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Sturk-Andreaggi K, Bodner M, Ring JD, Ameur A, Gyllensten U, Parson W, Marshall C, Allen M. Complete Mitochondrial DNA Genome Variation in the Swedish Population. Genes (Basel) 2023; 14:1989. [PMID: 38002932 PMCID: PMC10671102 DOI: 10.3390/genes14111989] [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: 09/03/2023] [Revised: 10/04/2023] [Accepted: 10/19/2023] [Indexed: 11/26/2023] Open
Abstract
The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies.
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Affiliation(s)
- Kimberly Sturk-Andreaggi
- Department of Immunology Genetics and Pathology, Uppsala University, 751 08 Uppsala, Sweden; (A.A.); (U.G.)
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA (C.M.)
- SNA International, LLC, Alexandria, VI 22314, USA
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.B.); (W.P.)
| | - Joseph D. Ring
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA (C.M.)
- SNA International, LLC, Alexandria, VI 22314, USA
| | - Adam Ameur
- Department of Immunology Genetics and Pathology, Uppsala University, 751 08 Uppsala, Sweden; (A.A.); (U.G.)
| | - Ulf Gyllensten
- Department of Immunology Genetics and Pathology, Uppsala University, 751 08 Uppsala, Sweden; (A.A.); (U.G.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.B.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16801, USA
| | - Charla Marshall
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA (C.M.)
- Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16801, USA
| | - Marie Allen
- Department of Immunology Genetics and Pathology, Uppsala University, 751 08 Uppsala, Sweden; (A.A.); (U.G.)
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Havaš Auguštin D, Šarac J, Reidla M, Tamm E, Grahovac B, Kapović M, Novokmet N, Rudan P, Missoni S, Marjanović D, Korolija M. Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates. Genes (Basel) 2023; 14:1614. [PMID: 37628665 PMCID: PMC10454736 DOI: 10.3390/genes14081614] [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: 06/29/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.
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Affiliation(s)
- Dubravka Havaš Auguštin
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Jelena Šarac
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Maere Reidla
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | - Erika Tamm
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | | | | | | | - Pavao Rudan
- Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Saša Missoni
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Faculty of Dental Medicine and Health, J. J. Strossmayer University, 31000 Osijek, Croatia
| | - Damir Marjanović
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Genetics and Bioengineering Department, International Burch University, 71000 Sarajevo, Bosnia and Herzegovina
| | - Marina Korolija
- Forensic Science Centre “Ivan Vučetić”, Ministry of the Interior, 10000 Zagreb, Croatia
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Malyarchuk B, Skonieczna K, Duleba A, Derenko M, Malyarchuk A, Grzybowski T. Mitogenomic diversity in Czechs and Slovaks. Forensic Sci Int Genet 2022; 59:102714. [PMID: 35468348 DOI: 10.1016/j.fsigen.2022.102714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 11/19/2022]
Affiliation(s)
- Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan 685000, Russian Federation.
| | - Katarzyna Skonieczna
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz 85-094, Poland
| | - Anna Duleba
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz 85-094, Poland
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan 685000, Russian Federation
| | - Alexandra Malyarchuk
- Center for Genetics and Genetic Technologies, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Russian Federation
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz 85-094, Poland
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Pham VH, Nguyen VL, Jung HE, Cho YS, Shin JG. The frequency of the known mitochondrial variants associated with drug-induced toxicity in a Korean population. BMC Med Genomics 2022; 15:3. [PMID: 34980117 PMCID: PMC8722126 DOI: 10.1186/s12920-021-01153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Few studies have annotated the whole mitochondrial DNA (mtDNA) genome associated with drug responses in Asian populations. This study aimed to characterize mtDNA genetic profiles, especially the distribution and frequency of well-known genetic biomarkers associated with diseases and drug-induced toxicity in a Korean population. METHOD Whole mitochondrial genome was sequenced for 118 Korean subjects by using a next-generation sequencing approach. The bioinformatic pipeline was constructed for variant calling, haplogroup classification and annotation of mitochondrial mutation. RESULTS A total of 681 variants was identified among all subjects. The MT-TRNP gene and displacement loop showed the highest numbers of variants (113 and 74 variants, respectively). The m.16189T > C allele, which is known to reduce the mtDNA copy number in human cells was detected in 25.4% of subjects. The variants (m.2706A > G, m.3010A > G, and m.1095T > C), which are associated with drug-induced toxicity, were observed with the frequency of 99.15%, 30.51%, and 0.08%, respectively. The m.2150T > A, a genotype associated with highly disruptive effects on mitochondrial ribosomes, was identified in five subjects. The D and M groups were the most dominant groups with the frequency of 34.74% and 16.1%, respectively. CONCLUSIONS Our finding was consistent with Korean Genome Project and well reflected the unique profile of mitochondrial haplogroup distribution. It was the first study to annotate the whole mitochondrial genome with drug-induced toxicity to predict the ADRs event in clinical implementation for Korean subjects. This approach could be extended for further study for validation of the potential ethnic-specific mitochondrial genetic biomarkers in the Korean population.
