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Jia M, Li Q, Zhang T, Dong B, Liang X, Fu S, Yu J. Genetic Diversity Analysis of the Chinese Daur Ethnic Group in Heilongjiang Province by Complete Mitochondrial Genome Sequencing. Front Genet 2022; 13:919063. [PMID: 35801081 PMCID: PMC9253502 DOI: 10.3389/fgene.2022.919063] [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: 04/13/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022] Open
Abstract
Mitochondrial DNA (mtDNA) has the characteristics of maternal inheritance, high mutation rate, high copy number, and no recombination. As the most powerful tool for studying the origin and evolution of modern humans, mtDNA has great significance in the research of population genetics and evolutionary genetics. Here, we provide new insights into the maternal genetic history of the Daur ethnic group by generating complete mitochondrial genomes from a total of 146 Daur individuals in China. We also collected the published complete mitochondrial genome sequences of 5,094 individuals from 56 worldwide populations as reference data to further explore the matrilineal genetic landscape of the Daur ethnic group. First, the haplotype diversity was 0.9943 ± 0.0019 and nucleotide diversity was 0.0428 ± 0.0210. The neutrality tests of the Daur group showed significant negative values and the mismatch distribution curve was obviously distributed in a unimodal pattern. The results showed that the Daur ethnic group has high genetic diversity and may have experienced recent population expansion. In addition, the main haplogroups of the Daur population were haplogroup D (31.51%), M* (20.55%), C (10.28%), F (7.53%), and B (6.85%), all of which were prevalent in northern China. It probably implies the northern Chinese origin of the Daur population. The PCA, FST, and phylogenetic analysis results indicated that the Daur group formed a cluster with East Asian populations, and had few genetic differences with the populations in northern China. More importantly, we found that disease-related mutation sites of the mitochondrial genome may be related to ethnic groups, which may have important implications for the prevention and occurrence of specific diseases. Overall, this study revealed the complexity and diversity of the matrilineal genetic background of the Daur ethnic group. Meanwhile, it provided meaningful data for the research on the diversity of the human genome.
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Affiliation(s)
- Mansha Jia
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qiuyan Li
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, China
- Editorial Department of International Journal of Genetics, Harbin Medical University, Harbin, China
| | - Tingting Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, China
| | - Bonan Dong
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, China
| | - Xiao Liang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, China
- *Correspondence: Songbin Fu, ; Jingcui Yu,
| | - Jingcui Yu
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, China
- *Correspondence: Songbin Fu, ; Jingcui Yu,
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Liu J, Cheng X, Liu F, Hao T, Wang J, Guo J, Li J, Liu Z, Li W, Shi J, Zhang X, Li J, Yan J, Zhang G. Identification of coding region SNPs from specific and sensitive mRNA biomarkers for the deconvolution of the semen donor in a body fluid mixture. Forensic Sci Int Genet 2021; 52:102483. [PMID: 33610949 DOI: 10.1016/j.fsigen.2021.102483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/27/2021] [Accepted: 02/10/2021] [Indexed: 11/29/2022]
Abstract
mRNA markers provide a very promising method for the identification of human body fluids or tissues in the context of forensic investigations. Previous studies have shown that different body fluids can be distinguished from each other according to their specific mRNA biomarkers. In this study, we evaluated eight semen-specific mRNA markers (KLK3, NKX3-1, CKB, KLK2, PRAC1, SEMG1, TGM4, and SORD) that encompass 12 coding single nucleotide polymorphisms (cSNPs) to identify the semen contributor in a mixed stain. Five highly specific and sensitive mRNA markers for blood, menstrual blood, saliva, vaginal secretions, and skin were also incorporated into the PCR system as body fluid-positive controls. Reverse transcription polymerase chain reaction (RT-PCR), multiplex PCR and SNaPshot mini-sequencing assays were established for the identification of semen-specific mRNA. The amplicon size ranged from 133 to 337 bp. The semen-specific system was examined against blood, menstrual blood, saliva, vaginal secretions, and skin swabs. The eight mRNA biomarkers were semen-specific and could be successfully typed in laboratory-generated mixtures composed of different body fluids supplemented with 1 ng of semen cDNA. This system possessed a high sensitivity that ranged from 1:10-1:100 for detecting trace amounts of semen in semen-containing body fluid mixtures. Additionally, our results demonstrated that the cSNPs polymorphisms included in the mRNA markers were concordant with genomic DNA (gDNA). Despite the presence of other body fluids, the system exhibited high sensitivity and specificity to the semen in the mixture. In future studies, we will add other cSNPs from the semen-specific genes using massively parallel sequencing to further improve our system.
