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Liu G, Zheng Y, Wu Q, Feng T, Xia Y, Chen D, Ren L, Bai X, Li Q, Chen D, Lv M, Liao M, Liang W, Zhang L, Qu S. Assessment of ForenSeq mtDNA Whole Genome Kit for forensic application. Int J Legal Med 2023; 137:1693-1703. [PMID: 37731065 DOI: 10.1007/s00414-023-03084-0] [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: 07/14/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
Mitochondrial DNA (mtDNA) is an indispensable genetic marker in forensic genetics. The emergence and development of massively parallel sequencing (MPS) makes it possible to obtain complete mitochondrial genome sequences more quickly and accurately. The study evaluated the advantages and limitations of the ForenSeq mtDNA Whole Genome Kit in the practical application of forensic genetics by detecting human genomic DNA standards and thirty-three case samples. We used control DNA with different amount to determine sensitivity of the assay. Even when the input DNA is as low as 2.5 pg, most of the mitochondrial genome sequences could still be covered. For the detection of buccal swabs and aged case samples (bloodstains, bones, teeth), most samples could achieve complete coverage of mitochondrial genome. However, when ancient samples and hair samples without hair follicles were sequenced by the kit, it failed to obtain sequence information. In general, the ForenSeq mtDNA Whole Genome Kit has certain applicability to forensic low template and degradation samples, and these results provide the data basis for subsequent forensic applications of the assay. The overall detection process and subsequent analysis are easy to standardize, and it has certain application potential in forensic cases.
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Affiliation(s)
- Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Tao Feng
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Yu Xia
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Dan Chen
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Li Ren
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Xiaogang Bai
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Qingqing Li
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
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Lee SE, Kim GE, Kim H, Chung DH, Lee SD, Kim MY. Comparison of Two Variant Analysis Programs for Next-Generation Sequencing Data of Whole Mitochondrial Genome. J Korean Med Sci 2023; 38:e297. [PMID: 37698211 PMCID: PMC10497357 DOI: 10.3346/jkms.2023.38.e297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/29/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND With advance of next-generation sequencing (NGS) techniques, the need for mitochondrial DNA analysis is increasing not only in the forensic area, but also in medical fields. METHODS Two commercial programs, Converge Software (CS) and Torrent Variant Caller for variant calling of NGS data, were compared with a considerable amount of sequence data of 50 samples with a homogeneous ethnicity. RESULTS About 2,300 variants were identified and the two programs showed about 90% of consistency. CS, a dedicated analysis program for mitochondrial DNA, showed some advantages for forensic use. By additional visual inspection, several causes of discrepancy in variant calling results were identified. Application of different notation rules for mitochondrial sequence and the minor allele frequency close to detection threshold were the two most significant reasons. CONCLUSION With prospective improvement of each program, researchers and practitioners should be aware of characteristics of the analysis program they use and prepare their own strategies to determine variants.
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Affiliation(s)
- Seung Eun Lee
- Laboratory of Forensic Medicine, Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Ga Eun Kim
- Laboratory of Forensic Medicine, Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Hajin Kim
- Laboratory of Forensic Medicine, Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Doo Hyun Chung
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Laboratory of Immune Regulation, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Young Kim
- Laboratory of Forensic Medicine, Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea.
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3
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Xavier C, Sutter C, Amory C, Niederstätter H, Parson W. NuMY-A qPCR Assay Simultaneously Targeting Human Autosomal, Y-Chromosomal, and Mitochondrial DNA. Genes (Basel) 2023; 14:1645. [PMID: 37628695 PMCID: PMC10454206 DOI: 10.3390/genes14081645] [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: 07/13/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The accurate quantification of DNA in forensic samples is of utmost importance. These samples are often present in limited amounts; therefore, it is indicated to use the appropriate analysis route with the optimum DNA amount (when possible). Also, DNA quantification can inform about the degradation stage and therefore support the decision on which downstream genotyping method to use. Consequently, DNA quantification aids in getting the best possible results from a forensic sample, considering both its DNA quantity and quality limitations. Here, we introduce NuMY, a new quantitative real-time PCR (qPCR) method for the parallel quantification of human nuclear (n) and mitochondrial (mt) DNA, assessing the male portion in mixtures of both sexes and testing for possible PCR inhibition. NuMY is based on previous work and follows the MIQE guidelines whenever applicable. Although quantification of nuclear (n)DNA by simultaneously analyzing autosomal and male-specific targets is available in commercial qPCR kits, tools that include the quantification of mtDNA are sparse. The quantification of mtDNA has proven relevant for samples with low nDNA content when conventional DNA fingerprinting techniques cannot be followed. Furthermore, the development and use of new massively parallel sequencing assays that combine multiple marker types, i.e., autosomal, Y-chromosomal, and mtDNA, can be optimized when precisely knowing the amount of each DNA component present in the input sample. For high-quality DNA extracts, NuMY provided nDNA results comparable to those of another quantification technique and has also proven to be a reliable tool for challenging, forensically relevant samples such as mixtures, inhibited, and naturally degraded samples.