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Affiliation(s)
- Vinh Hoa Pham
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea
| | - Van Lam Nguyen
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea
| | - Hye-Eun Jung
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea.,Department of Precision Medicine, SPMED Co., Ltd., Busan, 46508, Republic of Korea
| | - Yong-Soon Cho
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea.,Department of Pharmacology and Clinical Pharmacology, PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Jae-Gook Shin
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea. .,Department of Pharmacology and Clinical Pharmacology, PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea. .,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea.
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Santos CGM, Rolim-Filho NG, Domingues CA, Dornelas-Ribeiro M, King JL, Budowle B, Moura-Neto RS, Silva R. Association of whole mtDNA, an NADPH G11914A variant, and haplogroups with high physical performance in an elite military troop. ACTA ACUST UNITED AC 2021; 54:e10317. [PMID: 33909855 PMCID: PMC8075130 DOI: 10.1590/1414-431x202010317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/29/2020] [Indexed: 11/22/2022]
Abstract
Physical performance is a multifactorial and complex trait influenced by environmental and hereditary factors. Environmental factors alone have been insufficient to characterize all outstanding phenotypes. Recent advances in genomic technologies have enabled the investigation of whole nuclear and mitochondrial genome sequences, increasing our ability to understand interindividual variability in physical performance. Our objective was to evaluate the association of mitochondrial polymorphic loci with physical performance in Brazilian elite military personnel. Eighty-eight male military personnel who participated in the Command Actions Course of the Army were selected. Total DNA was obtained from blood samples and a complete mitochondrial genome (mtDNA) was sequenced using Illumina MiSeq platform. Twenty-nine subjects completed the training program (FINISHED, 'F'), and fifty-nine failed to complete (NOT_FINISHED, 'NF'). The mtDNA from NF was slightly more similar to genomes from African countries frequently related to endurance level. Twenty-two distinct mtDNA haplogroups were identified corroborating the intense genetic admixture of the Brazilian population, but their distribution was similar between the two groups (FST=0.0009). Of 745 polymorphisms detected in the mtDNA, the position G11914A within the NADPH gene component of the electron transport chain, was statistically different between F and NF groups (P=0.011; OR: 4.286; 95%CI: 1.198-16.719), with a higher frequency of the G allele in group F individuals). The high performance of military personnel may be mediated by performance-related genomic traits. Thus, mitochondrial genetic markers such as the ND4 gene may play an important role on physical performance variability.