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Affiliation(s)
- Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Xiaojuan Cheng
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Feng Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Ting Hao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiangling Guo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jintao Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Wenyan Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jie Shi
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Xiuying Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jing Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
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ElHefnawi M, Hegazy E, Elfiky A, Jeon Y, Jeon S, Bhak J, Mohamed Metwally F, Sugano S, Horiuchi T, Kazumi A, Blazyte A. Complete genome sequence and bioinformatics analysis of nine Egyptian females with clinical information from different geographic regions in Egypt. Gene 2020; 769:145237. [PMID: 33127537 DOI: 10.1016/j.gene.2020.145237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 08/03/2020] [Accepted: 10/11/2020] [Indexed: 10/23/2022]
Abstract
Egyptians are at a crossroad between Africa and Eurasia, providing useful genomic resources for analyzing both genetic and environmental factors for future personalized medicine. Two personal Egyptian whole genomes have been published previously by us and here nine female whole genome sequences with clinical information have been added to expand the genomic resource of Egyptian personal genomes. Here we report the analysis of whole genomes of nine Egyptian females from different regions using Illumina short-read sequencers. At 30x sequencing coverage, we identified 12 SNPs that were shared in most of the subjects associated with obesity which are concordant with their clinical diagnosis. Also, we found mtDNA mutation A4282G is common in all the samples and this is associated with chronic progressive external ophthalmoplegia (CPEO). Haplogroup and Admixture analyses revealed that most Egyptian samples are close to the other north Mediterranean, Middle Eastern, and European, respectively, possibly reflecting the into-Africa influx of human migration. In conclusion, we present whole-genome sequences of nine Egyptian females with personal clinical information that cover the diverse regions of Egypt. Although limited in sample size, the whole genomes data provides possible geno-phenotype candidate markers that are relevant to the region's diseases.
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Affiliation(s)
- Mahmoud ElHefnawi
- School of Information Technology and Computer Science, Nile University, Giza 12588, Egypt; Informatics & Systems Department, the National Research Centre, Cairo, Egypt; Biomedical Informatics and Chemoinformatics Group, Center of Excellence for Medical Research, National Research Centre, Cairo, Egypt.
| | - Elsayed Hegazy
- School of Information Technology and Computer Science, Nile University, Giza 12588, Egypt
| | - Asmaa Elfiky
- Environmental and Occupational Medicine Department, Environmental Research Division, National Research Centre, Cairo, Egypt
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), UNIST, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), UNIST, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), UNIST, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea; Personal Genomics Institute, Genome Research Foundation, Osong, Republic of Korea
| | - Fateheya Mohamed Metwally
- Environmental and Occupational Medicine Department, Environmental Research Division, National Research Centre, Cairo, Egypt
| | - Sumio Sugano
- The Institute of Medical Science, University of Tokyo, Japan
| | - Terumi Horiuchi
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Abe Kazumi
- The Institute of Medical Science, University of Tokyo, Japan
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), UNIST, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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Palencia-Madrid L, Cardoso S, Castro-Maestre F, Baroja-Careaga I, Rocandio AM, de Pancorbo MM. Development of a new screening method to determine the main 52 mitochondrial haplogroups through a single minisequencing reaction. Mitochondrion 2018; 45:46-51. [PMID: 29474835 DOI: 10.1016/j.mito.2018.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/23/2018] [Accepted: 02/15/2018] [Indexed: 12/17/2022]
Abstract
This work presents the design, development and optimization of a screening method based on single-base extension sequencing to simultaneously analyze a panel of 52 mitochondrial SNPs. This enables to recognize the main mitochondrial haplogroups and to discriminate even between lineages from the same phylogenetic branch that diverged in different continents. The unavailability of individuals harboring infrequent variants was a limitation to optimize the panel. To overcome this, we have modified DNA by site-directed mutagenesis to create the unavailable allelic variants. This allowed us to verify the reliability of this panel and its usefulness to be applied in biomedicine, forensic and population genetic studies.
