1
|
Weissensteiner H, Forer L, Kronenberg F, Schönherr S. mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics. Nucleic Acids Res 2024; 52:W102-W107. [PMID: 38709886 PMCID: PMC11223783 DOI: 10.1093/nar/gkae296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/08/2024] Open
Abstract
Over the past decade, mtDNA-Server established itself as one of the most widely used variant calling web-services for human mitochondrial genomes. The service accepts sequencing data in BAM format and returns an annotated variant analysis report for both homoplasmic and heteroplasmic variants. In this work we present mtDNA-Server 2, which includes several new features highly requested by the community. Most importantly, it includes (a) the integration of a novel variant calling mode that accurately call insertions, deletions and single nucleotide variants at once, (b) the integration of additional quality control and input validation modules, (c) a method to estimate the required coverage to minimize false positives and (d) an interactive analytics dashboard. Furthermore, we migrated the complete analysis workflow to the Nextflow workflow manager for improved parallelization, reproducibility and local execution. Recognizing the importance of insertions and deletions as well as offering novel quality control, validation and reporting features, mtDNA-Server 2 provides researchers and clinicians a new state-of-the-art analysis platform for interpreting mitochondrial genomes. mtDNA-Server 2 is available via mitoverse, our analysis platform that offers a centralized place for mtDNA analysis in the cloud. The web-service, source code and its documentation are freely accessible at https://mitoverse.i-med.ac.at.
Collapse
Affiliation(s)
- Hansi Weissensteiner
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
2
|
Parasayan O, Laurelut C, Bôle C, Bonnabel L, Corona A, Domenech-Jaulneau C, Paresys C, Richard I, Grange T, Geigl EM. Late Neolithic collective burial reveals admixture dynamics during the third millennium BCE and the shaping of the European genome. SCIENCE ADVANCES 2024; 10:eadl2468. [PMID: 38896620 PMCID: PMC11186501 DOI: 10.1126/sciadv.adl2468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
The third millennium BCE was a pivotal period of profound cultural and genomic transformations in Europe associated with migrations from the Pontic-Caspian steppe, which shaped the ancestry patterns in the present-day European genome. We performed a high-resolution whole-genome analysis including haplotype phasing of seven individuals of a collective burial from ~2500 cal BCE and of a Bell Beaker individual from ~2300 cal BCE in the Paris Basin in France. The collective burial revealed the arrival in real time of steppe ancestry in France. We reconstructed the genome of an unsampled individual through its relatives' genomes, enabling us to shed light on the early-stage admixture patterns, dynamics, and propagation of steppe ancestry in Late Neolithic Europe. We identified two major Neolithic/steppe-related ancestry admixture pulses around 3000/2900 BCE and 2600 BCE. These pulses suggest different population expansion dynamics with striking links to the Corded Ware and Bell Beaker cultural complexes.
Collapse
Affiliation(s)
- Oğuzhan Parasayan
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Christophe Laurelut
- INRAP Grand Est, Châlons-en-Champagne, France
- UMR 8215 Trajectoires (CNRS-University Paris I), Paris, France
| | - Christine Bôle
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 et INSERM US24/CNRS UAR3633, Paris Descartes Sorbonne Université Paris Cité, Paris, France
| | | | - Alois Corona
- Service archéologique interdépartemental, 78180 Montigny-le-Bretonneux, France
| | - Cynthia Domenech-Jaulneau
- Service Régional, Direction Régionale des Affaires culturelles d’Île-de-France, UMR 8215 Trajectoires (CNRS-University Paris I), Paris, France
| | - Cécile Paresys
- INRAP Grand Est, Châlons-en-Champagne, France
- UMR 6472 CEPAM (CNRS-Nice University), Nice, France
| | - Isabelle Richard
- INRAP Grand Est, Châlons-en-Champagne, France
- UMR 6472 CEPAM (CNRS-Nice University), Nice, France
| | - Thierry Grange
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Eva-Maria Geigl
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| |
Collapse
|
3
|
Dobner J, Nguyen T, Pavez-Giani MG, Cyganek L, Distelmaier F, Krutmann J, Prigione A, Rossi A. mtDNA analysis using Mitopore. Mol Ther Methods Clin Dev 2024; 32:101231. [PMID: 38572068 PMCID: PMC10988129 DOI: 10.1016/j.omtm.2024.101231] [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: 09/14/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
Mitochondrial DNA (mtDNA) analysis is crucial for the diagnosis of mitochondrial disorders, forensic investigations, and basic research. Existing pipelines are complex, expensive, and require specialized personnel. In many cases, including the diagnosis of detrimental single nucleotide variants (SNVs), mtDNA analysis is still carried out using Sanger sequencing. Here, we developed a simple workflow and a publicly available webserver named Mitopore that allows the detection of mtDNA SNVs, indels, and haplogroups. To simplify mtDNA analysis, we tailored our workflow to process noisy long-read sequencing data for mtDNA analysis, focusing on sequence alignment and parameter optimization. We implemented Mitopore with eliBQ (eliminate bad quality reads), an innovative quality enhancement that permits the increase of per-base quality of over 20% for low-quality data. The whole Mitopore workflow and webserver were validated using patient-derived and induced pluripotent stem cells harboring mtDNA mutations. Mitopore streamlines mtDNA analysis as an easy-to-use fast, reliable, and cost-effective analysis method for both long- and short-read sequencing data. This significantly enhances the accessibility of mtDNA analysis and reduces the cost per sample, contributing to the progress of mtDNA-related research and diagnosis.
Collapse
Affiliation(s)
- Jochen Dobner
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Thach Nguyen
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Mario Gustavo Pavez-Giani
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Lukas Cyganek
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jean Krutmann
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andrea Rossi
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| |
Collapse
|
4
|
Bulduk BK, Tortajada J, Valiente-Pallejà A, Callado LF, Torrell H, Vilella E, Meana JJ, Muntané G, Martorell L. High number of mitochondrial DNA alterations in postmortem brain tissue of patients with schizophrenia compared to healthy controls. Psychiatry Res 2024; 337:115928. [PMID: 38759415 DOI: 10.1016/j.psychres.2024.115928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024]
Abstract
Previous studies have shown mitochondrial dysfunction in schizophrenia (SZ) patients, which may be caused by mitochondrial DNA (mtDNA) alterations. However, there are few studies in SZ that have analyzed mtDNA in brain samples by next-generation sequencing (NGS). To address this gap, we used mtDNA-targeted NGS and qPCR to characterize mtDNA alterations in brain samples from patients with SZ (n = 40) and healthy controls (HC) (n = 40). 35 % of SZ patients showed mtDNA alterations, a significantly higher prevalence compared to 10 % of HC. Specifically, SZ patients had a significantly higher frequency of deletions (35 vs. 5 in HC), with a mean number of deletions of 3.8 in SZ vs. 1.0 in HC. Likely pathogenic missense variants were also significantly more frequent in patients with SZ than in HC (10 vs. three HC), encompassing 14 variants in patients and three in HC. The pathogenic tRNA variant m.3243A>G was identified in one SZ patient with a high heteroplasmy level of 32.2 %. While no significant differences in mtDNA copy number (mtDNA-CN) were observed between SZ and HC, antipsychotic users had significantly higher mtDNA-CN than non-users. These findings suggest a potential role for mtDNA alterations in the pathophysiology of SZ that require further validation and functional studies.