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Affiliation(s)
- Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
- i3S—Institute for Research and Innovation in Health, University of Porto, 4099-002 Porto, Portugal
| | - Charlotte Sutter
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
| | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
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4
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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.
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Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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5
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Kayser M, Sajantila A, Butler JM, Parson W, Salas A, Gill P, Parsons T, Phillips C, Egeland T, Marshall C. Special issue: Forensic Genetics: Unde venisti et quo vadis? Forensic Sci Int Genet 2023:102881. [PMID: 37173159 DOI: 10.1016/j.fsigen.2023.102881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, the Netherland.
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki and Finnish Institute for Health and Welfare, Helsinki, Finland
| | - John M Butler
- National Institute of Standards and Technology, Special Programs Office, Gaithersburg, MD, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Austria and Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Antonio Salas
- Forensic Genetics Unit, Institute of Forensic Sciences and GenPoB Research Group, Institute of Health Research, Clinic Hospital, University of Santiago de Compostela, Spain
| | - Peter Gill
- Forensic Genetics Research Group, Oslo University Hospital and Department of Clinical Medicine, University of Oslo, Norway
| | - Thomas Parsons
- International Commission on Missing Persons, Den Haag, the Netherlands
| | - Chris Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Thore Egeland
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Charla Marshall
- Emerging Technologies Section, Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE, USA
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6
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Peng D, Geng J, Yang J, Liu J, Wang N, Wu R, Sun H. Whole Mitochondrial Genome Detection and Analysis of Two- to Four-Generation Maternal Pedigrees Using a New Massively Parallel Sequencing Panel. Genes (Basel) 2023; 14:genes14040912. [PMID: 37107670 PMCID: PMC10137955 DOI: 10.3390/genes14040912] [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: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is an effective genetic marker in forensic practice, especially for aged bones and hair shafts. Detection of the whole mitochondrial genome (mtGenome) using traditional Sanger-type sequencing is laborious and time-consuming. Additionally, its ability to distinguish point heteroplasmy (PHP) and length heteroplasmy (LHP) is limited. The application of massively parallel sequencing in mtDNA detection helps researchers to study the mtGenome in-depth. The ForenSeq mtDNA Whole Genome Kit, which contains a total of 245 short amplicons, is one of the multiplex library preparation kits for the mtGenome. We used this system to detect the mtGenome in the blood samples and hair shafts of thirty-three individuals from eight two-generation pedigrees, one three-generation pedigree, and one four-generation pedigree. High-quality sequencing results were obtained. Ten unique mtGenome haplotypes were observed in the mothers from the ten pedigrees. A total of 26 PHPs were observed using the interpretation threshold of 6%. Eleven types of LHPs in six regions were evaluated in detail. When considering homoplasmic variants only, consistent mtGenome haplotypes were observed between the twice-sequenced libraries and between the blood and hair shafts from the same individual and among maternal relatives in the pedigrees. Four inherited PHPs were observed, and the remainder were de novo/disappearing PHPs in the pedigrees. Our results demonstrate the effective capability of the ForenSeq mtDNA Whole Genome Kit to generate the complete mtGenome in blood and hair shafts, as well as the complexity of mtDNA haplotype comparisons between different types of maternal relatives when heteroplasmy is considered.
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Affiliation(s)
- Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
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7
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Liu Z, Simayijiang H, Wang Q, Yang J, Sun H, Wu R, Yan J. DNA and protein analyses of hair in forensic genetics. Int J Legal Med 2023; 137:613-633. [PMID: 36732435 DOI: 10.1007/s00414-023-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China.
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8
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Borik-Heil L, Endler G, Parson W, Zuckermann A, Schnaller L, Uyanik-Ünal K, Jaksch P, Böhmig G, Cejka D, Staufer K, Hielle-Wittmann E, Rasoul-Rockenschaub S, Wolf P, Sunder-Plassmann R, Geusau A. Cumulative UV Exposure or a Modified SCINEXA™-Skin Aging Score Do Not Play a Substantial Role in Predicting the Risk of Developing Keratinocyte Cancers after Solid Organ Transplantation-A Case Control Study. Cancers (Basel) 2023; 15:cancers15030864. [PMID: 36765822 PMCID: PMC9913211 DOI: 10.3390/cancers15030864] [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: 12/21/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
The risk of keratinocyte cancer is determined by intrinsic and extrinsic factors, which also influence skin aging. Few studies have linked skin aging and UV exposure with the incidence of non-melanoma skin cancer (NMSC). We evaluated signs of actinic skin damage and aging, individual UV burden, and melanocortin-1 receptor (MC1R) variants. A total of 194 organ transplant recipients (OTR) who suffered from NMSC were compared to 194 tumor-free controls matched for gender, age, type of transplanted organ, post-transplantation (TX) period, and immunosuppressive therapy. Compared with the cases, the controls scored higher in all skin aging scores and there were no differences in UV burden except for intentional whole-body UV exposure for specific UV scenarios and periods of life in favor of cases. The number of NMSCs correlated with all types of skin aging scores, the extent of intentional sun exposure, older age, longer post-TX period, shorter interval from TX to first NMSC, and specific MC1R risk groups. Multivariable models revealed a 7.5-fold risk of developing NMSC in individuals with actinic keratosis; 4.1- or 3.6-fold in those with green or blue eyes, respectively; and a 1.9-fold increased risk in the MC1R medium- + high-risk group. In the absence of skin aging contributing to NMSC development, certain MC1R risk types may identify OTR at risk for high tumor burden.