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Affiliation(s)
- Leire Palencia-Madrid
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Sergio Cardoso
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Fernando Castro-Maestre
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Igor Baroja-Careaga
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Ana M Rocandio
- Department of Nutrition and Food Sciences, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain.
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Nunotani M, Sato N, Kamei S, Shiozaki T, Hayashi T, Asamura H. Development of Multiple Assays using 46 SNPs for Comprehensive mtDNA Haplogrouping and Application to Highly Degraded DNA. J Forensic Sci 2015; 61:472-477. [PMID: 26390120 DOI: 10.1111/1556-4029.12961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/26/2014] [Accepted: 03/29/2015] [Indexed: 11/30/2022]
Abstract
Six multiplex PCR systems using single-base extension reactions to analyze 46 mitochondrial DNA (mtDNA)-coding region single nucleotide polymorphisms (SNPs) that define 42 haplogroups, that is, 24 major mtDNA haplogroups and 18 subclades, were devised. To improve the usefulness of the established systems for the analysis of degraded DNA samples, novel primers to render amplicons with sizes <150 bp were designed. By applying these systems to 214 Japanese individuals, 24 different haplogroups (power of discrimination = 93.4%) were found. To assess the effectiveness of our systems in grouping degraded DNA, an ancient bone sample of a Jomon skeleton was analyzed and then classified as haplogroup N9b. We conclude that the present systems are powerful screening tools for major haplogroups of mtDNA in addition to the prevalent subhaplogroups in the Japanese population and that these systems are capable of analyzing highly degraded DNA samples in forensic studies.
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Affiliation(s)
- Miya Nunotani
- Department of Legal Medicine, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto, Nagano, 390-8621, Japan
| | - Noriko Sato
- Department of Legal Medicine, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto, Nagano, 390-8621, Japan
| | - Sayako Kamei
- Department of Legal Medicine, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto, Nagano, 390-8621, Japan
| | - Tetsuya Shiozaki
- Department of Legal Medicine, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto, Nagano, 390-8621, Japan
| | - Tokutaro Hayashi
- Department of Legal Medicine, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto, Nagano, 390-8621, Japan
| | - Hideki Asamura
- Department of Legal Medicine, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto, Nagano, 390-8621, Japan
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6
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Chaitanya L, van Oven M, Weiler N, Harteveld J, Wirken L, Sijen T, de Knijff P, Kayser M. Developmental validation of mitochondrial DNA genotyping assays for adept matrilineal inference of biogeographic ancestry at a continental level. Forensic Sci Int Genet 2014; 11:39-51. [PMID: 24631695 DOI: 10.1016/j.fsigen.2014.02.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 02/12/2014] [Accepted: 02/15/2014] [Indexed: 12/30/2022]
Abstract
Mitochondrial DNA (mtDNA) can be used for matrilineal biogeographic ancestry prediction and can thus provide investigative leads towards identifying unknown suspects, when conventional autosomal short tandem repeat (STR) profiling fails to provide a match. Recently, six multiplex genotyping assays targeting 62 ancestry-informative mitochondrial single nucleotide polymorphisms (mt-SNPs) were developed. This hierarchical system of assays allows detection of the major haplogroups present in Africa, America, Western Eurasia, Eastern Eurasia, Australia and Oceania, thus revealing the broad geographic region of matrilineal origin of a DNA donor. Here, we provide a forensic developmental validation study of five multiplex assays targeting all the 62 ancestry-informative mt-SNPs following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. We demonstrate that the assays are highly sensitive; being able to produce full profiles at input DNA amounts of as little as 1pg. The assays were shown to be highly robust and efficient in providing information from degraded samples and from simulated casework samples of different substrates such as blood, semen, hair, saliva and trace DNA samples. Reproducible results were successfully achieved from concordance testing across three independent laboratories depicting the ease and reliability of these assays. Overall, our results demonstrate the suitability of these five mt-SNP assays for application to forensic casework and other purposes aiming to establish an individual's matrilineal genetic ancestry. With this validated tool, it is now possible to determine the matrilineal biogeographic origin of unknown individuals on the level of continental resolution from forensic DNA samples to provide investigative leads in criminal and missing person cases where autosomal STR profiling is uninformative.