Collapse
Affiliation(s)
- Bengisu K Bulduk
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain
| | - Juan Tortajada
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain
| | - Alba Valiente-Pallejà
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Luís F Callado
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; Department of Pharmacology, University of the Basque Country, UPV/EHU, Leioa, and BioBizkaia Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Helena Torrell
- Centre for Omic Sciences (COS), Joint Unit URV-EURECAT Technology Centre of Catalonia, Unique Scientific and Technical Infrastructures, Reus, Catalonia, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - J Javier Meana
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; Department of Pharmacology, University of the Basque Country, UPV/EHU, Leioa, and BioBizkaia Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Gerard Muntané
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; Institut de Biologia Evolutiva (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain.
| | - Lourdes Martorell
- Hospital Universitari Institut Pere Mata (HUIPM), Reus, Catalonia, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV-CERCA), Universitat Rovira i Virgili (URV), Reus, Catalonia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
5
|
Zhu C, Tong T, Farrell JJ, Martin ER, Bush WS, Pericak-Vance MA, Wang LS, Schellenberg GD, Haines JL, Lunetta KL, Farrer LA, Zhang X. MitoH3: Mitochondrial Haplogroup and Homoplasmic/Heteroplasmic Variant Calling Pipeline for Alzheimer's Disease Sequencing Project. J Alzheimers Dis Rep 2024; 8:575-587. [PMID: 38746629 PMCID: PMC11091720 DOI: 10.3233/adr-230120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/21/2024] [Indexed: 07/13/2024] Open
Abstract
Background Mitochondrial DNA (mtDNA) is a double-stranded circular DNA and has multiple copies in each cell. Excess heteroplasmy, the coexistence of distinct variants in copies of mtDNA within a cell, may lead to mitochondrial impairments. Accurate determination of heteroplasmy in whole-genome sequencing (WGS) data has posed a significant challenge because mitochondria carrying heteroplasmic variants cannot be distinguished during library preparation. Moreover, sequencing errors, contamination, and nuclear mtDNA segments can reduce the accuracy of heteroplasmic variant calling. Objective To efficiently and accurately call mtDNA homoplasmic and heteroplasmic variants from the large-scale WGS data generated from the Alzheimer's Disease Sequencing Project (ADSP), and test their association with Alzheimer's disease (AD). Methods In this study, we present MitoH3-a comprehensive computational pipeline for calling mtDNA homoplasmic and heteroplasmic variants and inferring haplogroups in the ADSP WGS data. We first applied MitoH3 to 45 technical replicates from 6 subjects to define a threshold for detecting heteroplasmic variants. Then using the threshold of 5% ≤variant allele fraction≤95%, we further applied MitoH3 to call heteroplasmic variants from a total of 16,113 DNA samples with 6,742 samples from cognitively normal controls and 6,183 from AD cases. Results This pipeline is available through the Singularity container engine. For 4,311 heteroplasmic variants identified from 16,113 samples, no significant variant count difference was observed between AD cases and controls. Conclusions Our streamlined pipeline, MitoH3, enables computationally efficient and accurate analysis of a large number of samples.
Collapse
Affiliation(s)
- Congcong Zhu
- Department of Medicine (Biomedical Genetics), Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Tong Tong
- Department of Medicine (Biomedical Genetics), Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - John J. Farrell
- Department of Medicine (Biomedical Genetics), Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - William S. Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Kathryn L. Lunetta
- Departments of Biostatistics Boston University School of Public Health, Boston, MA, USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Departments of Biostatistics Boston University School of Public Health, Boston, MA, USA
- Departments of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Departments of Neurology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Departments of Ophthalmology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Boston University School of Medicine, Framingham, MA, USA
- Alzheimer’s Disease Research Center, Boston University School of Medicine, Boston, MA, USA
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Departments of Biostatistics Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Boston University School of Medicine, Framingham, MA, USA
- Alzheimer’s Disease Research Center, Boston University School of Medicine, Boston, MA, USA
| |
Collapse
|
6
|
Cortes-Figueiredo F, Asseyer S, Chien C, Zimmermann HG, Ruprecht K, Schmitz-Hübsch T, Bellmann-Strobl J, Paul F, Morais VA. CD4 + T cell mitochondrial genotype in Multiple Sclerosis: a cross-sectional and longitudinal analysis. Sci Rep 2024; 14:7507. [PMID: 38553515 PMCID: PMC10980703 DOI: 10.1038/s41598-024-57592-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Multiple Sclerosis (MS) is a chronic autoimmune demyelinating disease of the central nervous system (CNS), with a largely unknown etiology, where mitochondrial dysfunction likely contributes to neuroaxonal loss and brain atrophy. Mirroring the CNS, peripheral immune cells from patients with MS, particularly CD4+ T cells, show inappropriate mitochondrial phenotypes and/or oxidative phosphorylation (OxPhos) insufficiency, with a still unknown contribution of mitochondrial DNA (mtDNA). We hypothesized that mitochondrial genotype in CD4+ T cells might influence MS disease activity and progression. Thus, we performed a retrospective cross-sectional and longitudinal study on patients with a recent diagnosis of either Clinically Isolated Syndrome (CIS) or Relapsing-Remitting MS (RRMS) at two timepoints: 6 months (VIS1) and 36 months (VIS2) after disease onset. Our primary outcomes were the differences in mtDNA extracted from CD4+ T cells between: (I) patients with CIS/RRMS (PwMS) at VIS1 and age- and sex-matched healthy controls (HC), in the cross-sectional analysis, and (II) different diagnostic evolutions in PwMS from VIS1 to VIS2, in the longitudinal analysis. We successfully performed mtDNA whole genome sequencing (mean coverage: 2055.77 reads/base pair) in 183 samples (61 triplets). Nonetheless, mitochondrial genotype was not associated with a diagnosis of CIS/RRMS, nor with longitudinal diagnostic evolution.
Collapse
Affiliation(s)
- Filipe Cortes-Figueiredo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Susanna Asseyer
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Claudia Chien
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Hanna G Zimmermann
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center Digital Future, Berlin, Germany
| | - Klemens Ruprecht
- Department of Neurology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Tanja Schmitz-Hübsch
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Judith Bellmann-Strobl
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Friedemann Paul
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany.
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Vanessa A Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
| |
Collapse
|
7
|
Dobner J, Nguyen T, Dunkel A, Prigione A, Krutmann J, Rossi A. Mitochondrial DNA integrity and metabolome profile are preserved in the human induced pluripotent stem cell reference line KOLF2.1J. Stem Cell Reports 2024; 19:343-350. [PMID: 38402620 PMCID: PMC10937150 DOI: 10.1016/j.stemcr.2024.01.009] [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: 10/17/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/27/2024] Open
Abstract
Quality control of human induced pluripotent stem cells (iPSCs) is critical to ensure reproducibility of research. Recently, KOLF2.1J was characterized and published as a male iPSC reference line to study neurological disorders. Emerging evidence suggests potential negative effects of mtDNA mutations, but its integrity was not analyzed in the original publication. To assess mtDNA integrity, we conducted a targeted mtDNA analysis followed by untargeted metabolomics analysis. We found that KOLF2.1J mtDNA integrity was intact at the time of publication and is still preserved in the commercially distributed cell line. In addition, the basal KOLF2.1J metabolome profile was similar to that of the two commercially available iPSC lines IMR90 and iPSC12, but clearly distinct from an in-house-generated ERCC6R683X/R683X iPSC line modeling Cockayne syndrome. Conclusively, we validate KOLF2.1J as a reference iPSC line, and encourage scientists to conduct mtDNA analysis and unbiased metabolomics whenever feasible.
Collapse
Affiliation(s)
- Jochen Dobner
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany.
| | - Thach Nguyen
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Andreas Dunkel
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Jean Krutmann
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany; Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Andrea Rossi
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany.
| |
Collapse
|
8
|
Bennett EA, Parasayan O, Prat S, Péan S, Crépin L, Yanevich A, Grange T, Geigl EM. Genome sequences of 36,000- to 37,000-year-old modern humans at Buran-Kaya III in Crimea. Nat Ecol Evol 2023; 7:2160-2172. [PMID: 37872416 DOI: 10.1038/s41559-023-02211-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/06/2023] [Indexed: 10/25/2023]
Abstract
Populations genetically related to present-day Europeans first appeared in Europe at some point after 38,000-40,000 years ago, following a cold period of severe climatic disruption. These new migrants would eventually replace the pre-existing modern human ancestries in Europe, but initial interactions between these groups are unclear due to the lack of genomic evidence from the earliest periods of the migration. Here we describe the genomes of two 36,000-37,000-year-old individuals from Buran-Kaya III in Crimea as belonging to this newer migration. Both genomes share the highest similarity to Gravettian-associated individuals found several thousand years later in southwestern Europe. These genomes also revealed that the population turnover in Europe after 40,000 years ago was accompanied by admixture with pre-existing modern human populations. European ancestry before 40,000 years ago persisted not only at Buran-Kaya III but is also found in later Gravettian-associated populations of western Europe and Mesolithic Caucasus populations.
Collapse
Affiliation(s)
- E Andrew Bennett
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Oğuzhan Parasayan
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | - Sandrine Prat
- UMR 7194 (HNHP), MNHN/CNRS/UPVD, Alliance Sorbonne Université, Musée de l'Homme, Palais de Chaillot, Paris, France
| | - Stéphane Péan
- UMR 7194 (HNHP), MNHN/CNRS/UPVD, Muséum national d'Histoire naturelle, Alliance Sorbonne Université, Institut de Paléontologie Humaine, Paris, France
| | - Laurent Crépin
- UMR 7194 (HNHP), MNHN/CNRS/UPVD, Muséum national d'Histoire naturelle, Alliance Sorbonne Université, Institut de Paléontologie Humaine, Paris, France
| | - Alexandr Yanevich
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Thierry Grange
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France.