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Affiliation(s)
- Liliane Borik-Heil
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Georg Endler
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
| | - Andreas Zuckermann
- Department of Cardiac Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Lisa Schnaller
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Keziban Uyanik-Ünal
- Department of Thoracic Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Peter Jaksch
- Department of Thoracic Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Georg Böhmig
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, 1090 Vienna, Austria
| | - Daniel Cejka
- Department of Nephrology, Ordensklinikum Barmherzige Schwestern Linz, 4020 Linz, Austria
| | - Katharina Staufer
- Department of General Surgery, Division of Transplantation, Medical University of Vienna, 1090 Vienna, Austria
| | - Elisabeth Hielle-Wittmann
- Department of General Surgery, Division of Transplantation, Medical University of Vienna, 1090 Vienna, Austria
| | - Susanne Rasoul-Rockenschaub
- Department of General Surgery, Division of Transplantation, Medical University of Vienna, 1090 Vienna, Austria
| | - Peter Wolf
- Department of Dermatology, Medical University of Graz, 8036 Graz, Austria
| | | | - Alexandra Geusau
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence: ; Tel.: +43-1-40400-77690
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Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.
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10
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Xavier C, de la Puente M, Mosquera-Miguel A, Freire-Aradas A, Kalamara V, Ralf A, Revoir A, Gross T, Schneider P, Ames C, Hohoff C, Phillips C, Kayser M, Parson W. Development and inter-laboratory evaluation of the VISAGE Enhanced Tool for Appearance and Ancestry inference from DNA. Forensic Sci Int Genet 2022; 61:102779. [DOI: 10.1016/j.fsigen.2022.102779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/14/2022] [Accepted: 09/18/2022] [Indexed: 11/30/2022]
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Feng Y, Zhang H, Wang Q, Jin X, Le C, Liu Y, Wang X, Jiang H, Ren Z. Whole mitochondrial genome analysis of Tai-Kadai-speaking populations in Southwest China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1000493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
As a single matrilineal gene, human mitochondrial DNA plays a very important role in the study of population genetics. The whole mitogenome sequences of 287 individuals of the Tai-Kadai-speaking population in Guizhou were obtained. It was discovered that there were 82, 104, and 94 haplotypes in 83 Bouyei individuals, 107 Dong individuals, and 97 Sui individuals, respectively; and the haplotype diversity in Bouyei, Dong, and Sui groups was 1.000 ± 0.02, 0.9993 ± 0.0015, and 0.999 ± 0.002, respectively. The result of neutrality tests of the Tai-Kadai-speaking population in Guizhou showed significant negative values, and the analysis of mismatch distribution showed an obvious unimodal distribution. The results implied that Guizhou Tai-Kadai-speaking populations had high genetic diversities and may have experienced recent population expansion. In addition, the primary haplogroups of studied populations were M*, F, B, D, and R*, implying that they may origin from Southern China. The matrilineal genetic structure of the Tai-Kadai-speaking populations in Guizhou was analyzed by merging the mitogenome data of 79 worldwide populations as reference data. The results showed that there were close relationships between studied populations and other Tai-Kadai as well as some Austronesian populations in East and Southeast Asia. Overall, the mitogenome data generated in this study will provide important data for the study of genetic structure of Tai-Kadai speaking populations.
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Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample. Int J Mol Sci 2022; 23:ijms23126725. [PMID: 35743173 PMCID: PMC9223851 DOI: 10.3390/ijms23126725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.
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Fujii K, Mita Y, Watahiki H, Fukagawa T, Kitayama T, Mizuno N, Nakahara H, Sekiguchi K. Poly_NumtS_430 or HSA_NumtS_587 observed in massively parallel sequencing of the mitochondrial HV1 and HV2 regions. Forensic Sci Int Genet 2022; 59:102717. [DOI: 10.1016/j.fsigen.2022.102717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 03/12/2022] [Accepted: 05/01/2022] [Indexed: 11/04/2022]
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14
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Wang H, Chen M, Chen C, Fang Y, Cui W, Lei F, Zhu B. Genetic Background of Kirgiz Ethnic Group From Northwest China Revealed by Mitochondrial DNA Control Region Sequences on Massively Parallel Sequencing. Front Genet 2022; 13:729514. [PMID: 35281833 PMCID: PMC8906502 DOI: 10.3389/fgene.2022.729514] [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: 06/23/2021] [Accepted: 01/24/2022] [Indexed: 11/23/2022] Open
Abstract
The mitochondrial DNA (mtDNA) has been used to trace population evolution and apply to forensic identification due to the characteristics including lack of recombination, higher copy number and matrilineal inheritance comparing with nuclear genome DNA. In this study, mtDNA control region sequences of 91 Kirgiz individuals from the Northwest region of China were sequenced to identify genetic polymorphisms and gain insight into the genetic background of the Kirgiz ethnic group. MtDNA control region sequences of Kirgiz individuals presented relatively high genetic polymorphisms. The 1,122 bp sequences of mtDNA control region could differ among unrelated Kirgiz individuals, which suggested the mtDNA control region sequences have a good maternal pedigree tracing capability among different Kirgiz individuals. The neutrality test, mismatch distribution, Bayesian phylogenetic inference, Bayesian skyline analysis, and the median network analyses showed that the Kirgiz group might occurred population expansion, and the expansion could be observed at about ∼53.41 kilo years ago (kya) when ancestries of modern humans began to thrive in Eurasia. The pairwise population comparisons, principal component analyses, and median network analyses were performed based on haplogroup frequencies or mtDNA control region sequences of 5,886 individuals from the Kirgiz group and the 48 reference populations all over the world. And the most homologous haplotypes were found between Kirgiz individuals and the East Asian individuals, which indicated that the Kirgiz group might have gene exchanges with the East Asian populations.