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Affiliation(s)
- C G M Santos
- Instituto de Biologia do Exército, Rio de Janeiro, RJ, Brasil
| | - N G Rolim-Filho
- Centro de Instrução de Operações Especiais do Exército Brasileiro, Rio de Janeiro, RJ, Brasil
| | - C A Domingues
- Centro de Instrução de Operações Especiais do Exército Brasileiro, Rio de Janeiro, RJ, Brasil
| | | | - J L King
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - B Budowle
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - R S Moura-Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - R Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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Guevara EK, Palo JU, Översti S, King JL, Seidel M, Stoljarova M, Wendt FR, Bus MM, Guengerich A, Church WB, Guillén S, Roewer L, Budowle B, Sajantila A. Genetic assessment reveals no population substructure and divergent regional and sex-specific histories in the Chachapoyas from northeast Peru. PLoS One 2020; 15:e0244497. [PMID: 33382772 PMCID: PMC7774974 DOI: 10.1371/journal.pone.0244497] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/10/2020] [Indexed: 12/31/2022] Open
Abstract
Many native populations in South America have been severely impacted by two relatively recent historical events, the Inca and the Spanish conquest. However decisive these disruptive events may have been, the populations and their gene pools have been shaped markedly also by the history prior to the conquests. This study focuses mainly on the Chachapoya peoples that inhabit the montane forests on the eastern slopes of the northern Peruvian Andes, but also includes three distinct neighboring populations (the Jívaro, the Huancas and the Cajamarca). By assessing mitochondrial, Y-chromosomal and autosomal diversity in the region, we explore questions that have emerged from archaeological and historical studies of the regional culture (s). These studies have shown, among others, that Chachapoyas was a crossroads for Coast-Andes-Amazon interactions since very early times. In this study, we examine the following questions: 1) was there pre-Hispanic genetic population substructure in the Chachapoyas sample? 2) did the Spanish conquest cause a more severe population decline on Chachapoyan males than on females? 3) can we detect different patterns of European gene flow in the Chachapoyas region? and, 4) did the demographic history in the Chachapoyas resemble the one from the Andean area? Despite cultural differences within the Chachapoyas region as shown by archaeological and ethnohistorical research, genetic markers show no significant evidence for past or current population substructure, although an Amazonian gene flow dynamic in the northern part of this territory is suggested. The data also indicates a bottleneck c. 25 generations ago that was more severe among males than females, as well as divergent population histories for populations in the Andean and Amazonian regions. In line with previous studies, we observe high genetic diversity in the Chachapoyas, despite the documented dramatic population declines. The diverse topography and great biodiversity of the northeastern Peruvian montane forests are potential contributing agents in shaping and maintaining the high genetic diversity in the Chachapoyas region.
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Affiliation(s)
- Evelyn K. Guevara
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- * E-mail: (EKG); (AS)
| | - Jukka U. Palo
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Genetics Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Sanni Översti
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jonathan L. King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Maria Seidel
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Monika Stoljarova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Frank R. Wendt
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Psychiatry, Yale University School of Medicine and VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Magdalena M. Bus
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Anna Guengerich
- Eckerd College, Saint Petersburg, Florida, United States of America
| | - Warren B. Church
- Department of Earth and Space Sciences, Columbus State University, Columbus, Georgia, United States of America
| | | | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- * E-mail: (EKG); (AS)
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Cihlar JC, Amory C, Lagacé R, Roth C, Parson W, Budowle B. Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel. Genes (Basel) 2020; 11:E1345. [PMID: 33202822 PMCID: PMC7709034 DOI: 10.3390/genes11111345] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/21/2020] [Accepted: 11/10/2020] [Indexed: 01/10/2023] Open
Abstract
For the adoption of massively parallel sequencing (MPS) systems by forensic laboratories, validation studies on specific workflows are needed to support the feasibility of implementation and the reliability of the data they produce. As such, the whole mitochondrial genome sequencing methodology-Precision ID mtDNA Whole Genome Panel, Ion Chef, Ion S5, and Converge-has been subjected to a variety of developmental validation studies. These validation studies were completed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines and assessed reproducibility, repeatability, accuracy, sensitivity, specificity to human DNA, and ability to analyze challenging (e.g., mixed, degraded, or low quantity) samples. Intra- and inter-run replicates produced an average maximum pairwise difference in variant frequency of 1.2%. Concordance with data generated with traditional Sanger sequencing and an orthogonal MPS platform methodology was used to assess accuracy, and generation of complete and concordant haplotypes at DNA input levels as low as 37.5 pg of nuclear DNA or 187.5 mitochondrial genome copies illustrated the sensitivity of the system. Overall, data presented herein demonstrate that highly accurate and reproducible results were generated for a variety of sample qualities and quantities, supporting the reliability of this specific whole genome mitochondrial DNA MPS system for analysis of forensic biological evidence.
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Affiliation(s)
- Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA;
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
| | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.A.); (W.P.)
| | - Robert Lagacé
- Human Identification Group, Thermo Fisher Scientific, South San Francisco, CA 94080, USA; (R.L.); (C.R.)
| | - Chantal Roth
- Human Identification Group, Thermo Fisher Scientific, South San Francisco, CA 94080, USA; (R.L.); (C.R.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.A.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA;
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
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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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Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P. Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. ZOOLOGIA 2020. [DOI: 10.3897/zoologia.37.e49046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The whole mitochondrial genome ofLateolabrax maculatus(Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity ofL. maculatuswere 0.998 and 0.00169, respectively. Pairwise FSTvalues between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajima’s D values, Fu’s Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history ofL. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation ofL. maculatus.