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France.
| |
Collapse
|
9
|
Fähnrich A, Stephan I, Hirose M, Haarich F, Awadelkareem MA, Ibrahim S, Busch H, Wohlers I. North and East African mitochondrial genetic variation needs further characterization towards precision medicine. J Adv Res 2023; 54:59-76. [PMID: 36736695 DOI: 10.1016/j.jare.2023.01.021] [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: 10/04/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Mitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied. OBJECTIVES To address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial data set to date and use it for characterizing mitochondrial genetic variation in this region. METHODS We compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n = 2504) and the Human Genome Diversity Project (n = 828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples. RESULTS Using a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1. CONCLUSION Our findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.
Collapse
Affiliation(s)
- Anke Fähnrich
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Isabel Stephan
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Misa Hirose
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Franziska Haarich
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, and University Heart Center, Lübeck, Lübeck, Germany
| | - Mosab Ali Awadelkareem
- Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Saleh Ibrahim
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Khalifa University, Abu Dhabi, United Arab Emirates
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538 Lübeck, Germany
| | - Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Biomedical Data Science, Research Center Borstel, 23845 Borstel, Germany.
| |
Collapse
|
10
|
Gupta R, Kanai M, Durham TJ, Tsuo K, McCoy JG, Kotrys AV, Zhou W, Chinnery PF, Karczewski KJ, Calvo SE, Neale BM, Mootha VK. Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. Nature 2023; 620:839-848. [PMID: 37587338 PMCID: PMC10447254 DOI: 10.1038/s41586-023-06426-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
Mitochondrial DNA (mtDNA) is a maternally inherited, high-copy-number genome required for oxidative phosphorylation1. Heteroplasmy refers to the presence of a mixture of mtDNA alleles in an individual and has been associated with disease and ageing. Mechanisms underlying common variation in human heteroplasmy, and the influence of the nuclear genome on this variation, remain insufficiently explored. Here we quantify mtDNA copy number (mtCN) and heteroplasmy using blood-derived whole-genome sequences from 274,832 individuals and perform genome-wide association studies to identify associated nuclear loci. Following blood cell composition correction, we find that mtCN declines linearly with age and is associated with variants at 92 nuclear loci. We observe that nearly everyone harbours heteroplasmic mtDNA variants obeying two principles: (1) heteroplasmic single nucleotide variants tend to arise somatically and accumulate sharply after the age of 70 years, whereas (2) heteroplasmic indels are maternally inherited as mixtures with relative levels associated with 42 nuclear loci involved in mtDNA replication, maintenance and novel pathways. These loci may act by conferring a replicative advantage to certain mtDNA alleles. As an illustrative example, we identify a length variant carried by more than 50% of humans at position chrM:302 within a G-quadruplex previously proposed to mediate mtDNA transcription/replication switching2,3. We find that this variant exerts cis-acting genetic control over mtDNA abundance and is itself associated in-trans with nuclear loci encoding machinery for this regulatory switch. Our study suggests that common variation in the nuclear genome can shape variation in mtCN and heteroplasmy dynamics across the human population.
Collapse
Affiliation(s)
- Rahul Gupta
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Timothy J Durham
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristin Tsuo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jason G McCoy
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna V Kotrys
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wei Zhou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Konrad J Karczewski
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M Neale
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
11
|
Hernández CL. Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era. Genes (Basel) 2023; 14:1534. [PMID: 37628587 PMCID: PMC10453943 DOI: 10.3390/genes14081534] [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: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.
Collapse
Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| |
Collapse
|
12
|
Bjørnetrø T, Bousquet PA, Redalen KR, Trøseid AMS, Lüders T, Stang E, Sanabria AM, Johansen C, Fuglestad AJ, Kersten C, Meltzer S, Ree AH. Next-generation sequencing reveals mitogenome diversity in plasma extracellular vesicles from colorectal cancer patients. BMC Cancer 2023; 23:650. [PMID: 37438741 DOI: 10.1186/s12885-023-11092-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 06/19/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Recent reports have demonstrated that the entire mitochondrial genome can be secreted in extracellular vesicles (EVs), but the biological attributes of this cell-free mitochondrial DNA (mtDNA) remain insufficiently understood. We used next-generation sequencing to compare plasma EV-derived mtDNA to that of whole blood (WB), peripheral blood mononuclear cells (PBMCs), and formalin-fixed paraffin-embedded (FFPE) tumor tissue from eight rectal cancer patients and WB and fresh-frozen (FF) tumor tissue from eight colon cancer patients. METHODS Total DNA was isolated before the mtDNA was enriched by PCR with either two primer sets generating two long products or multiple primer sets (for the FFPE tumors), prior to the sequencing. mtDNA diversity was assessed as the total variant number, level of heteroplasmy (mutant mtDNA copies mixed with wild-type copies), variant distribution within the protein-coding genes, and the predicted functional effect of the variants in the different sample types. Differences between groups were compared by paired Student's t-test or ANOVA with Dunnett's multiple comparison tests when comparing matched samples from patients. Mann-Whitney U test was used when comparing differences between the cancer types and patient groups. Pearson correlation analysis was performed. RESULTS In both cancer types, EV mtDNA presented twice as many variants and had significantly more low-level heteroplasmy than WB mtDNA. The EV mtDNA variants were clustered in the coding regions, and the proportion of EV mtDNA variants that were missense mutations (i.e., estimated to moderately affect the mitochondrial protein function) was significantly higher than in WB and tumor tissues. Nonsense mutations (i.e., estimated to highly affect the mitochondrial protein function) were only observed in the tumor tissues and EVs. CONCLUSION Taken together, plasma EV mtDNA in CRC patients exhibits a high degree of diversity. TRIAL REGISTRATION ClinicalTrials.gov: NCT01816607 . Registered 22 March 2013.
Collapse
Affiliation(s)
- Tonje Bjørnetrø
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478, Lørenskog, Norway.
| | - Paula A Bousquet
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478, Lørenskog, Norway
| | - Kathrine Røe Redalen
- Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Torben Lüders
- Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Espen Stang
- Department of Pathology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Adriana M Sanabria
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478, Lørenskog, Norway
| | - Christin Johansen
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478, Lørenskog, Norway
| | - Anniken Jørlo Fuglestad
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Research, Southern Hospital Trust, Kristiansand, Norway
| | - Christian Kersten
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478, Lørenskog, Norway
- Department of Research, Southern Hospital Trust, Kristiansand, Norway
| | - Sebastian Meltzer
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478, Lørenskog, Norway
| | - Anne Hansen Ree
- Department of Oncology, Akershus University Hospital, P.O. Box 1000, 1478, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| |
Collapse
|
13
|
Aizpurua-Iraola J, Rasal R, Prieto L, Comas D, Bonet N, Casals F, Calafell F, Vásquez P. Population analysis of complete mitogenomes for 334 samples from El Salvador. Forensic Sci Int Genet 2023; 66:102906. [PMID: 37364481 DOI: 10.1016/j.fsigen.2023.102906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
The use of mitochondrial DNA (mtDNA) in the field of forensic genetics is widely spread mainly due to its advantages when identifying highly degraded samples. In this sense, massive parallel sequencing has made the analysis of the whole mitogenome more accessible, noticeably increasing the informativeness of mtDNA haplotypes. The civil war (1980-1992) in El Salvador caused many deaths and disappearances (including children) all across the country and the economic and social instability after the war forced many people to emigration. For this reason, different organizations have collected DNA samples from relatives with the aim of identifying missing people. Thus, we present a dataset containing 334 complete mitogenomes from the Salvadoran general population. To the best of our knowledge, this is the first publication of a nationwide forensic-quality complete mitogenome database of any Latin American country. We found 293 different haplotypes, with a random match probability of 0.0041 and 26.6 mean pairwise differences, which is similar to other Latin American populations, and which represent a marked improvement from the values obtained with just control region sequences. These haplotypes belong to 54 different haplogroups, being 91% of them of Native American origin. Over a third (35.9%) of the individuals carried at least a heteroplasmic site (excluding length heteroplasmies). Ultimately, the present database aims to represent mtDNA haplotype diversity in the general Salvadoran populations as a basis for the identification of people that disappeared during or after the civil war.