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Affiliation(s)
- Hongdan Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Yating Fang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, China
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15
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McElhoe JA, Wilton PR, Parson W, Holland MM. Exploring statistical weight estimates for mitochondrial DNA matches involving heteroplasmy. Int J Legal Med 2022; 136:671-685. [PMID: 35243529 DOI: 10.1007/s00414-022-02774-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022]
Abstract
Massively parallel sequencing (MPS) of mitochondrial (mt) DNA allows forensic laboratories to report heteroplasmy on a routine basis. Statistical approaches will be needed to determine the relative frequency of observing an mtDNA haplotype when including the presence of a heteroplasmic site. Here, we examined 1301 control region (CR) sequences, collected from individuals in four major population groups (European, African, Asian, and Latino), and covering 24 geographically distributed haplogroups, to assess the rates of point heteroplasmy (PHP) on an individual and nucleotide position (np) basis. With a minor allele frequency (MAF) threshold of 2%, the data was similar across population groups, with an overall PHP rate of 37.7%, and the majority of heteroplasmic individuals (77.3%) having only one site of heteroplasmy. The majority (75.2%) of identified PHPs had an MAF of 2-10%, and were observed at 12.6% of the nps across the CR. Both the broad and phylogenetic testing suggested that in many cases the low number of observations of heteroplasmy at any one np results in a lack of statistical association. The posterior frequency estimates, which skew conservative to a degree depending on the sample size in a given haplogroup, had a mean of 0.152 (SD 0.134) and ranged from 0.031 to 0.83. As expected, posterior frequency estimates decreased in accordance with 1/n as the sample size (n) increased. This provides a proposed conservative statistical framework for assessing haplotype/heteroplasmy matches when applying an MPS technique in forensic cases and will allow for continual refinement as more data is generated, both within the CR and across the mitochondrial genome.
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Affiliation(s)
- Jennifer A McElhoe
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA.
| | - Peter R Wilton
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- 23andMe Inc, Sunnyvale, CA, 94086, USA
| | - Walther Parson
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
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16
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Simão F, Ribeiro J, Vullo C, Catelli L, Gomes V, Xavier C, Huber G, Bodner M, Quiroz A, Ferreira AP, Carvalho EF, Parson W, Gusmão L. The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture. Genes (Basel) 2021; 12:1788. [PMID: 34828394 PMCID: PMC8625094 DOI: 10.3390/genes12111788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/25/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.
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Affiliation(s)
- Filipa Simão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Julyana Ribeiro
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team, Córdoba 14001, Argentina; (C.V.); (L.C.)
| | - Laura Catelli
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team, Córdoba 14001, Argentina; (C.V.); (L.C.)
| | - Verónica Gomes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal;
- Institute of Pathology and Molecular Immunology, University of Porto (IPATIMUP), 4099-002 Porto, Portugal
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Alfredo Quiroz
- Instituto de Previsión Social, Asunción 100153, Paraguay;
| | - Ana Paula Ferreira
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Elizeu F. Carvalho
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
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17
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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.
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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.)
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18
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Faccinetto C, Sabbatini D, Serventi P, Rigato M, Salvoro C, Casamassima G, Margiotta G, De Fanti S, Sarno S, Staiti N, Luiselli D, Marino A, Vazza G. Internal validation and improvement of mitochondrial genome sequencing using the Precision ID mtDNA Whole Genome Panel. Int J Legal Med 2021; 135:2295-2306. [PMID: 34491421 PMCID: PMC8523450 DOI: 10.1007/s00414-021-02686-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/13/2021] [Indexed: 12/26/2022]
Abstract
With the recent advances in next-generation sequencing (NGS), mitochondrial whole-genome sequencing has begun to be applied to the field of the forensic biology as an alternative to the traditional Sanger-type sequencing (STS). However, experimental workflows, commercial solutions, and output data analysis must be strictly validated before being implemented into the forensic laboratory. In this study, we performed an internal validation for an NGS-based typing of the entire mitochondrial genome using the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific) on the Ion S5 sequencer (Thermo Fisher Scientific). Concordance, repeatability, reproducibility, sensitivity, and heteroplasmy detection analyses were assessed using the 2800 M and 9947A standard control DNA as well as typical casework specimens, and results were compared with conventional Sanger sequencing and another NGS sequencer in a different laboratory. We discuss the strengths and limitations of this approach, highlighting some issues regarding noise thresholds and heteroplasmy detection, and suggesting solutions to mitigate these effects and improve overall data interpretation. Results confirmed that the Precision ID Whole mtDNA Genome Panel is highly reproducible and sensitive, yielding useful full mitochondrial DNA sequences also from challenging DNA specimens, thus providing further support for its use in forensic practice.