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Davidovic S, Malyarchuk B, Grzybowski T, Aleksic JM, Derenko M, Litvinov A, Rogalla-Ładniak U, Stevanovic M, Kovacevic-Grujicic N. Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases. Int J Legal Med 2020; 134:1581-1590. [PMID: 32504149 DOI: 10.1007/s00414-020-02324-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/28/2020] [Indexed: 11/24/2022]
Abstract
Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, 11060, Serbia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Jelena M Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Urszula Rogalla-Ładniak
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia.,Serbian Academy of Sciences and Arts, Kneza Mihaila 35, Belgrade, 11000, Serbia
| | - Natasa Kovacevic-Grujicic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.
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11
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Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China. Genes (Basel) 2020; 11:genes11050564. [PMID: 32443545 PMCID: PMC7290686 DOI: 10.3390/genes11050564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/27/2022] Open
Abstract
The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group.
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12
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Wei YY, Ren ZP, Jin XY, Cui W, Chen C, Guo YX, Meng HT, Zhu BF. Haplogroup Structure and Genetic Variation Analyses of 60 Mitochondrial DNA Markers in Southern Shaanxi Han Population. Biochem Genet 2019; 58:279-293. [PMID: 31696339 DOI: 10.1007/s10528-019-09942-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 10/24/2019] [Indexed: 12/30/2022]
Abstract
Mitochondrial DNA (mtDNA) has been widely employed as one tool for the studies of human migration and phylogenetic evolution owing to the characteristics of its lack of recombination and matrilineal inheritance. In this study, we analyze genetic distributions of 60 mtDNA markers in 126 unrelated individuals of Southern Shaanxi Han population and classify their haplogroups. Genetic distribution comparisons between Southern Shaanxi Han and other populations from different continents are conducted based on the same mtDNA markers. The majority of 60 mtDNA markers are polymorphic in Southern Shaanxi Han population. The most common haplogroups observed in Southern Shaanxi Han population are B5, followed by D5, A, D4e, and N9a1'3. Obtained matching probability for these 60 mtDNA markers indicates that the panel could be used as a valuable tool in forensic caseworks. Results of genetic distances (Fst) and multidimensional scaling analysis show that Southern Shaanxi Han population has relatively close genetic relationships with other Han populations in different regions. In conclusion, the panel comprising 60 mtDNA markers could be utilized for forensic applications in Southern Shaanxi Han population.
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Affiliation(s)
- Yuan-Yuan Wei
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Zhan-Ping Ren
- Department of Cranio-Maxillofacial Trauma Plastic Surgery, Stomatology Hospital of Xi'an Jiaotong University College of Medicine, Xi'an, China
| | - Xiao-Ye Jin
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wei Cui
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chong Chen
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yu-Xin Guo
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Hao-Tian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Bo-Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China. .,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China. .,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China.
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13
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Lan Q, Xie T, Jin X, Fang Y, Mei S, Yang G, Zhu B. MtDNA polymorphism analyses in the Chinese Mongolian group: Efficiency evaluation and further matrilineal genetic structure exploration. Mol Genet Genomic Med 2019; 7:e00934. [PMID: 31478599 PMCID: PMC6785450 DOI: 10.1002/mgg3.934] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 05/26/2019] [Accepted: 07/07/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Profiling of mitochondrial DNA is surely to provide valuable investigative clues for forensic cases involving highly degraded specimens or complex maternal lineage kinship determination. But traditionally used hypervariable region sequencing of mitochondrial DNA is less frequently suggested by the forensic community for insufficient informativeness. Genome-wide sequencing of mitochondrial DNA can provide considerable amount of variant information but can be high cost at the same time. METHODS Efficiency of the 60 mitochondrial DNA polymorphic sites dispersing across the control region and coding region of mitochondrial DNA genome was evaluated with 106 Mongolians recruited from the Xinjiang Uyghur Autonomous Region, China, and allele-specific PCR technique was employed for mitochondrial DNA typing. RESULTS Altogether 58 haplotypes were observed and the haplotypic diversity, discrimination power and random match probability were calculated to be 0.981, 0.972, and 0.028, respectively. Mitochondrial DNA haplogroup affiliation exhibited an exceeding percentage (12.26%) of west Eurasian lineage (H haplogroup) in the studied Mongolian group, which needed to be further verified with more samples. Furthermore, the genetic relationships between the Xinjiang Mongolian group and the comparison populations were also investigated and the genetic affinity was discovered between the Xinjiang Mongolian group and the Xinjiang Kazak group in this study. CONCLUSION It was indicated that the panel was potentially enough to be used as a supplementary tool for forensic applications. And the matrilineal genetic structure analyses based on mitochondrial DNA variants in the Xinjiang Mongolian group could be helpful for subsequent anthropological studies.