Collapse
Affiliation(s)
- Julen Aizpurua-Iraola
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Lourdes Prieto
- Instituto de Ciencias Forenses, Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Comisaría General de Policía Científica. DNA Laboratory, Madrid, Spain
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, San Salvador, El Salvador
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Vandiver AR, Hoang AN, Herbst A, Lee CC, Aiken JM, McKenzie D, Teitell MA, Timp W, Wanagat J. Nanopore sequencing identifies a higher frequency and expanded spectrum of mitochondrial DNA deletion mutations in human aging. Aging Cell 2023; 22:e13842. [PMID: 37132288 PMCID: PMC10265159 DOI: 10.1111/acel.13842] [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: 01/09/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 05/04/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletion mutations cause many human diseases and are linked to age-induced mitochondrial dysfunction. Mapping the mutation spectrum and quantifying mtDNA deletion mutation frequency is challenging with next-generation sequencing methods. We hypothesized that long-read sequencing of human mtDNA across the lifespan would detect a broader spectrum of mtDNA rearrangements and provide a more accurate measurement of their frequency. We employed nanopore Cas9-targeted sequencing (nCATS) to map and quantitate mtDNA deletion mutations and develop analyses that are fit-for-purpose. We analyzed total DNA from vastus lateralis muscle in 15 males ranging from 20 to 81 years of age and substantia nigra from three 20-year-old and three 79-year-old men. We found that mtDNA deletion mutations detected by nCATS increased exponentially with age and mapped to a wider region of the mitochondrial genome than previously reported. Using simulated data, we observed that large deletions are often reported as chimeric alignments. To address this, we developed two algorithms for deletion identification which yield consistent deletion mapping and identify both previously reported and novel mtDNA deletion breakpoints. The identified mtDNA deletion frequency measured by nCATS correlates strongly with chronological age and predicts the deletion frequency as measured by digital PCR approaches. In substantia nigra, we observed a similar frequency of age-related mtDNA deletions to those observed in muscle samples, but noted a distinct spectrum of deletion breakpoints. NCATS-mtDNA sequencing allows the identification of mtDNA deletions on a single-molecule level, characterizing the strong relationship between mtDNA deletion frequency and chronological aging.
Collapse
Affiliation(s)
- Amy R. Vandiver
- Division of Dermatology, Department of MedicineUCLALos AngelesCaliforniaUSA
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
| | - Austin N. Hoang
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
| | - Allen Herbst
- US Geological Survey National Wildlife Health CenterMadisonWisconsinUSA
| | - Cathy C. Lee
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
| | - Judd M. Aiken
- Department of Agricultural, Food and Nutritional SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Debbie McKenzie
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Michael A. Teitell
- Molecular Biology InstituteUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Pathology and Laboratory Medicine, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Bioengineering, California NanoSystems Institute, Broad Center for Regenerative Medicine and Stem Cell ResearchUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Pediatrics, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Jonsson Comprehensive Cancer Center, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
| | - Winston Timp
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jonathan Wanagat
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
| |
Collapse
|
16
|
Gupta R, Kanai M, Durham TJ, Tsuo K, McCoy JG, Chinnery PF, Karczewski KJ, Calvo SE, Neale BM, Mootha VK. Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.19.23284696. [PMID: 36711677 PMCID: PMC9882621 DOI: 10.1101/2023.01.19.23284696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Human mitochondria contain a high copy number, maternally transmitted genome (mtDNA) that encodes 13 proteins required for oxidative phosphorylation. Heteroplasmy arises when multiple mtDNA variants co-exist in an individual and can exhibit complex dynamics in disease and in aging. As all proteins involved in mtDNA replication and maintenance are nuclear-encoded, heteroplasmy levels can, in principle, be under nuclear genetic control, however this has never been shown in humans. Here, we develop algorithms to quantify mtDNA copy number (mtCN) and heteroplasmy levels using blood-derived whole genome sequences from 274,832 individuals of diverse ancestry and perform GWAS to identify nuclear loci controlling these traits. After careful correction for blood cell composition, we observe that mtCN declines linearly with age and is associated with 92 independent nuclear genetic loci. We find that nearly every individual carries heteroplasmic variants that obey two key patterns: (1) heteroplasmic single nucleotide variants are somatic mutations that accumulate sharply after age 70, while (2) heteroplasmic indels are maternally transmitted as mtDNA mixtures with resulting levels influenced by 42 independent nuclear loci involved in mtDNA replication, maintenance, and novel pathways. These nuclear loci do not appear to act by mtDNA mutagenesis, but rather, likely act by conferring a replicative advantage to specific mtDNA molecules. As an illustrative example, the most common heteroplasmy we identify is a length variant carried by >50% of humans at position m.302 within a G-quadruplex known to serve as a replication switch. We find that this heteroplasmic variant exerts cis -acting genetic control over mtDNA abundance and is itself under trans -acting genetic control of nuclear loci encoding protein components of this regulatory switch. Our study showcases how nuclear haplotype can privilege the replication of specific mtDNA molecules to shape mtCN and heteroplasmy dynamics in the human population.
Collapse
Affiliation(s)
- Rahul Gupta
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Timothy J Durham
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
| | - Kristin Tsuo
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Jason G McCoy
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
| | - Patrick F Chinnery
- Department of Clinical Neurosciences & MRC Mitochondrial Biology Unit, University of Cambridge, United Kingdom
| | - Konrad J Karczewski
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
| | - Benjamin M Neale
- Broad Institute of MIT and Harvard, United States
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, United States
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, United States
- Broad Institute of MIT and Harvard, United States
- Department of Systems Biology, Harvard Medical School, United States
| |
Collapse
|
17
|
Fleskes RE, Cabana GS, Gilmore JK, Juarez C, Karcher E, Oubré L, Mishoe G, Ofunniyin AA, Schurr TG. Community-engaged ancient DNA project reveals diverse origins of 18th-century African descendants in Charleston, South Carolina. Proc Natl Acad Sci U S A 2023; 120:e2201620120. [PMID: 36623185 PMCID: PMC9934026 DOI: 10.1073/pnas.2201620120] [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: 01/28/2022] [Accepted: 11/18/2022] [Indexed: 01/11/2023] Open
Abstract
In this study, we present the results of community-engaged ancient DNA research initiated after the remains of 36 African-descended individuals dating to the late 18th century were unearthed in the port city of Charleston, South Carolina. The Gullah Society of Charleston, along with other Charleston community members, initiated a collaborative genomic study of these ancestors of presumed enslaved status, in an effort to visibilize their histories. We generated 18 low-coverage genomes and 31 uniparental haplotypes to assess their genetic origins and interrelatedness. Our results indicate that they have predominantly West and West-Central African genomic ancestry, with one individual exhibiting some genomic affiliation with populations in the Americas. Most were assessed as genetic males, and no autosomal kin were identified among them. Overall, this study expands our understanding of the colonial histories of African descendant populations in the US South.
Collapse
Affiliation(s)
- Raquel E. Fleskes
- Department of Anthropology, University of Connecticut, Storrs, CT06269
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
| | | | - Joanna K. Gilmore
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
- Department of Sociology and Anthropology, The College of Charleston, Charleston, SC29424
| | - Chelsey Juarez
- Department of Anthropology, California State University, Fresno, CA93740
| | - Emilee Karcher
- Department of Anthropology, University of California, Davis, CA95616
| | - La’Sheia Oubré
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
| | - Grant Mishoe
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
| | - Ade A. Ofunniyin
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
- Department of Sociology and Anthropology, The College of Charleston, Charleston, SC29424
| | - Theodore G. Schurr
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA19104
| |
Collapse
|
18
|
KAHYA H, KARADUMAN T. Sık Kullanılan Bazı Hücre Hatları için Kalite Kontrol: Mikoplazma Kontaminasyon Tespiti, Sitokrom B ve Sitokrom Oksidaz Alt Birim I Genlerinin DNA Dizi Analizlerinin Gerçekleştirilmesi. İSTANBUL GELIŞIM ÜNIVERSITESI SAĞLIK BILIMLERI DERGISI 2022. [DOI: 10.38079/igusabder.1114239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Amaç: Laboratuvarlarda sık kullanılan serviks epitelyal karsinom (HeLa), insan periferal kan promiyelösitik lösemi (HL-60), fare C3/bağ dokusu (L929), Madin Darby köpek böbrek (MDCK), fare nöroblastom (Neuro-2a) gibi bazı hücre hatlarının mikoplazma kontaminasyon kontrollerinin yapılması, kimlik doğrulamalarının gerçekleştirilmesi ve klonalitelerinin belirlenmesidir.Yöntem: Bu çalışmada üç farklı türe ait beş hücre hattı kullanılmıştır. Çalışılan tüm hatların Bisbenzimid (Hoechst 33258) ile deoksiribonükleik asit (DNA) floresan işaretlemesi yapılarak mikoplazma kontaminasyonu kontrolleri gerçekleştirilmiştir. Hücre hatlarından DNA izolasyonları yapılmış, elde edilen DNA örneklerinden sitokrom B (CYTB) geninin bölgesel amplifikasyonu için L14816 ve H15173 primerleri; sitokrom oksidaz alt birim I (COI) geni için ise LCO 1490 and HCO 2198 primerleri kullanılmıştır. İlgili amplifikasyonların DNA dizi analiz sonuçları, biyoinformatik araçlar kullanılarak referans dizilerle karşılaştırmalı olarak değerlendirilmiştir.Bulgular: Çalışmada ilgili hücrelerin, Bisbenzimid (Hoechst 33258) ile üretici firmanın protokollerine göre belirlenen konsantrasyon ve sürede yapılan boyama sonucunda mikoplazma kontaminasyonuna rastlanılmamıştır. Ayrıca CYTB gen bölgesi için veritabanında yer alan referans dizi ile yapılan karşılaştırma sonucu HL-60 için %97; "HeLa, L929, MDCK, Neuro-2a” hücre hatları için ise %98 oranında benzerlik bulunmuştur. COI gen bölgesi için ise bu benzerlik oranları “HeLa, HL-60, L929, MDCK ve Neuro-2a” hücre hatları için sırasıyla %95, %99, %96, %96 ve %98 olarak bulunmuştur.Sonuç: Bu bağlamda, çalışmadan elde edilen Bisbenzimid (Hoechst 33258) işaretleme ve DNA dizi analiz sonuçları, pek çok araştırmada kullanılan bu hücre hatlarının kalitesi konusunda kabul edilebilir bir belirteç ve güven sağlamıştır.