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Affiliation(s)
- Lakshmi Chaitanya
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, Zuid-Holland, The Netherlands
| | - Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, Zuid-Holland, The Netherlands
| | - Natalie Weiler
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands
| | - Joyce Harteveld
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands
| | - Laura Wirken
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden, University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Titia Sijen
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands
| | - Peter de Knijff
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden, University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, Zuid-Holland, The Netherlands.
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Kim EH, Shin KJ, Kim HY, Park SJ, Yang WI, Lee HY. Rapid and Simple Screening of Mitochondrial DNA in Koreans by the Analysis of Highly Variable Control Region SNPs. ACTA ACUST UNITED AC 2013. [DOI: 10.7580/kjlm.2013.37.4.183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Eun Hye Kim
- Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hye Yeon Kim
- DNA Forensic Division, Supreme Prosecutors' Office, Seoul, Korea
| | - Su Jeong Park
- DNA Forensic Division, Supreme Prosecutors' Office, Seoul, Korea
| | - Woo Ick Yang
- Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hwan Young Lee
- Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
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Ren Z, Luo H, Song F, Zhang J, Zhu H, Hou Y. Screening of mtDNA SNPs in Chinese Han population using pyrosequencing. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2013. [DOI: 10.1016/j.fsigss.2013.10.161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lee HY, Yoon JA, Yang WI, Shin KJ. A one step multiplex PCR assay for rapid screening of East Asian mtDNA haplogroups on forensic samples. Leg Med (Tokyo) 2012; 15:50-4. [PMID: 22981178 DOI: 10.1016/j.legalmed.2012.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 08/03/2012] [Accepted: 08/04/2012] [Indexed: 10/27/2022]
Abstract
The mitochondrial DNA (mtDNA) haplogroup typing has become an essential tool to study human evolutionary history and to infer the matrilineal bio-geographic ancestry. In forensic field, the screening of mtDNA haplogroups by genotyping of mtDNA single nucleotide polymorphisms (SNPs) can help guarantee the quality of mtDNA sequence data as well as can reduce the need to sequence samples that do not match. Here, a multiplex mutagenically separated (MS) polymerase chain reaction (PCR) system was developed for simultaneous rapid detection of 14 coding region SNPs and one deletion motif representing common mtDNA haplogroups of East Asia. The multiplex MS PCR system we developed has the advantage of being a one step procedure that requires only a single PCR amplification with allele-specific primers and allowing straightforward designation of haplogroups along the branches of the phylogenetic tree. Therefore, it would be a simple, rapid, and reliable detection method useful for large-scale screening of mtDNA variations to determine East Asian mtDNA haplogroups.
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Affiliation(s)
- Hwan Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, South Korea
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Zubizarreta J, Davis MC, Hampikian G. The Y-STR genetic diversity of an Idaho Basque population, with comparison to European Basques and US Caucasians. Hum Biol 2012; 83:685-94. [PMID: 22276968 DOI: 10.3378/027.083.0602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Fifty unrelated Basque males from southwest Idaho were typed for the 17 Y-STR loci in the Yfiler multiplex kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA H4.1 and DYS385a/b). In total, 42 haplotypes were identified, with no more than two individuals sharing a single haplotype. The haplotype diversity (HD) was 0.9935, and gene diversity (D) over loci was 0.457 ± 0.137. The Idaho Basque population was compared to the source population from the Basque autonomous region of Northern Spain and Southern France, as well as a United States Caucasian population. The haplotype diversity for the immigrant Basque sample is within 0.4% of the haplotype diversity of the European Basques (0.9903); thus the power of discrimination is similar for each population. The Idaho Basque population has less diversity in 9 out of 16 loci (considering DYS385a/b together) and 3% less diversity across all loci, compared to the European Basque population. A multidimensional scaling analysis (MDS) was created using pairwise R(ST) values to compare the Idaho Basques to other populations. Based upon R(ST) and F(ST) measures, no significant differentiation was found between the Idaho and source European Basque population.