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Affiliation(s)
- Christian Faccinetto
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy.
| | - Daniele Sabbatini
- Department of Neurosciences DNS, University of Padova, Padova, Italy
| | - Patrizia Serventi
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Martina Rigato
- Department of Biology, University of Padova, Padova, Italy
| | | | - Gianluca Casamassima
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Gianluca Margiotta
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Sara De Fanti
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Interdepartmental Centre Alma Mater Research Institute On Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy
| | - Stefania Sarno
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Nicola Staiti
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Alberto Marino
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Giovanni Vazza
- Department of Biology, University of Padova, Padova, Italy.
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19
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Ta MTA, Nguyen NN, Tran DM, Nguyen TH, Vu TA, Le DT, Le PT, Do TTH, Hoang H, Chu HH. Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5™ system. Int J Legal Med 2021; 135:2285-2294. [PMID: 34196785 DOI: 10.1007/s00414-021-02649-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
Mitochondrial DNA (mtDNA) analysis using Sanger sequencing has been a routine practice for the identification of human skeletal remains. However, this process is usually challenging since DNA from the remains is highly degraded and at low concentration. Recently, the advent and implementation of massively parallel sequencing (MPS) have been offered the ability to improve mtDNA sequence data for forensic analysis. To assess the utility of the Ion S5™ system - an MPS platform for mtDNA analysis in challenging samples, we sequenced the mitochondrial control region of 52 age-old skeletal remains. Using the Precision ID mtDNA Control Region Panel, 50 full and two partial control region haplotypes at relatively high mean coverage of 2494 × were achieved for variant calling. Further variant analysis at 10% threshold for point heteroplasmy showed high degradation degree in terms of DNA damage in our bone samples. A higher point heteroplasmy threshold of 20% was required to diminish most of background noise caused by the damage. The results from this study indicated the potential application of the Ion S5™ system in sequencing degraded samples in Vietnam and provided valuable data sources for forensic analyses in the future.
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Affiliation(s)
- May Thi Anh Ta
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nam Ngoc Nguyen
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Duc Minh Tran
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Trang Hong Nguyen
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Tuan Anh Vu
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dung Thi Le
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Phuong Thi Le
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thu Thi Hong Do
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Hoang Ha Chu
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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20
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Holt CL, Stephens KM, Walichiewicz P, Fleming KD, Forouzmand E, Wu SF. Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software. Genes (Basel) 2021; 12:genes12040599. [PMID: 33921728 PMCID: PMC8073089 DOI: 10.3390/genes12040599] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGxTM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.
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21
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Lutz-Bonengel S, Niederstätter H, Naue J, Koziel R, Yang F, Sänger T, Huber G, Berger C, Pflugradt R, Strobl C, Xavier C, Volleth M, Weiß SC, Irwin JA, Romsos EL, Vallone PM, Ratzinger G, Schmuth M, Jansen-Dürr P, Liehr T, Lichter P, Parsons TJ, Pollak S, Parson W. Evidence for multi-copy Mega-NUMTs in the human genome. Nucleic Acids Res 2021; 49:1517-1531. [PMID: 33450006 PMCID: PMC7897518 DOI: 10.1093/nar/gkaa1271] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022] Open
Abstract
The maternal mode of mitochondrial DNA (mtDNA) inheritance is central to human genetics. Recently, evidence for bi-parental inheritance of mtDNA was claimed for individuals of three pedigrees that suffered mitochondrial disorders. We sequenced mtDNA using both direct Sanger and Massively Parallel Sequencing in several tissues of eleven maternally related and other affiliated healthy individuals of a family pedigree and observed mixed mitotypes in eight individuals. Cells without nuclear DNA, i.e. thrombocytes and hair shafts, only showed the mitotype of haplogroup (hg) V. Skin biopsies were prepared to generate ρ° cells void of mtDNA, sequencing of which resulted in a hg U4c1 mitotype. The position of the Mega-NUMT sequence was determined by fluorescence in situ hybridization and two different quantitative PCR assays were used to determine the number of contributing mtDNA copies. Thus, evidence for the presence of repetitive, full mitogenome Mega-NUMTs matching haplogroup U4c1 in various tissues of eight maternally related individuals was provided. Multi-copy Mega-NUMTs mimic mixtures of mtDNA that cannot be experimentally avoided and thus may appear in diverse fields of mtDNA research and diagnostics. We demonstrate that hair shaft mtDNA sequencing provides a simple but reliable approach to exclude NUMTs as source of misleading results.