Collapse
|
19
|
García-Olivares V, Rubio-Rodríguez LA, Muñoz-Barrera A, Díaz-de Usera A, Jáspez D, Iñigo-Campos A, Rodríguez Pérez MDC, Cabrera de León A, Lorenzo-Salazar JM, González-Montelongo R, Cabrera VM, Flores C. Digging into the admixture strata of current-day Canary Islanders based on mitogenomes. iScience 2022; 26:105907. [PMID: 36647378 PMCID: PMC9840145 DOI: 10.1016/j.isci.2022.105907] [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: 06/15/2022] [Revised: 10/18/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
The conquest of the Canary Islands by Europeans began at the beginning of the 15th century and culminated in 1496 with the surrender of the aborigines. The collapse of the aboriginal population during the conquest and the arrival of settlers caused a drastic change in the demographic composition of the archipelago. To shed light on this historical process, we analyzed 896 mitogenomes of current inhabitants from the seven main islands. Our findings confirm the continuity of aboriginal maternal contributions and the persistence of their genetic footprints in the current population, even at higher levels (>60% on average) than previously evidenced. Moreover, the age estimates for most autochthonous founder lineages support a first aboriginal arrival to the islands at the beginning of the first millennium. We also revealed for the first time that the main recognizable genetic influences from Europe are from Portuguese and Galicians.
Collapse
Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain,Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | - Luis A. Rubio-Rodríguez
- 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
| | - 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
| | | | - Antonio Cabrera de León
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain,Área de Medicina Preventiva y Salud Pública, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- 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,Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | | | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain,Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain,Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain,Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Las Palmas de Gran Canaria, Spain,Corresponding author
| |
Collapse
|
20
|
Campelo dos Santos AL, Owings A, Sullasi HSL, Gokcumen O, DeGiorgio M, Lindo J. Genomic evidence for ancient human migration routes along South America's Atlantic coast. Proc Biol Sci 2022; 289:20221078. [PMID: 36322514 PMCID: PMC9629774 DOI: 10.1098/rspb.2022.1078] [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] [Indexed: 11/23/2022] Open
Abstract
An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.
Collapse
Affiliation(s)
- Andre Luiz Campelo dos Santos
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA,Department of Archaeology, Federal University of Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | - Amanda Owings
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | | | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
21
|
Caporali L, Fiorini C, Palombo F, Romagnoli M, Baccari F, Zenesini C, Visconti P, Posar A, Scaduto MC, Ormanbekova D, Battaglia A, Tancredi R, Cameli C, Viggiano M, Olivieri A, Torroni A, Maestrini E, Rochat MJ, Bacchelli E, Carelli V, Maresca A. Dissecting the multifaceted contribution of the mitochondrial genome to autism spectrum disorder. Front Genet 2022; 13:953762. [PMID: 36419830 PMCID: PMC9676943 DOI: 10.3389/fgene.2022.953762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2023] Open
Abstract
Autism spectrum disorder (ASD) is a clinically heterogeneous class of neurodevelopmental conditions with a strong, albeit complex, genetic basis. The genetic architecture of ASD includes different genetic models, from monogenic transmission at one end, to polygenic risk given by thousands of common variants with small effects at the other end. The mitochondrial DNA (mtDNA) was also proposed as a genetic modifier for ASD, mostly focusing on maternal mtDNA, since the paternal mitogenome is not transmitted to offspring. We extensively studied the potential contribution of mtDNA in ASD pathogenesis and risk through deep next generation sequencing and quantitative PCR in a cohort of 98 families. While the maternally-inherited mtDNA did not seem to predispose to ASD, neither for haplogroups nor for the presence of pathogenic mutations, an unexpected influence of paternal mtDNA, apparently centered on haplogroup U, came from the Italian families extrapolated from the test cohort (n = 74) when compared to the control population. However, this result was not replicated in an independent Italian cohort of 127 families and it is likely due to the elevated paternal age at time of conception. In addition, ASD probands showed a reduced mtDNA content when compared to their unaffected siblings. Multivariable regression analyses indicated that variants with 15%-5% heteroplasmy in probands are associated to a greater severity of ASD based on ADOS-2 criteria, whereas paternal super-haplogroups H and JT were associated with milder phenotypes. In conclusion, our results suggest that the mtDNA impacts on ASD, significantly modifying the phenotypic expression in the Italian population. The unexpected finding of protection induced by paternal mitogenome in term of severity may derive from a role of mtDNA in influencing the accumulation of nuclear de novo mutations or epigenetic alterations in fathers' germinal cells, affecting the neurodevelopment in the offspring. This result remains preliminary and needs further confirmation in independent cohorts of larger size. If confirmed, it potentially opens a different perspective on how paternal non-inherited mtDNA may predispose or modulate other complex diseases.
Collapse
Affiliation(s)
- Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Claudio Fiorini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Flavia Palombo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Martina Romagnoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Flavia Baccari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Epidemiologia e Statistica, Bologna, Italy
| | - Corrado Zenesini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Epidemiologia e Statistica, Bologna, Italy
| | - Paola Visconti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Maria Cristina Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Danara Ormanbekova
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Agatino Battaglia
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa, Italy
| | - Raffaella Tancredi
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa, Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Viggiano
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Magali Jane Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma Diagnostica Funzionale Neuroradiologica, Bologna, Italy
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| |
Collapse
|
22
|
The kringle IV type 2 domain variant 4925G>A causes the elusive association signal of the LPA pentanucleotide repeat. J Lipid Res 2022; 63:100306. [PMID: 36309064 PMCID: PMC9700027 DOI: 10.1016/j.jlr.2022.100306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 11/23/2022] Open
Abstract
Lipoprotein(a) [Lp(a)] concentrations are regulated by the LPA gene mainly via the large kringle IV-type 2 (KIV-2) copy number variation and multiple causal variants. Early studies suggested an effect of long pentanucleotide repeat (PNR) alleles (10 and 11 repeats, PNR10 and PNR11) in the LPA promoter on gene transcription and found an association with lower Lp(a). Subsequent in vitro studies showed no effects on mRNA transcription, but the association with strongly decreased Lp(a) remained consistent. We investigated the isolated and combined effect of PNR10, PNR11, and the frequent splice site variant KIV-2 4925G>A on Lp(a) concentrations in the Cooperative Health Research in the Region of Augsburg F4 study by multiple quantile regression in single-SNP and joint models. Data on Lp(a), apolipoprotein(a) Western blot isoforms, and variant genotypes were available for 2,858 individuals. We found a considerable linkage disequilibrium between KIV-2 4925G>A and the alleles PNR10 and PNR11. In single-variant analysis adjusted for age, sex, and the shorter apo(a) isoform, we determined that both PNR alleles were associated with a highly significant Lp(a) decrease (PNR10: β = -14.43 mg/dl, 95% CI: -15.84, -13.02, P = 3.33e-84; PNR11: β = -17.21 mg/dl, 95% CI: -20.19, -14.23, P = 4.01e-29). However, a joint model, adjusting the PNR alleles additionally for 4925G>A, abolished the effect on Lp(a) (PNR10: β = +0.44 mg/dl, 95% CI: -1.73, 2.60, P = 0.69; PNR11: β = -1.52 mg/dl, 95% CI: -6.05, 3.00, P = 0.51). Collectively, we conclude that the previously reported Lp(a) decrease observed in pentanucleotide alleles PNR10 or PNR11 carriers results from a linkage disequilibrium with the frequent splicing mutation KIV-2 4925G>A.
