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Almohammed EK, Hadi A, Al-Asmakh M, Lazim H. The Qatari population's genetic structure and gene flow as revealed by the Y chromosome. PLoS One 2023; 18:e0290844. [PMID: 37656680 PMCID: PMC10473524 DOI: 10.1371/journal.pone.0290844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023] Open
Abstract
The Y-chromosome has been widely used in forensic genetic applications and human population genetic studies due to its uniparental origins. A large database on the Qatari population was created for comparison with other databases from the Arabian Peninsula, the Middle East, and Africa. We provide a study of 23 Y-STR loci included in PowerPlex Y23 (Promega, USA) that were genotyped to produce haplotypes in 379 unrelated males from Qatar, a country at the crossroads of migration patterns. Overall, the most polymorphic locus provided by the Promega kit was DYS458, with a genetic diversity value of 0.85 and a haplotype diversity of 0.998924. Athey's Haplogroup Predictor tool was used to predict haplogroups from Y-STR haplotypes in the Qatari population. In a median-joining network, the haplogroup J1 predominance (49%) in Qatar generated a star-like expansion cluster. The graph of population Q-matrix was developed using Y-STR data from 38 Middle Eastern and 97 African populations (11,305 individuals), and it demonstrated a stronger sub-grouping of countries within each ethnic group and showed the effect of Arabs on the indigenous Berbers of North Africa. The estimated migration rate between the Qatari and other Arabian populations was inferred using Bayesian coalescence theory in the Migrate-n program. According to the Gene Flow study, the main migration route was from Yemen to Kuwait through Qatar. Our research, using the PowerPlex Y23 database, shows the importance of gene diversity, as well as regional and social structuring, in determining the utility of demographic and forensic databases.
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Affiliation(s)
- Eida Khalaf Almohammed
- Ministry of Interior of Qatar, Doha, Qatar
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Abdullah Hadi
- University of Central Lancashire Medical School, Preston, United Kingdom
| | - Maha Al-Asmakh
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hayder Lazim
- School of Medicine, Faculty of Health, Social Care and Medicine (FHSCM), Edge Hill University, Ormskirk, United Kingdom
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Wepeba PP, Abaidoo CS, Goodwin WH. Haplogroup prediction in the Ghanaian population using haplotype data of 27 Yfiler® Plus loci and TaqMan SNP genotyping. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Zeye MMJ, Li J, Ouedraogo SY, Zha L, Simpore J, Jifeng C. Population data and genetic structure analysis based on 29 Y-STR loci among the ethnolinguistic groups in Burkina Faso. Int J Legal Med 2021; 135:1767-1769. [PMID: 33677620 DOI: 10.1007/s00414-021-02544-9] [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: 01/15/2021] [Accepted: 02/15/2021] [Indexed: 10/22/2022]
Abstract
Burkina Faso (BF) is a landlocked Sahelian country located in the middle of West Africa. Sixty-three local languages are spoken in BF. Despite this high diversity, the BF population remains poorly investigated, and updated forensic parameters with a large number of Y chromosome short tandem repeats (Y-STRs) are still missing. Herein, 447 DNA samples were typed for a cocktail of 29 Y-STR loci. None of these 447 individuals in total shared a common haplotype. The overall Y-STR haplotypes were successfully uploaded online on the Y-STR Haplotype Reference Database (YHRD) with the accession numbers YA004690 and YA004691. The main haplotype diversity was 0.9999999965, which is much higher than that obtained with 12 Y-STRs in a previous study. Haploid Match Probability for the whole dataset was 0.002237. The phylogenetic analysis of 24 ethnic groups of BF shows that the ethnic group named BISSA is closer to Gur speakers than Mande speakers, where they belong. In addition, genetic structure analysis of 49 African subpopulations sheds light on the fact that geographic proximity turns out to be one of the best predictors of genetic affinity between populations.