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Affiliation(s)
- Qiong Lan
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Tong Xie
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of StomatologyXi'an Jiaotong UniversityXi'anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of StomatologyXi'an Jiaotong UniversityXi'anChina
| | - Yating Fang
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Shuyan Mei
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Guang Yang
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of StomatologyXi'an Jiaotong UniversityXi'anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of StomatologyXi'an Jiaotong UniversityXi'anChina
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14
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Insights into matrilineal genetic structure, differentiation and ancestry of Armenians based on complete mitogenome data. Mol Genet Genomics 2019; 294:1547-1559. [DOI: 10.1007/s00438-019-01596-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023]
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15
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Strobl C, Churchill Cihlar J, Lagacé R, Wootton S, Roth C, Huber N, Schnaller L, Zimmermann B, Huber G, Lay Hong S, Moura-Neto R, Silva R, Alshamali F, Souto L, Anslinger K, Egyed B, Jankova-Ajanovska R, Casas-Vargas A, Usaquén W, Silva D, Barletta-Carrillo C, Tineo DH, Vullo C, Würzner R, Xavier C, Gusmão L, Niederstätter H, Bodner M, Budowle B, Parson W. Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel. Forensic Sci Int Genet 2019; 42:244-251. [PMID: 31382159 DOI: 10.1016/j.fsigen.2019.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/09/2019] [Accepted: 07/21/2019] [Indexed: 12/24/2022]
Abstract
The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.
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Affiliation(s)
- Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Robert Lagacé
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Sharon Wootton
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Chantal Roth
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Lisa Schnaller
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Seah Lay Hong
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Rodrigo Moura-Neto
- Laboratório de Biologia Molecular Forense, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rosane Silva
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Farida Alshamali
- Dubai Police, Gen. Dept. Forensic Science & Criminology, Dubai, United Arab Emirates
| | - Luis Souto
- Laboratorio de Genética Aplicada, Departamento de Biologia, Universidade de Aveiro, Portugal
| | | | - Balazs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Renata Jankova-Ajanovska
- Institute of Forensic Medicine, Criminalistic and Medical Deontology, Medical Faculty, University "St. Cyril and Methodius", Skopje, Macedonia
| | - Andrea Casas-Vargas
- Group of Population Genetics and Identification, Genetics Institute, National University of Colombia, Bogotá, Colombia
| | - Wiliam Usaquén
- Group of Population Genetics and Identification, Genetics Institute, National University of Colombia, Bogotá, Colombia
| | - Dayse Silva
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | | | - Dean Herman Tineo
- Universidad Nacional Mayor de San Marcos, Instituto de Medicina Legal del Perú, Lima, Peru
| | - Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology team (EAAF), Córdoba, Argentina
| | - Reinhard Würzner
- Division of Hygiene & Med. Microbiology, Medical University of Innsbruck, Austria
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, TX, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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16
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Connell JR, Ghaiyed AP, Chaseling J, Mellick GD, Bernie A, Brownlie JC, Wright KM. Establishing historical sample data is essential for identification of unaccounted Australian soldiers from WWI, WWII, and the Korean War. AUST J FORENSIC SCI 2019. [DOI: 10.1080/00450618.2019.1623320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Jasmine R. Connell
- School of Environment and Science, Griffith University, Queensland, Australia
| | - Andrew P. Ghaiyed
- School of Environment and Science, Griffith University, Queensland, Australia
| | - Janet Chaseling
- School of Environment and Science, Griffith University, Queensland, Australia
| | - George D. Mellick
- School of Environment and Science, Griffith University, Queensland, Australia
- Griffith Institute for Drug Discovery, Griffith University, Queensland, Australia
| | - Andrew Bernie
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, Australian Capital Territory
| | - Jeremy C. Brownlie
- School of Environment and Science, Griffith University, Queensland, Australia
| | - Kirsty M. Wright
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, Australian Capital Territory
- Genomics Research Centre, School of Biomedical Science, Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
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17
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Xie T, Hu L, Guo YX, Li YC, Chen F, Zhu BF. Genetic polymorphism analysis of mitochondrial DNA from Chinese Xinjiang Kazak ethnic group by a novel mitochondrial DNA genotyping panel. Mol Biol Rep 2018; 46:17-25. [DOI: 10.1007/s11033-018-4375-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/10/2018] [Indexed: 11/24/2022]