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Affiliation(s)
- Sabine Lutz-Bonengel
- Institute of Forensic Medicine, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Jana Naue
- Institute of Forensic Medicine, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Rafal Koziel
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck 6020, Austria
| | - Fengtang Yang
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Timo Sänger
- Institute of Forensic Medicine, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - René Pflugradt
- State Investigation Department of Lower Saxony, Hannover 30169, Germany
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Marianne Volleth
- Magdeburg University Hospital, Institute of Human Genetics, Otto von Guericke University, Magdeburg 39120, Germany
| | - Sandra Carina Weiß
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany
| | - Jodi A Irwin
- DNA Support Unit, FBI Laboratory, Quantico, VA 22135, USA
| | - Erica L Romsos
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, MD 20899, USA
| | - Peter M Vallone
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, MD 20899, USA
| | - Gudrun Ratzinger
- Department of Dermatology, Venereology and Allergy, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Matthias Schmuth
- Department of Dermatology, Venereology and Allergy, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Pidder Jansen-Dürr
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck 6020, Austria
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena 07747, Germany
| | - Peter Lichter
- German Cancer Research Center, Molecular Genetics, Heidelberg 69120, Germany
| | - Thomas J Parsons
- International Commission on Missing Persons, The Hague 2514 AA, Netherlands
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Stefan Pollak
- Institute of Forensic Medicine, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
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Smart U, Cihlar JC, Mandape SN, Muenzler M, King JL, Budowle B, Woerner AE. A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures. Genes (Basel) 2021; 12:128. [PMID: 33498312 PMCID: PMC7909279 DOI: 10.3390/genes12020128] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the benefits of quantitative data generated by massively parallel sequencing, resolving mitotypes from mixtures occurring in certain ratios remains challenging. In this study, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated. The method was first tested on 270 in silico two-person mixtures varying in mixture proportions. An assortment of external reference panels containing information on haplotypic variation (from similar and different haplogroups) was leveraged to assess the effect of panel composition on phasing accuracy. Building on these simulations, mitochondrial genomes from the Human Mitochondrial DataBase were sourced to populate the panels and key parameter values were identified by deconvolving an additional 7290 in silico two-person mixtures. Finally, employing an optimized reference panel and phasing parameters, the approach was validated with in vitro two-person mixtures with differing proportions. Deconvolution was most accurate when the haplotypes in the mixture were similar to haplotypes present in the reference panel and when the mixture ratios were neither highly imbalanced nor subequal (e.g., 4:1). Overall, errors in haplotype estimation were largely bounded by the accuracy of the mixture's genotype results. The proposed framework is the first available approach that automates the reconstruction of complete individual mitotypes from mixtures, even in ratios that have traditionally been considered problematic.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Sammed N. Mandape
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Melissa Muenzler
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Jonathan L. King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - August E. Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Cihlar JC, Amory C, Lagacé R, Roth C, Parson W, Budowle B. Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel. Genes (Basel) 2020; 11:E1345. [PMID: 33202822 PMCID: PMC7709034 DOI: 10.3390/genes11111345] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/21/2020] [Accepted: 11/10/2020] [Indexed: 01/10/2023] Open
Abstract
For the adoption of massively parallel sequencing (MPS) systems by forensic laboratories, validation studies on specific workflows are needed to support the feasibility of implementation and the reliability of the data they produce. As such, the whole mitochondrial genome sequencing methodology-Precision ID mtDNA Whole Genome Panel, Ion Chef, Ion S5, and Converge-has been subjected to a variety of developmental validation studies. These validation studies were completed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines and assessed reproducibility, repeatability, accuracy, sensitivity, specificity to human DNA, and ability to analyze challenging (e.g., mixed, degraded, or low quantity) samples. Intra- and inter-run replicates produced an average maximum pairwise difference in variant frequency of 1.2%. Concordance with data generated with traditional Sanger sequencing and an orthogonal MPS platform methodology was used to assess accuracy, and generation of complete and concordant haplotypes at DNA input levels as low as 37.5 pg of nuclear DNA or 187.5 mitochondrial genome copies illustrated the sensitivity of the system. Overall, data presented herein demonstrate that highly accurate and reproducible results were generated for a variety of sample qualities and quantities, supporting the reliability of this specific whole genome mitochondrial DNA MPS system for analysis of forensic biological evidence.