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Affiliation(s)
- Josu Zubizarreta
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
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Paneto G, Köhnemann S, Martins J, Cicarelli R, Pfeiffer H. A single multiplex SNaPshot reaction of 42 SNPs to classify admixture populations into mitochondrial DNA haplogroups. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.08.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Ballantyne KN, van Oven M, Ralf A, Stoneking M, Mitchell RJ, van Oorschot RAH, Kayser M. MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania. Forensic Sci Int Genet 2011; 6:425-36. [PMID: 21940232 DOI: 10.1016/j.fsigen.2011.08.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/18/2011] [Accepted: 08/25/2011] [Indexed: 01/22/2023]
Abstract
Human mitochondrial DNA (mtDNA) is a convenient marker for tracing matrilineal bio-geographic ancestry and is widely applied in forensic, genealogical and anthropological studies. In forensic applications, DNA-based ancestry inference can be useful for finding unknown suspects by concentrating police investigations in cases where autosomal STR profiling was unable to provide a match, or can help provide clues in missing person identification. Although multiplexed mtDNA single nucleotide polymorphism (SNP) assays to infer matrilineal ancestry at a (near) continental level are already available, such tools are lacking for the Oceania region. Here, we have developed a hierarchical system of three SNaPshot multiplexes for genotyping 26 SNPs defining all major mtDNA haplogroups for Oceania (including Australia, Near Oceania and Remote Oceania). With this system, it was possible to conclusively assign 74% of Oceanian individuals to their Oceanian matrilineal ancestry in an established literature database (after correcting for obvious external admixture). Furthermore, in a set of 161 genotyped individuals collected in Australia, Papua New Guinea and Fiji, 87.6% were conclusively assigned an Oceanian matrilineal origin. For the remaining 12.4% of the genotyped samples either a Eurasian origin was detected indicating likely European admixture (1.9%), the identified haplogroups are shared between Oceania and S/SE-Asia (5%), or the SNPs applied did not allow a geographic inference to be assigned (5.6%). Sub-regional assignment within Oceania was possible for 32.9% of the individuals genotyped: 49.5% of Australians were assigned an Australian origin and 13.7% of the Papua New Guineans were assigned a Near Oceanian origin, although none of the Fijians could be assigned a specific Remote Oceanian origin. The low assignment rates of Near and Remote Oceania are explained by recent migrations from Asia via Near Oceania into Remote Oceania. Combining the mtDNA multiplexes for Oceania introduced here with those we developed earlier for all other continental regions, global matrilineal bio-geographic ancestry assignment from DNA is now achievable in a highly efficient way that is also suitable for applications with limited material such as forensic case work.
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Affiliation(s)
- Kaye N Ballantyne
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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van Oven M, Vermeulen M, Kayser M. Multiplex genotyping system for efficient inference of matrilineal genetic ancestry with continental resolution. INVESTIGATIVE GENETICS 2011; 2:6. [PMID: 21429198 PMCID: PMC3078086 DOI: 10.1186/2041-2223-2-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 03/23/2011] [Indexed: 12/17/2022]
Abstract
Background In recent years, phylogeographic studies have produced detailed knowledge on the worldwide distribution of mitochondrial DNA (mtDNA) variants, linking specific clades of the mtDNA phylogeny with certain geographic areas. However, a multiplex genotyping system for the detection of the mtDNA haplogroups of major continental distribution that would be desirable for efficient DNA-based bio-geographic ancestry testing in various applications is still missing. Results Three multiplex genotyping assays, based on single-base primer extension technology, were developed targeting a total of 36 coding-region mtDNA variants that together differentiate 43 matrilineal haplo-/paragroups. These include the major diagnostic haplogroups for Africa, Western Eurasia, Eastern Eurasia and Native America. The assays show high sensitivity with respect to the amount of template DNA: successful amplification could still be obtained when using as little as 4 pg of genomic DNA and the technology is suitable for medium-throughput analyses. Conclusions We introduce an efficient and sensitive multiplex genotyping system for bio-geographic ancestry inference from mtDNA that provides resolution on the continental level. The method can be applied in forensics, to aid tracing unknown suspects, as well as in population studies, genealogy and personal ancestry testing. For more complete inferences of overall bio-geographic ancestry from DNA, the mtDNA system provided here can be combined with multiplex systems for suitable autosomal and, in the case of males, Y-chromosomal ancestry-sensitive DNA markers.
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Affiliation(s)
- Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.