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18
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Current and emerging tools for the recovery of genetic information from post mortem samples: New directions for disaster victim identification. Forensic Sci Int Genet 2018; 37:270-282. [DOI: 10.1016/j.fsigen.2018.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/27/2018] [Accepted: 08/27/2018] [Indexed: 01/14/2023]
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19
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Neparáczki E, Maróti Z, Kalmár T, Kocsy K, Maár K, Bihari P, Nagy I, Fóthi E, Pap I, Kustár Á, Pálfi G, Raskó I, Zink A, Török T. Mitogenomic data indicate admixture components of Central-Inner Asian and Srubnaya origin in the conquering Hungarians. PLoS One 2018; 13:e0205920. [PMID: 30335830 PMCID: PMC6193700 DOI: 10.1371/journal.pone.0205920] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/02/2018] [Indexed: 01/07/2023] Open
Abstract
It has been widely accepted that the Finno-Ugric Hungarian language, originated from proto Uralic people, was brought into the Carpathian Basin by the conquering Hungarians. From the middle of the 19th century this view prevailed against the deep-rooted Hungarian Hun tradition, maintained in folk memory as well as in Hungarian and foreign written medieval sources, which claimed that Hungarians were kinsfolk of the Huns. In order to shed light on the genetic origin of the Conquerors we sequenced 102 mitogenomes from early Conqueror cemeteries and compared them to sequences of all available databases. We applied novel population genetic algorithms, named Shared Haplogroup Distance and MITOMIX, to reveal past admixture of maternal lineages. Our results show that the Conquerors assembled from various nomadic groups of the Eurasian steppe. Population genetic results indicate that they had closest connection to the Onogur-Bulgar ancestors of Volga Tatars. Phylogenetic results reveal that more than one third of the Conqueror maternal lineages were derived from Central-Inner Asia and their most probable ultimate sources were the Asian Scythians and Asian Huns, giving support to the Hungarian Hun tradition. The rest of the lineages most likely originated from the Bronze Age Potapovka-Poltavka-Srubnaya cultures of the Pontic-Caspian steppe. Available data imply that the Conquerors did not have a major contribution to the gene pool of the Carpathian Basin.
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Affiliation(s)
| | - Zoltán Maróti
- Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, Hungary
| | - Tibor Kalmár
- Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, Hungary
| | - Klaudia Kocsy
- Department of Genetics, University of Szeged, Szeged, Hungary
| | - Kitti Maár
- Department of Genetics, University of Szeged, Szeged, Hungary
| | | | - István Nagy
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Erzsébet Fóthi
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - Ágnes Kustár
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - István Raskó
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Albert Zink
- Institute for Mummies and the Iceman, EURAC, Bolzano, Italy
| | - Tibor Török
- Department of Genetics, University of Szeged, Szeged, Hungary
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20
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Malyarchuk B, Derenko M, Denisova G, Litvinov A, Rogalla U, Skonieczna K, Grzybowski T, Pentelényi K, Guba Z, Zeke T, Molnár MJ. Whole mitochondrial genome diversity in two Hungarian populations. Mol Genet Genomics 2018; 293:1255-1263. [PMID: 29948329 DOI: 10.1007/s00438-018-1458-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/06/2018] [Indexed: 11/28/2022]
Abstract
Complete mitochondrial genomics is an effective tool for studying the demographic history of human populations, but there is still a deficit of mitogenomic data in European populations. In this paper, we present results of study of variability of 80 complete mitochondrial genomes in two Hungarian populations from eastern part of Hungary (Szeged and Debrecen areas). The genetic diversity of Hungarian mitogenomes is remarkably high, reaching 99.9% in a combined sample. According to the analysis of molecular variance (AMOVA), European populations showed a low, but statistically significant level of between-population differentiation (Fst = 0.61%, p = 0), and two Hungarian populations demonstrate lack of between-population differences. Phylogeographic analysis allowed us to identify 71 different mtDNA sub-clades in Hungarians, sixteen of which are novel. Analysis of ancestry-informative mtDNA sub-clades revealed a complex genetic structure associated with the genetic impact of populations from different parts of Eurasia, though the contribution from European populations is the most pronounced. At least 8% of ancestry-informative haplotypes found in Hungarians demonstrate similarity with East and West Slavic populations (sub-clades H1c23a, H2a1c1, J2b1a6, T2b25a1, U4a2e, K1c1j, and I1a1c), while the influence of Siberian populations is not so noticeable (sub-clades A12a, C4a1a, and probably U4b1a4).