Collapse
|
23
|
Harerimana NV, Paliwali D, Romero-Molina C, Bennett DA, Pa J, Goate A, Swerdlow RH, Andrews SJ. The role of mitochondrial genome abundance in Alzheimer's disease. Alzheimers Dement 2022; 19:2069-2083. [PMID: 36224040 DOI: 10.1002/alz.12812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/1912] [Revised: 12/12/1912] [Accepted: 12/12/1912] [Indexed: 11/05/2022]
Abstract
Mitochondrial dysfunction is an early and prominent feature of Alzheimer's disease (AD), with impaired energy metabolism preceding the onset of clinical symptoms. Here we propose an update to the mitochondrial dysfunction hypothesis of AD based on recent results examining the role of mitochondrial genome abundance in AD. In a large post mortem study, we show that lower brain mitochondrial genome abundance is associated with a greater odds of AD neuropathological change and worse cognitive performance. We hypothesize that lower mitochondrial genome abundance impairs mitochondrial function by reducing mitochondrial bioenergetics, thereby impacting neuronal and glial cell function. However, it remains to be determined if mitochondrial dysfunction causes, mediates, or is a by-product of AD pathogenesis. Additional support for this hypothesis will be generated by linking peripheral blood mitochondrial genome abundance to AD and establishing clinical trials of compounds that upregulate total mitochondrial genome abundance or boost mitochondrial mass.
Collapse
Affiliation(s)
- Nadia V Harerimana
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Devashi Paliwali
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Carmen Romero-Molina
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Judy Pa
- Department of Neurosciences, Alzheimer's Disease Cooperative Study (ADCS), University of California, San Diego, California, USA
| | - Alison Goate
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Russell H Swerdlow
- University of Kansas Alzheimer's Disease Research Center, Kansas City, Kansas, USA
| | - Shea J Andrews
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, California, USA
| |
Collapse
|
24
|
Keraite I, Becker P, Canevazzi D, Frias-López C, Dabad M, Tonda-Hernandez R, Paramonov I, Ingham MJ, Brun-Heath I, Leno J, Abulí A, Garcia-Arumí E, Heath SC, Gut M, Gut IG. A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome. Nat Commun 2022; 13:5902. [PMID: 36202811 PMCID: PMC9537161 DOI: 10.1038/s41467-022-33530-3] [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: 04/27/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Here we describe a method to target, multiplex and sequence at high coverage full-length human mitochondrial genomes as native single-molecules, utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks, that define the mtDNA beginning and end of the sequencing reads, as barcodes, we achieve high demultiplexing specificity and delineation of the full-length of the mtDNA, regardless of the structural variant pattern. The long-read sequencing data is analysed with a pipeline where our custom-developed software, baldur, efficiently detects single nucleotide heteroplasmy to below 1%, physically determines phase and can accurately disentangle complex deletions. Our workflow is a tool for studying mtDNA variation and will accelerate mitochondrial research. Accurate analysis of mitochondrial DNA is important for mitochondrial disease clinical research and diagnostics. Here, authors present a method using Cas9 cleavage, nanopore sequencing and a custom pipeline to identify pathogenic variants, deletions and accurately quantify heteroplasmy to below 1%.
Collapse
Affiliation(s)
- Ieva Keraite
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Philipp Becker
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Qiagen, Hilden, Germany
| | - Davide Canevazzi
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cristina Frias-López
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Raúl Tonda-Hernandez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ida Paramonov
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Matthew John Ingham
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Joint IRB-BSC Program in Computational Biology, Barcelona, Spain
| | - Jordi Leno
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Anna Abulí
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Elena Garcia-Arumí
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Research Group on Neuromuscular and Mitochondrial Disorders, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Simon Charles Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
| | - Ivo Glynne Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
| |
Collapse
|
25
|
Battle SL, Puiu D, Verlouw J, Broer L, Boerwinkle E, Taylor KD, Rotter JI, Rich SS, Grove ML, Pankratz N, Fetterman JL, Liu C, Arking D. A bioinformatics pipeline for estimating mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data. NAR Genom Bioinform 2022; 4:lqac034. [PMID: 35591888 PMCID: PMC9112767 DOI: 10.1093/nargab/lqac034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/16/2022] [Accepted: 04/25/2022] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial diseases are a heterogeneous group of disorders that can be caused by mutations in the nuclear or mitochondrial genome. Mitochondrial DNA (mtDNA) variants may exist in a state of heteroplasmy, where a percentage of DNA molecules harbor a variant, or homoplasmy, where all DNA molecules have the same variant. The relative quantity of mtDNA in a cell, or copy number (mtDNA-CN), is associated with mitochondrial function, human disease, and mortality. To facilitate accurate identification of heteroplasmy and quantify mtDNA-CN, we built a bioinformatics pipeline that takes whole genome sequencing data and outputs mitochondrial variants, and mtDNA-CN. We incorporate variant annotations to facilitate determination of variant significance. Our pipeline yields uniform coverage by remapping to a circularized chrM and by recovering reads falsely mapped to nuclear-encoded mitochondrial sequences. Notably, we construct a consensus chrM sequence for each sample and recall heteroplasmy against the sample's unique mitochondrial genome. We observe an approximately 3-fold increased association with age for heteroplasmic variants in non-homopolymer regions and, are better able to capture genetic variation in the D-loop of chrM compared to existing software. Our bioinformatics pipeline more accurately captures features of mitochondrial genetics than existing pipelines that are important in understanding how mitochondrial dysfunction contributes to disease.
Collapse
Affiliation(s)
- Stephanie L Battle
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Joost Verlouw
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Linda Broer
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephan S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Megan L Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Jessica L Fetterman
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Chunyu Liu
- Framingham Heart Study, Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
26
|
Lüth T, Schaake S, Grünewald A, May P, Trinh J, Weissensteiner H. Benchmarking Low-Frequency Variant Calling With Long-Read Data on Mitochondrial DNA. Front Genet 2022; 13:887644. [PMID: 35664331 PMCID: PMC9161029 DOI: 10.3389/fgene.2022.887644] [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: 03/01/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Sequencing quality has improved over the last decade for long-reads, allowing for more accurate detection of somatic low-frequency variants. In this study, we used mixtures of mitochondrial samples with different haplogroups (i.e., a specific set of mitochondrial variants) to investigate the applicability of nanopore sequencing for low-frequency single nucleotide variant detection. Methods: We investigated the impact of base-calling, alignment/mapping, quality control steps, and variant calling by comparing the results to a previously derived short-read gold standard generated on the Illumina NextSeq. For nanopore sequencing, six mixtures of four different haplotypes were prepared, allowing us to reliably check for expected variants at the predefined 5%, 2%, and 1% mixture levels. We used two different versions of Guppy for base-calling, two aligners (i.e., Minimap2 and Ngmlr), and three variant callers (i.e., Mutserve2, Freebayes, and Nanopanel2) to compare low-frequency variants. We used F1 score measurements to assess the performance of variant calling. Results: We observed a mean read length of 11 kb and a mean overall read quality of 15. Ngmlr showed not only higher F1 scores but also higher allele frequencies (AF) of false-positive calls across the mixtures (mean F1 score = 0.83; false-positive allele frequencies < 0.17) compared to Minimap2 (mean F1 score = 0.82; false-positive AF < 0.06). Mutserve2 had the highest F1 scores (5% level: F1 score >0.99, 2% level: F1 score >0.54, and 1% level: F1 score >0.70) across all callers and mixture levels. Conclusion: We here present the benchmarking for low-frequency variant calling with nanopore sequencing by identifying current limitations.