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Paneto GG, Köhnemann S, Martins JA, Cicarelli RMB, Pfeiffer H. A single multiplex PCR and SNaPshot minisequencing reaction of 42 SNPs to classify admixture populations into mitochondrial DNA haplogroups. Mitochondrion 2010; 11:296-302. [PMID: 21172459 DOI: 10.1016/j.mito.2010.12.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 11/02/2010] [Accepted: 12/03/2010] [Indexed: 11/24/2022]
Abstract
SNaPshot minisequencing reaction is in increasing use because of its fast detection of many polymorphisms in a single assay. In this work we described a highly sensitive single nucleotide polymorphisms (SNPs) typing method with detection of 42 mitochondrial DNA (mtDNA) SNPs in a single PCR and SNaPshot multiplex reaction, in order to allow haplogroup classification in Latin American admixture population. We validated the panel typing 160 Brazilian individuals. Complete SNP profiles were obtained from 10 pg of total DNA. We conclude that it is possible to build and genotype more than forty mtDNA SNPs in a single multiplex PCR and SNaPshot reaction, with sensitivity and reliability, resolving haplogroup classification in admixture populations.
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Affiliation(s)
- Greiciane G Paneto
- Faculdade de Ciências Farmacêuticas, Unesp-Univ Estadual Paulista, Araraquara, SP, Brazil.
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15
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Tobe SS, Linacre A. DNA typing in wildlife crime: recent developments in species identification. Forensic Sci Med Pathol 2010; 6:195-206. [PMID: 20526699 DOI: 10.1007/s12024-010-9168-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2010] [Indexed: 11/27/2022]
Abstract
Species identification has become a tool in the investigation of acts of alleged wildlife crimes. This review details the steps required in DNA testing in wildlife crime investigations and highlights recent developments where not only can individual species be identified within a mixture of species but multiple species can be identified simultaneously. 'What species is this?' is a question asked frequently in wildlife crime investigations. Depending on the material being examined, DNA analysis may offer the best opportunity to answer this question. Species testing requires the comparison of the DNA type from the unknown sample to DNA types on a database. The areas of DNA tested are on the mitochondria and include predominantly the cytochrome b gene and the cytochrome oxidase I gene. Standard analysis requires the sequencing of part of one of these genes and comparing the sequence to that held on a repository of DNA sequences such as the GenBank database. Much of the DNA sequence of either of these two genes is conserved with only parts being variable. A recent development is to target areas of those sequences that are specific to a species; this can increase the sensitivity of the test with no loss of specificity. The benefit of targeting species specific sequences is that within a mixture of two of more species, the individual species within the mixture can be identified. This identification would not be possible using standard sequencing. These new developments can lead to a greater number of samples being tested in alleged wildlife crimes.
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Affiliation(s)
- Shanan S Tobe
- Centre for Forensic Science, Strathclyde University, WestCHEM, Glasgow, UK
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16
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Identification and genotyping of Mycobacterium tuberculosis complex species by use of a SNaPshot Minisequencing-based assay. J Clin Microbiol 2010; 48:1758-66. [PMID: 20220173 DOI: 10.1128/jcm.02255-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of the present study was to investigate the use of the SNaPshot minisequencing method for the identification of Mycobacterium tuberculosis complex (MTBC) isolates to the species level and for further genotyping of M. tuberculosis isolates. We developed an innovative strategy based on two multiplex allele-specific minisequencing assays that allowed detection of eight species-specific and eight lineage-specific single nucleotide polymorphisms (SNPs). Each assay consisted of an eightplex PCR amplification, followed by an eightplex minisequencing reaction with the SNaPshot multiplex kit (Applied Biosystems) and, finally, analysis of the extension products by capillary electrophoresis. The whole strategy was developed with a panel of 56 MTBC strains and 15 negative controls. All MTBC strains tested except one M. africanum clinical isolate were accurately identified to the species level, and all M. tuberculosis isolates were successfully further genotyped. This two-step strategy based on SNaPshot minisequencing allows the simultaneous differentiation of closely related members of the MTBC, the distinction between principal genetic groups, and the characterization of M. tuberculosis isolates into one of the seven prominent SNP cluster groups (SCGs) and could be a useful tool for diagnostic and epidemiological purposes.
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