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Affiliation(s)
- Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA;
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
| | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.A.); (W.P.)
| | - Robert Lagacé
- Human Identification Group, Thermo Fisher Scientific, South San Francisco, CA 94080, USA; (R.L.); (C.R.)
| | - Chantal Roth
- Human Identification Group, Thermo Fisher Scientific, South San Francisco, CA 94080, USA; (R.L.); (C.R.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.A.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA;
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
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Melchionda F, Stanciu F, Buscemi L, Pesaresi M, Tagliabracci A, Turchi C. Searching the undetected mtDNA variants in forensic MPS data. Forensic Sci Int Genet 2020; 49:102399. [PMID: 33038616 DOI: 10.1016/j.fsigen.2020.102399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/27/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
The efficiency of MPS in forensic mtDNA analysis has been thoroughly proven, although a reliable and well established data evaluation still remains a critical point. Numerous bioinformatics tools have been developed, but most of them require specific operating systems and high costs, while free open-source programs with user-friendly interfaces are few. In this study, 43 full mtGenomes were sequenced using the Ion Personal Genome Machine™ (PGM™) System and analyzed utilizing the plug-in Variant Caller (TVC) of the Ion Torrent Software Suite and the mtDNA-Server (mDS), a free web-based mitochondrial analysis tool for MPS data. The outcomes of these two different analysis tools were compared to variants noted after manual inspection of the aligned reads performed using Integrative Genomics Viewer (IGV). The comparison highlighted the presence of thirty-nine discordant variant calls, which were resolved by Sanger sequencing that confirmed the presence of all variants, except for 7 deletions. The combined adoption of IGV and Sanger type sequencing confirmatory steps, in addition of TVC and mDS analysis, resulted in a more accurate variants assignment with the detection of 32 additional true polymorphisms, which were noted in the final dataset. Regarding the heteroplasmy issue, out of a total of thirty heteroplasmic variants, twenty-eight were detected by the TVC, while the mDS detected twenty-two. Overall, none of the used bioinformatics tools were the perfect choice and a secondary analysis with an expert's opinion in complete mtGenome MPS data evaluation is still required in forensic genetic analysis.
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Affiliation(s)
- Filomena Melchionda
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Florin Stanciu
- Romanian National DNA Database, National Forensic Science Institute, General Inspectorate of Romanian Police, Bucharest, Romania.
| | - Loredana Buscemi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Mauro Pesaresi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Adriano Tagliabracci
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Chiara Turchi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
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Distinguishing mitochondrial DNA and NUMT sequences amplified with the precision ID mtDNA whole genome panel. Mitochondrion 2020; 55:122-133. [PMID: 32949792 DOI: 10.1016/j.mito.2020.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 11/22/2022]
Abstract
Nuclear mitochondrial DNA segments (NUMTs) are generated via transfer of portions of the mitochondrial genome into the nuclear genome. Given their common origin, there is the possibility that both the mitochondrial and NUMT segments may co-amplify using the same set of primers. Thus, analysis of the variation of the mitochondrial genome must take into account this co-amplification of mitochondrial and NUMT sequences. The study herein builds on data from the study by Strobl et al. (Strobl et al., 2019), in which multiple point heteroplasmies were called with an "N" to prevent labeling NUMT sequences mimicking mitochondrial heteroplasmy and being interpreted as true mitochondrial in origin sequence variants. Each of these point heteroplasmies was studied in greater detail, both molecularly and bioinformatically, to determine whether NUMT or true mitochondrial DNA variation was present. The bioinformatic and molecular tools available to help distinguish between NUMT and mitochondrial DNA and the effect of NUMT sequences on interpretation were discussed.
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Woerner AE, Cihlar JC, Smart U, Budowle B. Numt identification and removal with RtN! Bioinformatics 2020; 36:5115-5116. [DOI: 10.1093/bioinformatics/btaa642] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/15/2020] [Accepted: 07/18/2020] [Indexed: 12/30/2022] Open
Abstract
Abstract
Motivation
Assays in mitochondrial genomics rely on accurate read mapping and variant calling. However, there are known and unknown nuclear paralogs that have fundamentally different genetic properties than that of the mitochondrial genome. Such paralogs complicate the interpretation of mitochondrial genome data and confound variant calling.
Results
Remove the Numts! (RtN!) was developed to categorize reads from massively parallel sequencing data not based on the expected properties and sequence identities of paralogous nuclear encoded mitochondrial sequences, but instead using sequence similarity to a large database of publicly available mitochondrial genomes. RtN! removes low-level sequencing noise and mitochondrial paralogs while not impacting variant calling, while competing methods were shown to remove true variants from mitochondrial mixtures.
Availability and implementation
https://github.com/Ahhgust/RtN
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- August E Woerner
- Department of Microbiology, Immunology and Genetics
- Center for Human Identification, University of North Texas Health Science Center (UNTHSC), Fort Worth, TX 76107, USA
| | - Jennifer Churchill Cihlar
- Department of Microbiology, Immunology and Genetics
- Center for Human Identification, University of North Texas Health Science Center (UNTHSC), Fort Worth, TX 76107, USA
| | - Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center (UNTHSC), Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Department of Microbiology, Immunology and Genetics
- Center for Human Identification, University of North Texas Health Science Center (UNTHSC), Fort Worth, TX 76107, USA
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England R, Nancollis G, Stacey J, Sarman A, Min J, Harbison S. Compatibility of the ForenSeq™ DNA Signature Prep Kit with laser microdissected cells: An exploration of issues that arise with samples containing low cell numbers. Forensic Sci Int Genet 2020; 47:102278. [DOI: 10.1016/j.fsigen.2020.102278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/05/2020] [Accepted: 03/15/2020] [Indexed: 12/27/2022]
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Cihlar JC, Peters D, Strobl C, Parson W, Budowle B. The lot-to-lot variability in the mitochondrial genome of controls. Forensic Sci Int Genet 2020; 47:102298. [PMID: 32464353 DOI: 10.1016/j.fsigen.2020.102298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/28/2022]
Abstract
Current research in the biomedical field has illustrated how cell lines used as reference standards can change over time and, more importantly, can affect research and diagnostic results obtained from these cell lines. With the use of increasingly sensitive and highly resolving technologies (e.g., massively parallel sequencing), forensic scientists must be aware of and account for potential variability in the cell lines used as controls in their validation studies and day-to-day casework. In this study, multiple lot numbers from four commonly-used control cell line DNAs were sequenced with massively parallel sequencing on the Ion S5. The variability among these different lots was evaluated, and the effect on forensic laboratory work discussed.