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Affiliation(s)
- Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia.
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Galina Denisova
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Urszula Rogalla
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094, Bydgoszcz, Poland
| | - Katarzyna Skonieczna
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094, Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094, Bydgoszcz, Poland
| | - Klára Pentelényi
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, 1085, Hungary
| | - Zsuzsanna Guba
- Hungarian Molecular Anthropological Research Group, Debrecen, 4030, Hungary
| | - Tamás Zeke
- Hungarian Molecular Anthropological Research Group, Debrecen, 4030, Hungary
| | - Mária Judit Molnár
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, 1085, Hungary
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21
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Evaluation of the precision ID whole MtDNA genome panel for forensic analyses. Forensic Sci Int Genet 2018; 35:21-25. [PMID: 29626805 DOI: 10.1016/j.fsigen.2018.03.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/20/2018] [Accepted: 03/28/2018] [Indexed: 12/18/2022]
Abstract
Mitochondrial DNA (mtDNA) amplification and Massively Parallel Sequencing (MPS) using an early access version of the Precision ID Whole MtDNA Genome Panel (Thermo Fisher Scientific) and the Ion Personal Genome Machine (PGM) were evaluated using 15 forensically relevant samples. Samples were selected to represent typical forensic specimens for mtDNA analysis including hairs, hair shafts, swabs and ancient solid tissue samples (bones and teeth) that were stored in the freezer for up to several years after having been typed with conventional Sanger-type Sequencing and Capillary Electrophoresis. The MPS haplotypes confirmed the earlier results in all samples and provided additional sequence information that improved discrimination power and haplogroup estimation. The results raised the appetite for further experiments to validate and apply the new technology in forensic practice.
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22
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Identification and analysis of mtDNA genomes attributed to Finns reveal long-stagnant demographic trends obscured in the total diversity. Sci Rep 2017; 7:6193. [PMID: 28733587 PMCID: PMC5522469 DOI: 10.1038/s41598-017-05673-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 06/01/2017] [Indexed: 01/08/2023] Open
Abstract
In Europe, modern mitochondrial diversity is relatively homogeneous and suggests an ubiquitous rapid population growth since the Neolithic revolution. Similar patterns also have been observed in mitochondrial control region data in Finland, which contrasts with the distinctive autosomal and Y-chromosomal diversity among Finns. A different picture emerges from the 843 whole mitochondrial genomes from modern Finns analyzed here. Up to one third of the subhaplogroups can be considered as Finn-characteristic, i.e. rather common in Finland but virtually absent or rare elsewhere in Europe. Bayesian phylogenetic analyses suggest that most of these attributed Finnish lineages date back to around 3,000–5,000 years, coinciding with the arrival of Corded Ware culture and agriculture into Finland. Bayesian estimation of past effective population sizes reveals two differing demographic histories: 1) the ‘local’ Finnish mtDNA haplotypes yielding small and dwindling size estimates for most of the past; and 2) the ‘immigrant’ haplotypes showing growth typical of most European populations. The results based on the local diversity are more in line with that known about Finns from other studies, e.g., Y-chromosome analyses and archaeology findings. The mitochondrial gene pool thus may contain signals of local population history that cannot be readily deduced from the total diversity.