Collapse
Affiliation(s)
- Theresa Lüth
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Anne Grünewald
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- *Correspondence: Joanne Trinh, ; Hansi Weissensteiner,
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- *Correspondence: Joanne Trinh, ; Hansi Weissensteiner,
| |
Collapse
|
27
|
Ip EKK, Troup M, Xu C, Winlaw DS, Dunwoodie SL, Giannoulatou E. Benchmarking the Effectiveness and Accuracy of Multiple Mitochondrial DNA Variant Callers: Practical Implications for Clinical Application. Front Genet 2022; 13:692257. [PMID: 35350246 PMCID: PMC8957813 DOI: 10.3389/fgene.2022.692257] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/27/2022] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations contribute to human disease across a range of severity, from rare, highly penetrant mutations causal for monogenic disorders to mutations with milder contributions to phenotypes. mtDNA variation can exist in all copies of mtDNA or in a percentage of mtDNA copies and can be detected with levels as low as 1%. The large number of copies of mtDNA and the possibility of multiple alternative alleles at the same DNA nucleotide position make the task of identifying allelic variation in mtDNA very challenging. In recent years, specialized variant calling algorithms have been developed that are tailored to identify mtDNA variation from whole-genome sequencing (WGS) data. However, very few studies have systematically evaluated and compared these methods for the detection of both homoplasmy and heteroplasmy. A publicly available synthetic gold standard dataset was used to assess four mtDNA variant callers (Mutserve, mitoCaller, MitoSeek, and MToolBox), and the commonly used Genome Analysis Toolkit “best practices” pipeline, which is included in most current WGS pipelines. We also used WGS data from 126 trios and calculated the percentage of maternally inherited variants as a metric of calling accuracy, especially for homoplasmic variants. We additionally compared multiple pathogenicity prediction resources for mtDNA variants. Although the accuracy of homoplasmic variant detection was high for the majority of the callers with high concordance across callers, we found a very low concordance rate between mtDNA variant callers for heteroplasmic variants ranging from 2.8% to 3.6%, for heteroplasmy thresholds of 5% and 1%. Overall, Mutserve showed the best performance using the synthetic benchmark dataset. The analysis of mtDNA pathogenicity resources also showed low concordance in prediction results. We have shown that while homoplasmic variant calling is consistent between callers, there remains a significant discrepancy in heteroplasmic variant calling. We found that resources like population frequency databases and pathogenicity predictors are now available for variant annotation but still need refinement and improvement. With its peculiarities, the mitochondria require special considerations, and we advocate that caution needs to be taken when analyzing mtDNA data from WGS data.
Collapse
Affiliation(s)
- Eddie K K Ip
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, Sydney, NSW, Australia
| | - Michael Troup
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Colin Xu
- School of Computer Science and Engineering, Sydney, NSW, Australia
| | - David S Winlaw
- Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Centre, Heart Institute, Cincinnati, OH, United States
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, Sydney, NSW, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, Sydney, NSW, Australia
| |
Collapse
|
28
|
Sturk-Andreaggi K, Ring JD, Ameur A, Gyllensten U, Bodner M, Parson W, Marshall C, Allen M. The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes. Int J Mol Sci 2022; 23:ijms23042244. [PMID: 35216360 PMCID: PMC8876724 DOI: 10.3390/ijms23042244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612–13,105 and 16,390–16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.
Collapse
Affiliation(s)
- Kimberly Sturk-Andreaggi
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala 751 08, Sweden; (A.A.); (U.G.)
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.D.R.); (C.M.)
- SNA International, LLC, Alexandria, VA 22314, USA
- Correspondence: (K.S.-A.); (M.A.)
| | - Joseph D. Ring
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.D.R.); (C.M.)
- SNA International, LLC, Alexandria, VA 22314, USA
| | - Adam Ameur
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala 751 08, Sweden; (A.A.); (U.G.)
| | - Ulf Gyllensten
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala 751 08, Sweden; (A.A.); (U.G.)
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria; (M.B.); (W.P.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria; (M.B.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
| | - Charla Marshall
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.D.R.); (C.M.)
- SNA International, LLC, Alexandria, VA 22314, USA
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
| | - Marie Allen
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala 751 08, Sweden; (A.A.); (U.G.)
- Correspondence: (K.S.-A.); (M.A.)
| |
Collapse
|
29
|
Laricchia KM, Lake NJ, Watts NA, Shand M, Haessly A, Gauthier L, Benjamin D, Banks E, Soto J, Garimella K, Emery J, Rehm HL, MacArthur DG, Tiao G, Lek MV, Mootha VK, Calvo SE. Mitochondrial DNA variation across 56,434 individuals in gnomAD. Genome Res 2022; 32:569-582. [PMID: 35074858 PMCID: PMC8896463 DOI: 10.1101/gr.276013.121] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/19/2022] [Indexed: 11/25/2022]
Abstract
Genomic databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial genome (mtDNA). Here we present a pipeline to call mtDNA variants that addresses three technical challenges: (i) detecting homoplasmic and heteroplasmic variants, present respectively in all or a fraction of mtDNA molecules, (ii) circular mtDNA genome, and (iii) misalignment of nuclear sequences of mitochondrial origin (NUMTs). We observed that mtDNA copy number per cell varied across gnomAD cohorts and influenced the fraction of NUMT-derived false-positive variant calls, which can account for the majority of putative heteroplasmies. To avoid false positives, we excluded contaminated samples, cell lines, and samples prone to NUMT misalignment due to few mtDNA copies. Furthermore, we report variants with heteroplasmy greater than 10%. We applied this pipeline to 56,434 whole genome sequences in the gnomAD v3.1 database that includes individuals of European (58%), African (25%), Latino (10%), and Asian (5%) ancestry. Our gnomAD v3.1 release contains population frequencies for 10,850 unique mtDNA variants at more than half of all mtDNA bases. We report frequencies within each nuclear ancestral population and mitochondrial haplogroup. Homoplasmic variants account for most variant calls (98%) and unique variants (85%). We observed that 1/250 individuals carry a pathogenic mtDNA variant with heteroplasmy above 10%. These mtDNA population allele frequencies are freely accessible and will aid in diagnostic interpretation and research studies.
Collapse
|
30
|
Su L, Guo S, Guo W, Ji X, Liu Y, Zhang H, Huang Q, Zhou K, Guo X, Gu X, Xing J. mitoDataclean: A machine learning approach for the accurate identification of cross-contamination-derived tumor mitochondrial DNA mutations. Int J Cancer 2022; 150:1677-1689. [PMID: 35001369 DOI: 10.1002/ijc.33927] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/03/2021] [Accepted: 12/22/2021] [Indexed: 11/06/2022]
Abstract
Next-generation sequencing (NGS) of mitochondrial DNA (mtDNA) has widespread applications in aging and cancer studies. However, cross-contamination of mtDNA constitutes a major concern. Previous methods for the detection of mtDNA contamination mainly focus on haplogroup-level phylogeny, but neglect haplotype-level differences, leading to limited sensitivity and accuracy. In this study, we present mitoDataclean, a random-forest-based machine learning package for accurate identification of cross-contamination, evaluation of contamination levels and detection of contamination-derived variants in mtDNA NGS data. Comprehensive optimization of mitoDataclean revealed that training simulation with mixtures of small haplogroup distance and low polymorphic difference was critical for optimal modeling. Compared with existing methods, mitoDataclean exhibited significantly improved sensitivity and accuracy for the detection of sample contamination in simulated data. In addition, mitoDataclean achieved area under the curve values of 0.91 and 0.97 for discerning genuine and contamination-derived mtDNA variants in a simulated Western dataset and private sequencing contamination data, respectively, suggesting that this tool may be applicable for different populations and samples with different sources of contamination. Finally, mitoDataclean was further evaluated in several private and public datasets and showed a robust ability for contamination detection. Altogether, our study demonstrates that mitoDataclean may be used for accurate detection of contaminated samples and contamination-derived variants in mtDNA NGS data. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Liping Su
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Shanshan Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Wenjie Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xiaoying Ji
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Yang Liu
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Huanqin Zhang
- College of Medical Technology, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Qichao Huang
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Kaixiang Zhou
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xu Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xiwen Gu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| |
Collapse
|
31
|
An J, Min KI, Ju YS. Identifying Somatic Mitochondrial DNA Mutations. Methods Mol Biol 2022; 2493:153-165. [PMID: 35751814 DOI: 10.1007/978-1-0716-2293-3_10] [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] [Indexed: 06/15/2023]
Abstract
Mitochondria are cellular organelles that play an essential role in eukaryotes, producing the energy needed for a cell to survive. Beyond the ~3.2 Gb of nuclear genomic DNA, each human cell has hundreds of mitochondria which carry one or a few copies of the 16.5 kb circular mitochondria DNA (mtDNA). Despite its small size, the circular genome encodes 37 genes, including 13 proteins that generate respiratory chain complexes together with other proteins of nuclear origin. Similar to nuclear genome, mtDNA in cancer cells frequently harbor somatically acquired alterations. Whole-genome or whole-exome sequencing of the tumor and its matched normal tissues (frequently blood or adjacent non-tumor tissues) enables sensitive and efficient detection of somatic mtDNA mutations. Because each cancer cell commonly carries hundreds to thousands of mtDNA copies, detection of mtDNA mutations is dependent on the heteroplasmic level of each mutation. Here, we describe strategies to accurately identify somatic mtDNA mutations in cancer genome studies.