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Affiliation(s)
- Moutanou Modeste Judes Zeye
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.,Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, Ouagadougou 01, 01 BP: 364, Burkina Faso.,Directorate General of the National Police of Burkina Faso, Directorate of Technical and Scientific Police, Ouagadougou 01, 01 BP: 22, Burkina Faso
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Serge Yannick Ouedraogo
- Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, Ouagadougou 01, 01 BP: 364, Burkina Faso.,Department of Biochemistry and molecular biology, School of Life sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.
| | - Jacques Simpore
- Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, Ouagadougou 01, 01 BP: 364, Burkina Faso.
| | - Cai Jifeng
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No:172, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.
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Bouakaze C, Delehelle F, Saenz-Oyhéréguy N, Moreira A, Schiavinato S, Croze M, Delon S, Fortes-Lima C, Gibert M, Bujan L, Huyghe E, Bellis G, Calderon R, Hernández CL, Avendaño-Tamayo E, Bedoya G, Salas A, Mazières S, Charioni J, Migot-Nabias F, Ruiz-Linares A, Dugoujon JM, Thèves C, Mollereau-Manaute C, Noûs C, Poulet N, King T, D'Amato ME, Balaresque P. Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters. Forensic Sci Int Genet 2020; 48:102342. [PMID: 32818722 DOI: 10.1016/j.fsigen.2020.102342] [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: 12/19/2019] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022]
Abstract
We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.
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Affiliation(s)
- Caroline Bouakaze
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Franklin Delehelle
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France; REVA Unit, UMR 5505 - CNRS & Université de Toulouse, Institut de Recherche en Informatique de Toulouse, 31400 Toulouse, France
| | - Nancy Saenz-Oyhéréguy
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Andreia Moreira
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Stéphanie Schiavinato
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Myriam Croze
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Solène Delon
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Cesar Fortes-Lima
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Morgane Gibert
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Louis Bujan
- Equipe d'acceuil EA3694, Hôpital Paule de Viguier, 330 Avenue de Grande Bretagne, TSA 70034, 31059 Toulouse Cedex 9, France
| | - Eric Huyghe
- Equipe d'acceuil EA3694, Hôpital Paule de Viguier, 330 Avenue de Grande Bretagne, TSA 70034, 31059 Toulouse Cedex 9, France
| | - Gil Bellis
- INED Institut National d'Etudes Démographiques, 133 Boulevard Davout, 75980 Paris cedex 20, France
| | - Rosario Calderon
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University. 28040 Madrid, Spain
| | - Candela Lucia Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University. 28040 Madrid, Spain
| | - Efren Avendaño-Tamayo
- Grupo de Ciencias Básicas Aplicadas del Tecnológico de Antioquia, Tecnológico de Antioquia, Institución Universitaria, Medellín 050034, Colombia
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Instituto de Biología, Universidad de Antioquia Medellín Colombia, Colombia
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, GenPoB Research Group, Instituto de Investigaciones, Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | | | - Jacques Charioni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France; Etablissement Français du Sang PACA Corse, Marseille, France
| | | | - Andres Ruiz-Linares
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France; Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jean-Michel Dugoujon
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Catherine Thèves
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Catherine Mollereau-Manaute
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Camille Noûs
- Laboratoire Cogitamous, CNRS & Université Toulouse III, 31000 Toulouse, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400 Toulouse, France
| | - Turi King
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of Western Cape, Cape Town, South Africa
| | - Patricia Balaresque
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France.
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5
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Kofi AE, Hakim HM, Khan HO, Ismail SA, Ghansah A, David AA, Mat NFC, Chambers GK, Edinur HA. Population data of 23 Y chromosome STR loci for the five major human subpopulations of Ghana. Int J Legal Med 2019; 134:1313-1315. [PMID: 31154498 DOI: 10.1007/s00414-019-02099-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 05/27/2019] [Indexed: 11/29/2022]
Abstract
In this study, 268 samples for unrelated males belonging to the five major human subpopulation groups in Ghana (Akan, Ewe, Mole-Dagbon, Ga-Dangme and Guang) were genetically characterised for 23 Y chromosome short tandem repeat (STR) loci using the Powerplex® Y23 STR kit. A total of 263 complete haplotypes were recorded of which 258 were unique. The haplotype diversity, discriminating capacity and match probability for the pooled population data were 0.9998, 0.9627 and 0.0039, respectively. The pairwise genetic distance (RST) for the Ghanaian datasets and other reference populations deposited in the Y-STR Haplotype Reference Database (YHRD) were estimated and mapped using multidimensional scaling (MDS) plot. The Guang and Ewe were significantly different from the Akan, Mole-Dagbon and Ga-Dangme. However, the five Ghanaian datasets were all plotted close together with other African populations in the MDS data mapping.
