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Genome Analysis Using Whole-Exome Sequencing of Non-Syndromic Cleft Lip and/or Palate from Malagasy Trios Identifies Variants Associated with Cilium-Related Pathways and Asian Genetic Ancestry. Genes (Basel) 2023; 14:genes14030665. [PMID: 36980938 PMCID: PMC10048728 DOI: 10.3390/genes14030665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 03/10/2023] Open
Abstract
Background: Orofacial clefts (OFCs) are common congenital disabilities that can occur as isolated non-syndromic events or as part of Mendelian syndromes. OFC risk factors vary due to differences in regional environmental exposures, genetic variants, and ethnicities. In recent years, significant progress has been made in understanding OFCs, due to advances in sequencing and genotyping technologies. Despite these advances, very little is known about the genetic interplay in the Malagasy population. Methods: Here, we performed high-resolution whole-exome sequencing (WES) on non-syndromic cleft lip with or without palate (nCL/P) trios in the Malagasy population (78 individuals from 26 families (trios)). To integrate the impact of genetic ancestry admixture, we computed both global and local ancestries. Results: Participants demonstrated a high percentage of both African and Asian admixture. We identified damaging variants in primary cilium-mediated pathway genes WNT5B (one family), GPC4 (one family), co-occurrence in MSX1 (five families), WDR11 (one family), and tubulin stabilizer SEPTIN9 (one family). Furthermore, we identified an autosomal homozygous damaging variant in PHGDH (one family) gene that may impact metabiotic activity. Lastly, all variants were predicted to reside on local Asian genetic ancestry admixed alleles. Conclusion: Our results from examining the Malagasy genome provide limited support for the hypothesis that germline variants in primary cilia may be risk factors for nCL/P, and outline the importance of integrating local ancestry components better to understand the multi-ethnic impact on nCL/P.
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Heiske M, Alva O, Pereda-Loth V, Van Schalkwyk M, Radimilahy C, Letellier T, Rakotarisoa JA, Pierron D. Genetic evidence and historical theories of the Asian and African origins of the present Malagasy population. Hum Mol Genet 2021; 30:R72-R78. [PMID: 33481023 DOI: 10.1093/hmg/ddab018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/23/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
The origin of the Malagasy population has been a subject of speculation since the 16th century. Contributions of African, Asian, Indian, Melanesian, Arabic and Persian populations have been suggested based on physical and cultural anthropology, oral tradition, linguistics and later also by archaeology. In the mid-20th century, increased knowledge of heredity rules and technical progress enabled the identification of African and Asian populations as main contributors. Recent access to the genomic landscape of Madagascar demonstrated pronounced regional variability in the relative contributions of these two ancestries, yet with significant presence of both African and Asian components throughout Madagascar. This article reviews the extent to which genetic results have settled historical questions concerning the origin of the Malagasy population. After an overview of the early literature, the genetic results of the 20th and 21th centuries are discussed and then complemented by the latest results in genome-wide analyses. While there is still much uncertainty regarding when, how and the circumstances under which the ancestors of the modern Malagasy population arrived on the island, we propose a scenario based on historical texts and genomic results.
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Affiliation(s)
- Margit Heiske
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | - Omar Alva
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | - Veronica Pereda-Loth
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | - Matthew Van Schalkwyk
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Chantal Radimilahy
- Musée d'Art et d'Archéologie, University of Antananarivo, Antananarivo, Madagascar
| | - Thierry Letellier
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | | | - Denis Pierron
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
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Fortes-Lima C, Dugoujon JM, Hernández CL, Reales G, Calderón R. Immunoglobulin genes in Andalusia (Spain). Genetic diversity in the Mediterranean space. C R Biol 2014; 337:646-56. [PMID: 25444709 DOI: 10.1016/j.crvi.2014.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/15/2014] [Accepted: 08/13/2014] [Indexed: 11/29/2022]
Abstract
Andalusia is the most densely populated region of Spain since ancient times, and has a rich history of contacts across the Mediterranean. Earlier studies have underlined the relatively high frequency of the Sub-Saharan GM 1,17 5* haplotype in western Andalusia (Huelva province, n=252) and neighbouring Atlantic regions. Here, we provide novel data on GM/KM markers in eastern Andalusians (n=195) from Granada province, where African GM*1,17 5* frequency is relatively high (0.044). The most frequent GM haplotypes in Andalusia parallel the most common in Europe. Altogether, these data allow us to gain insight into the genetic diversity of southern Iberia. Additionally, we assess population structure by comparing our Iberian samples with 41 Mediterranean populations. GM haplotype variation across the Mediterranean reflects intense and complex interactions between North Africans and South Europeans along human history, highlighting that African influence over the Iberian Peninsula does not follow an isotropic pattern.
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Affiliation(s)
- César Fortes-Lima
- Laboratoire D'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique (CNRS), Université Toulouse-3-Paul-Sabatier, Toulouse, France
| | - Jean-Michel Dugoujon
- Laboratoire D'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique (CNRS), Université Toulouse-3-Paul-Sabatier, Toulouse, France.
| | - Candela L Hernández
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Guillermo Reales
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Rosario Calderón
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain.
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Capredon M, Brucato N, Tonasso L, Choesmel-Cadamuro V, Ricaut FX, Razafindrazaka H, Rakotondrabe AB, Ratolojanahary MA, Randriamarolaza LP, Champion B, Dugoujon JM. Tracing Arab-Islamic inheritance in Madagascar: study of the Y-chromosome and mitochondrial DNA in the Antemoro. PLoS One 2013; 8:e80932. [PMID: 24278350 PMCID: PMC3838347 DOI: 10.1371/journal.pone.0080932] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/08/2013] [Indexed: 11/19/2022] Open
Abstract
Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.
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Affiliation(s)
- Mélanie Capredon
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
- Centre de recherche littéraire et historique de l’Océan Indien (CRLHOI), Département d’ethnologie, Université de La Réunion, Saint-Denis, France
- Department of Pediatrics, CHU Sainte Justine, Faculty of Medecine, University of Montreal, Quebec, Canada
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| | - Nicolas Brucato
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Laure Tonasso
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - Valérie Choesmel-Cadamuro
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - François-Xavier Ricaut
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - Harilanto Razafindrazaka
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | | | - Mamisoa Adelta Ratolojanahary
- Laboratoire d'Anthropologie Patrimoine -Transformations sociales- Transculturalité (LAP2T), Université Antananarivo, Antananarivo, Madagascar
| | - Louis-Paul Randriamarolaza
- Laboratoire d'Anthropologie Patrimoine -Transformations sociales- Transculturalité (LAP2T), Université Antananarivo, Antananarivo, Madagascar
| | - Bernard Champion
- Centre de recherche littéraire et historique de l’Océan Indien (CRLHOI), Département d’ethnologie, Université de La Réunion, Saint-Denis, France
| | - Jean-Michel Dugoujon
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
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