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23
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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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Park S, Cho S, Seo HJ, Lee JH, Kim MY, Lee SD. Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population. J Korean Med Sci 2017; 32:587-592. [PMID: 28244283 PMCID: PMC5334155 DOI: 10.3346/jkms.2017.32.4.587] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/15/2017] [Indexed: 12/02/2022] Open
Abstract
Mitochondrial DNA (mtDNA) genome analysis has been a potent tool in forensic practice as well as in the understanding of human phylogeny in the maternal lineage. The traditional mtDNA analysis is focused on the control region, but the introduction of massive parallel sequencing (MPS) has made the typing of the entire mtDNA genome (mtGenome) more accessible for routine analysis. The complete mtDNA information can provide large amounts of novel genetic data for diverse populations as well as improved discrimination power for identification. The genetic diversity of the mtDNA sequence in different ethnic populations has been revealed through MPS analysis, but the Korean population not only has limited MPS data for the entire mtGenome, the existing data is mainly focused on the control region. In this study, the complete mtGenome data for 186 Koreans, obtained using Ion Torrent Personal Genome Machine (PGM) technology and retrieved from rather common mtDNA haplogroups based on the control region sequence, are described. The results showed that 24 haplogroups, determined with hypervariable regions only, branched into 47 subhaplogroups, and point heteroplasmy was more frequent in the coding regions. In addition, sequence variations in the coding regions observed in this study were compared with those presented in other reports on different populations, and there were similar features observed in the sequence variants for the predominant haplogroups among East Asian populations, such as Haplogroup D and macrohaplogroups M9, G, and D. This study is expected to be the trigger for the development of Korean specific mtGenome data followed by numerous future studies.
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Affiliation(s)
- Sohyung Park
- Medical Examiner's Office, National Forensic Service, Wonju, Korea
| | - Sohee Cho
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
| | - Hee Jin Seo
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Moon Young Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Soong Deok Lee
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea.
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Bhatti S, Aslamkhan M, Abbas S, Attimonelli M, Aydin HH, de Souza EMS. Genetic analysis of mitochondrial DNA control region variations in four tribes of Khyber Pakhtunkhwa, Pakistan. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:687-697. [PMID: 27159729 DOI: 10.3109/24701394.2016.1174222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Due to its geo strategic position at the crossroad of Asia, Pakistan has gained crucial importance of playing its pivotal role in subsequent human migratory events, both prehistoric and historic. This human movement became possible through an ancient overland network of trails called "The Silk Route" linking Asia Minor, Middle East China, Central Asia and Southeast Asia. This study was conducted to analyze complete mitochondrial control region samples of 100 individuals of four major Pashtun tribes namely, Bangash, Khattak, Mahsuds and Orakzai in the province of Khyber Pakhtunkhwa, Pakistan. All Pashtun tribes revealed high genetic diversity which is comparable to the other Central Asian, Southeast Asian and European populations. The configuration of genetic variation and heterogeneity further unveiled through Multidimensional Scaling, Principal Component Analysis and phylogenetic analysis. The results revealed that Pashtun are the composite mosaic of West Eurasian ancestry of numerous geographic origin. They received substantial gene flow during different invasive movements and have a high element of the Western provenance. The most common haplogroups reported in this study are: South Asian haplogroups M (28%) and R (8%); whereas, West Asians haplogroups are present, albeit in high frequencies (67%) and widespread over all; HV (15%), U (17%), H (9%), J (8%), K (8%), W (4%), N (3%) and T (3%). Moreover, we linked the unexplored genetic connection between Ashkenazi Jews and Pashtun. The presence of specific haplotypes J1b (4%) and K1a1b1a (5%) pointed to a genetic connection of Jewish conglomeration in Khattak tribe. This was a result of an ancient genetic influx in the early Neolithic period that led to the formation of a diverse genetic substratum in present day Pashtun.
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Affiliation(s)
- Shahzad Bhatti
- a Department of Human Genetics and Molecular Biology , University of Health Sciences Lahore , Pakistan.,b Institute of Molecular Biology and Biotechnology, University of Lahore , Lahore , Pakistan
| | - M Aslamkhan
- a Department of Human Genetics and Molecular Biology , University of Health Sciences Lahore , Pakistan
| | - Sana Abbas
- b Institute of Molecular Biology and Biotechnology, University of Lahore , Lahore , Pakistan
| | - Marcella Attimonelli
- c Department of Biosciences, Biotechnologies and Biopharmaceutics , University of Bari , Italy
| | - Hikmet Hakan Aydin
- d Department of Medical Biochemistry , Ege University School of Medicine , Bornova Izmir , Turkey
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