable region I/II (HV I/II) and control region (CR). This study demonstrates the substantially higher degree of haplotype resolution with whole-mtGenome sequences in comparison to HV I/II or CR that historically targeted for forensic testing, which shows the potential value of mtGenome typing in forensic testing in the future.
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Affiliation(s)
- Ke Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Yu Cao
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China.,State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Xuejun Zhao
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Xueying Zhao
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
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48
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Strategies for complete mitochondrial genome sequencing on Ion Torrent PGM™ platform in forensic sciences. Forensic Sci Int Genet 2016; 22:11-21. [DOI: 10.1016/j.fsigen.2016.01.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 12/30/2015] [Accepted: 01/08/2016] [Indexed: 01/08/2023]
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49
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Weissensteiner H, Pacher D, Kloss-Brandstätter A, Forer L, Specht G, Bandelt HJ, Kronenberg F, Salas A, Schönherr S. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res 2016; 44:W58-63. [PMID: 27084951 PMCID: PMC4987869 DOI: 10.1093/nar/gkw233] [Citation(s) in RCA: 551] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics. With the extensive growth of the underlying phylogenetic tree summarizing the published mtDNA sequences, the manual process of haplogroup classification would be too time-consuming. The previously published classification tool HaploGrep provided an automatic way to address this issue. Here, we present the completely updated version HaploGrep 2 offering several advanced features, including a generic rule-based system for immediate quality control (QC). This allows detecting artificial recombinants and missing variants as well as annotating rare and phantom mutations. Furthermore, the handling of high-throughput data in form of VCF files is now directly supported. For data output, several graphical reports are generated in real time, such as a multiple sequence alignment format, a VCF format and extended haplogroup QC reports, all viewable directly within the application. In addition, HaploGrep 2 generates a publication-ready phylogenetic tree of all input samples encoded relative to the revised Cambridge Reference Sequence. Finally, new distance measures and optimizations of the algorithm increase accuracy and speed-up the application. HaploGrep 2 can be accessed freely and without any registration at http://haplogrep.uibk.ac.at.
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Affiliation(s)
- Hansi Weissensteiner
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck 6020, Austria
| | - Dominic Pacher
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Anita Kloss-Brandstätter
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Lukas Forer
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Günther Specht
- Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck 6020, Austria
| | | | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Calle San Francisco s/n, C.P. 15872, Galicia, Spain
| | - Sebastian Schönherr
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria
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50
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Csákyová V, Szécsényi-Nagy A, Csősz A, Nagy M, Fusek G, Langó P, Bauer M, Mende BG, Makovický P, Bauerová M. Maternal Genetic Composition of a Medieval Population from a Hungarian-Slavic Contact Zone in Central Europe. PLoS One 2016; 11:e0151206. [PMID: 26963389 PMCID: PMC4786151 DOI: 10.1371/journal.pone.0151206] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/23/2016] [Indexed: 02/07/2023] Open
Abstract
The genetic composition of the medieval populations of Central Europe has been poorly investigated to date. In particular, the region of modern-day Slovakia is a blank spot in archaeogenetic research. This paper reports the study of mitochondrial DNA (mtDNA) in ancient samples from the 9th–12th centuries originating from the cemeteries discovered in Nitra-Šindolka and Čakajovce, located in western Slovakia (Central Europe). This geographical region is interesting to study because its medieval multi-ethnic population lived in the so-called contact zone of the territory of the Great Moravian and later Hungarian state formations. We described 16 different mtDNA haplotypes in 19 individuals, which belong to the most widespread European mtDNA haplogroups: H, J, T, U and R0. Using comparative statistical and population genetic analyses, we showed the differentiation of the European gene pool in the medieval period. We also demonstrated the heterogeneous genetic characteristics of the investigated population and its affinity to the populations of modern Europe.
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Affiliation(s)
- Veronika Csákyová
- Department of Botany and Genetics, Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nitra, Slovakia
- * E-mail:
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Aranka Csősz
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Melinda Nagy
- Department of Biology, Faculty of Education, J. Selye University in Komárno, Komárno, Slovakia
| | - Gabriel Fusek
- Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Péter Langó
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Miroslav Bauer
- Department of Botany and Genetics, Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nitra, Slovakia
- Research Institute for Animal Production, NAFC, Nitra, Slovakia
| | - Balázs Gusztáv Mende
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Pavol Makovický
- Department of Biology, Faculty of Education, J. Selye University in Komárno, Komárno, Slovakia
| | - Mária Bauerová
- Department of Botany and Genetics, Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nitra, Slovakia
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