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Affiliation(s)
- Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA.
| | - Dixie Peters
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
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29
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Mengge W, Guanglin H, Yongdong S, Shouyu W, Xing Z, Jing L, Zheng W, Hou Y. Massively parallel sequencing of mitogenome sequences reveals the forensic features and maternal diversity of tai-kadai-speaking hlai islanders. Forensic Sci Int Genet 2020; 47:102303. [PMID: 32361554 DOI: 10.1016/j.fsigen.2020.102303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 03/30/2020] [Accepted: 04/16/2020] [Indexed: 12/11/2022]
Abstract
As a single maternally inherited locus, human mitochondrial DNA (mtDNA) is geographically arranged and plays a key role in forensic applications. Hlai population has been evidenced as the most typical and unmixed representative of the Tai-Kadai-speaking populations via genome-wide analyses. However, forensic features and maternal diversity of the complete mitogenomes in this Tai-Kadai ancestrally related population are scarce. Thus, we sequenced the complete mitogenomes in 127 Hainan Hlais and found 109 distinct haplotypes belonging to 43 terminal haplogroups resulting in the haplotype diversity of 0.9970. Our results of comprehensive population comparisons showed that Hlai islanders had a close genetic affinity with Tai-Kadai-speaking populations from Southeast Asia, which is consistent with the back-migration of Chinese Neolithic farmers into this region via the inland route. Besides, maternally genetic evidence further revealed a close genetic relationship between Tai-Kadai-speaking and Austronesian-speaking populations when only East Asian dataset was considered, which is consistent with the common origin from Yangtze rice farmers and then spread southward along the inland and coastal routes, respectively. In the reconstructed phylogenetic tree and median-joining networks, the vast majority of Hlais were clustered in exclusive clades, which demonstrated that Hlai people probably had undergone founder effect or genetic bottleneck in their history, and remained genetically isolated for a long time. Collectively, Hainan Hlai did not exhibit detectable maternal gene flow from surrounding or incoming populations. Mitogenome information generated in this study is a contribution in mitigating the underrepresentation of Chinese data in forensic mitogenetics and will assist geography-, metapopulation-, as well as phylogeny-based queries.
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Affiliation(s)
- Wang Mengge
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - He Guanglin
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Su Yongdong
- Forensic Identification Center, Public Security Bureau of Tibet Tibetan Autonomous Region, Lhasa, Tibet Tibetan Autonomous Region, 850000, China
| | - Wang Shouyu
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zou Xing
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Liu Jing
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Wang Zheng
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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García Ó, Alonso S, Huber N, Bodner M, Parson W. Forensically relevant phylogeographic evaluation of mitogenome variation in the Basque Country. Forensic Sci Int Genet 2020; 46:102260. [PMID: 32062111 DOI: 10.1016/j.fsigen.2020.102260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/26/2019] [Accepted: 02/01/2020] [Indexed: 11/19/2022]
Abstract
The Basque Country has been the focus of population (genetic) and evolutionary studies for decades, as it represents an interesting evolutionary feature: it is the only European country where a non-Indo-European language is still spoken today and, for which there are no known living or extinct relatives. Early studies that were based on anatomical and serological methods, along with subsequent molecular genetic investigations, contain controversial interpretations of their data. Additionally, the analysis of mitochondrial DNA, which is maternally inherited and thus suitable for the examination of the maternal phylogeny of the population, was the focus of some studies. Early mtDNA studies were however restricted to the information provided by the control region or its hypervariable segments only. These are known to harbour little phylogenetic information, particularly for haplogroup H that is dominant in Westeurasian populations including the Basques. Later studies analysed complete mitogenome sequences. Their information content is however limited, either because the number of samples was low, or because these studies only considered particular haplogroups. In this study we present the full mitogenome sequences of 178 autochthonous Basque individuals that were carefully selected based on their familial descent and discuss the observed phylogenetic signals in the light of earlier published findings. We confirm the presence of Basque-specific mtDNA lineages and extend the knowledge of these lineages by providing data on their distribution in comparison to other Basque and non-Basque populations. This dataset improves our understanding of the Basque mtDNA phylogeny and serves as a high-quality dataset that is provided via EMPOP for forensic genetic purposes.
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Affiliation(s)
- Óscar García
- Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio (Bizkaia), Spain.
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Spain.
| | - Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania, USA.
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