Collapse
Affiliation(s)
- Jisong An
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kyoung Il Min
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
| |
Collapse
|
32
|
Yoon CJ, Kim SY, Nam CH, Lee J, Park JW, Mun J, Park S, Lee S, Yi B, Min KI, Wiley B, Bolton KL, Lee JH, Kim E, Yoo HJ, Jun JK, Choi JS, Griffith M, Griffith OL, Ju YS. Estimation of intrafamilial DNA contamination in family trio genome sequencing using deviation from Mendelian inheritance. Genome Res 2022; 32:2134-2144. [PMID: 36617634 PMCID: PMC9808622 DOI: 10.1101/gr.276794.122] [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: 03/28/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022]
Abstract
With the increasing number of sequencing projects involving families, quality control tools optimized for family genome sequencing are needed. However, accurately quantifying contamination in a DNA mixture is particularly difficult when genetically related family members are the sources. We developed TrioMix, a maximum likelihood estimation (MLE) framework based on Mendel's law of inheritance, to quantify DNA mixture between family members in genome sequencing data of parent-offspring trios. TrioMix can accurately deconvolute any intrafamilial DNA contamination, including parent-offspring, sibling-sibling, parent-parent, and even multiple familial sources. In addition, TrioMix can be applied to detect genomic abnormalities that deviate from Mendelian inheritance patterns, such as uniparental disomy (UPD) and chimerism. A genome-wide depth and variant allele frequency plot generated by TrioMix facilitates tracing the origin of Mendelian inheritance deviations. We showed that TrioMix could accurately deconvolute genomes in both simulated and real data sets.
Collapse
Affiliation(s)
- Christopher J. Yoon
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,Research Center for Natural Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,McDonnell Genome Institute, St. Louis, Missouri 63108, USA
| | - Su Yeon Kim
- Research Center for Natural Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Chang Hyun Nam
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | - Jung Woo Park
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | - Jihyeob Mun
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | | | - Soyoung Lee
- GENOME INSIGHT Incorporated, Daejeon 34051, Korea
| | - Boram Yi
- GENOME INSIGHT Incorporated, Daejeon 34051, Korea
| | - Kyoung Il Min
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Brian Wiley
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Kelly L. Bolton
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon 34141, Korea
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam 13620, Korea;,Department of Psychiatry, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jong Kwan Jun
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Ji Seon Choi
- Department of Laboratory Medicine, International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon 22711, Korea
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,McDonnell Genome Institute, St. Louis, Missouri 63108, USA
| | - Obi L. Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,McDonnell Genome Institute, St. Louis, Missouri 63108, USA
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,GENOME INSIGHT Incorporated, Daejeon 34051, Korea
| |
Collapse
|
33
|
Cortes-Figueiredo F, Carvalho FS, Fonseca AC, Paul F, Ferro JM, Schönherr S, Weissensteiner H, Morais VA. From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel. Int J Mol Sci 2021; 22:12031. [PMID: 34769461 PMCID: PMC8584537 DOI: 10.3390/ijms222112031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 02/06/2023] Open
Abstract
Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS's variants (TSS found 57.92% of PCP's variants), with a significant correlation between the variant levels of variants found with both pipelines.
Collapse
Affiliation(s)
- Filipe Cortes-Figueiredo
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Filipa S. Carvalho
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
| | - Ana Catarina Fonseca
- José Ferro Lab—Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.C.F.); (J.M.F.)
- Serviço de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-035 Lisbon, Portugal
| | - Friedemann Paul
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - José M. Ferro
- José Ferro Lab—Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.C.F.); (J.M.F.)
- Serviço de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-035 Lisbon, Portugal
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Vanessa A. Morais
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
| |
Collapse
|
34
|
Emery MV, Bolhofner K, Ghafoor S, Winingear S, Buikstra JE, Fulginiti LC, Stone AC. Whole mitochondrial genomes assembled from thermally altered forensic bones and teeth. Forensic Sci Int Genet 2021; 56:102610. [PMID: 34735939 DOI: 10.1016/j.fsigen.2021.102610] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/29/2021] [Accepted: 10/18/2021] [Indexed: 12/17/2022]
Abstract
The recovery and analysis of genetic material obtained from thermally altered human bones and teeth are increasingly important to forensic investigations, especially in cases where soft-tissue identification is no longer possible. Although little is known about how these fire-related processes affect DNA degradation over time, next-generation sequencing technology in combination with traditional osteobiographical applications may provide us clues to these questions. In this study, we compare whole mitochondrial genome data generated using two different DNA extraction methods from 27 thermally altered samples obtained from fire victims (Maricopa County, Arizona) . DNA extracts were converted to double-stranded DNA libraries and enriched for whole mitochondrial DNA (mtDNA) using synthetic biotinylated RNA baits, then sequenced on an Illumina MiSeq. We processed the mitochondrial data using an in-house computational pipeline (MitoPipe1.0) composed of ancient DNA and modern genomics applications, then compared the resulting information across the two extraction types and five burn categories. Our analysis shows that DNA fragmentation increases with temperature, but that the acute insult from fire combined with the lack of water is insufficient to produce 5' and 3' terminal deamination characteristic of ancient DNA. Our data also suggest an acute and significant point of DNA degradation between 350 °C and 550 °C, and that the likelihood of generating high quality mtDNA haplogroup calls decreases significantly at temperatures > 550 °C. This research is part of a concerted effort to understand how fire affects our ability to generate genetic profiles suitable for forensic identification purposes.
Collapse
Affiliation(s)
- M V Emery
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States.
| | - K Bolhofner
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Bioarchaeology, Arizona State University, United States; Maricopa County Office of the Medical Examiner, Phoenix, AZ, United States; School of Life Sciences, Arizona State University, United States; School of Mathematical and Natural Sciences, Arizona State University, United States
| | - S Ghafoor
- Center for Evolution and Medicine, Arizona State University, United States; School of Life Sciences, Arizona State University, United States
| | - S Winingear
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; School of Life Sciences, Arizona State University, United States
| | - J E Buikstra
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; Center for Bioarchaeology, Arizona State University, United States; School of Life Sciences, Arizona State University, United States
| | - L C Fulginiti
- School of Human Evolution and Social Change, Arizona State University, United States; Maricopa County Office of the Medical Examiner, Phoenix, AZ, United States; School of Life Sciences, Arizona State University, United States
| | - A C Stone
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; Center for Bioarchaeology, Arizona State University, United States.
| |
Collapse
|
35
|
An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia. Sci Rep 2021; 11:10816. [PMID: 34031453 PMCID: PMC8144189 DOI: 10.1038/s41598-021-90145-2] [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: 03/25/2021] [Accepted: 05/07/2021] [Indexed: 11/08/2022] Open
Abstract
Cambodia harbours a variety of human aboriginal populations that have scarcely been studied in terms of genetic diversity of entire mitochondrial genomes. Here we present the matrilineal gene pool of 299 Cambodian refugees from three different ethnic groups (Cham, Khmer, and Khmer Loeu) deriving from 16 Cambodian districts. After establishing a DNA-saving high-throughput strategy for mitochondrial whole-genome Sanger sequencing, a HaploGrep based workflow was used for quality control, haplogroup classification and phylogenetic reconstruction. The application of diverse phylogenetic algorithms revealed an exciting picture of the genetic diversity of Cambodia, especially in relation to populations from Southeast Asia and from the whole world. A total of 224 unique haplotypes were identified, which were mostly classified under haplogroups B5a1, F1a1, or categorized as newly defined basal haplogroups or basal sub-branches of R, N and M clades. The presence of autochthonous maternal lineages could be confirmed as reported in previous studies. The exceptional homogeneity observed between and within the three investigated Cambodian ethnic groups indicates genetic isolation of the whole population. Between ethnicities, genetic barriers were not detected. The mtDNA data presented here increases the phylogenetic resolution in Cambodia significantly, thereby highlighting the need for an update of the current human mtDNA phylogeny.
Collapse
|