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Affiliation(s)
- Abban Edward Kofi
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.,Forensic Science Laboratory, Criminal Investigation Department, Ghana Police Service, 00233, Accra, Ghana
| | - Hashom Mohd Hakim
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysian Police, 43200, Cheras, Selangor, Malaysia.,School of Industrial Technologies, Universiti Sains Malaysia, 11800, Gelugor, Pulau Pinang, Malaysia
| | - Hussein Omar Khan
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysian Police, 43200, Cheras, Selangor, Malaysia
| | - Siti Afifah Ismail
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysian Police, 43200, Cheras, Selangor, Malaysia
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, 00233, Accra, Ghana
| | - Agyemang Adjem David
- Forensic Science Laboratory, Criminal Investigation Department, Ghana Police Service, 00233, Accra, Ghana
| | - Nor Fazila Che Mat
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Geoffrey Keith Chambers
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Hisham Atan Edinur
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia. .,Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia. .,Environmental Futures Research Institute, Griffith University, Nathan, Queensland, 4111, Australia.
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6
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Jagadeesan A, Gunnarsdóttir ED, Ebenesersdóttir SS, Guðmundsdóttir VB, Thordardottir EL, Einarsdóttir MS, Jónsson H, Dugoujon JM, Fortes-Lima C, Migot-Nabias F, Massougbodji A, Bellis G, Pereira L, Másson G, Kong A, Stefánsson K, Helgason A. Reconstructing an African haploid genome from the 18th century. Nat Genet 2018; 50:199-205. [PMID: 29335549 DOI: 10.1038/s41588-017-0031-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 12/18/2017] [Indexed: 01/15/2023]
Abstract
A genome is a mosaic of chromosome fragments from ancestors who existed some arbitrary number of generations earlier. Here, we reconstruct the genome of Hans Jonatan (HJ), born in the Caribbean in 1784 to an enslaved African mother and European father. HJ migrated to Iceland in 1802, married and had two children. We genotyped 182 of his 788 descendants using single-nucleotide polymorphism (SNP) chips and whole-genome sequenced (WGS) 20 of them. Using these data, we reconstructed 38% of HJ's maternal genome and inferred that his mother was from the region spanned by Benin, Nigeria and Cameroon.
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Affiliation(s)
- Anuradha Jagadeesan
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | - S Sunna Ebenesersdóttir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Valdis B Guðmundsdóttir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | - Margrét S Einarsdóttir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | - Jean-Michel Dugoujon
- Laboratoire d'Eco-Anthropologie et Ethnobiologie, Equipe d'Anthropologie Evolutive, UMR 7206, Centre National de la Recherche Scientifique (CNRS) et Université Diderot Paris 7, Paris, France
| | - Cesar Fortes-Lima
- Laboratoire d'Eco-Anthropologie et Ethnobiologie, Equipe d'Anthropologie Evolutive, UMR 7206, Centre National de la Recherche Scientifique (CNRS) et Université Diderot Paris 7, Paris, France
| | - Florence Migot-Nabias
- Institut de Recherche pour le Développement, UMR D216 MERIT (Mère et enfant face aux infections tropicales), Paris, France
- COMUE Sorbonne Paris Cité, Faculté de Pharmacie, Université Paris Descartes, Paris, France
| | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et l'Enfance (CERPAGE), Cotonou, Benin
- Laboratoire de Parasitologie, Faculté des Sciences de la Santé, Université d'Abomey-Calavi, Cotonou, Benin
| | - Gil Bellis
- Institut National d'Etudes Démographiques (INED), Paris, France
| | - Luisa Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | | | | | - Kári Stefánsson
- deCODE Genetics/Amgen, Reykjavik, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
| | - Agnar Helgason
- deCODE Genetics/Amgen, Reykjavik, Iceland.
- Department of Anthropology, University of Iceland, Reykjavik, Iceland.
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