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Sánchez S, Juárez U, Domínguez J, Molina B, Barrientos R, Martínez-Hernández A, Carnevale A, Grether-González P, Mayen DG, Villarroel C, Lieberman E, Yokoyama E, Del Castillo V, Torres L, Frias S. Frequent copy number variants in a cohort of Mexican-Mestizo individuals. Mol Cytogenet 2023; 16:2. [PMID: 36631885 PMCID: PMC9835318 DOI: 10.1186/s13039-022-00631-z] [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: 11/01/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The human genome presents variation at distinct levels, copy number variants (CNVs) are DNA segments of variable lengths that range from several base pairs to megabases and are present at a variable number of copies in human genomes. Common CNVs have no apparent influence on the phenotype; however, some rare CNVs have been associated with phenotypic traits, depending on their size and gene content. CNVs are detected by microarrays of different densities and are generally visualized, and their frequencies analysed using the HapMap as default reference population. Nevertheless, this default reference is inadequate when the samples analysed are from people from Mexico, since population with a Hispanic genetic background are minimally represented. In this work, we describe the variation in the frequencies of four common CNVs in Mexican-Mestizo individuals. RESULTS In a cohort of 147 unrelated Mexican-Mestizo individuals, we found that the common CNVs 2p11.2 (99.6%), 8p11.22 (54.5%), 14q32.33 (100%), and 15q11.2 (71.1%) appeared with unexpectedly high frequencies when contrasted with the HapMap reference (ChAS). Yet, while when comparing to an ethnically related reference population, these differences were significantly reduced or even disappeared. CONCLUSION The findings in this work contribute to (1) a better description of the CNVs characteristics of the Mexican Mestizo population and enhance the knowledge of genome variation in different ethnic groups. (2) emphasize the importance of contrasting CNVs identified in studied individuals against a reference group that-as best as possible-share the same ethnicity while keeping this relevant information in mind when conducting CNV studies at the population or clinical level.
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Affiliation(s)
- Silvia Sánchez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México ,grid.9486.30000 0001 2159 0001Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ulises Juárez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Julieta Domínguez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Bertha Molina
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Rehotbevely Barrientos
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Angélica Martínez-Hernández
- grid.452651.10000 0004 0627 7633Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Alessandra Carnevale
- grid.452651.10000 0004 0627 7633Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Patricia Grether-González
- grid.419218.70000 0004 1773 5302Departamento de Genética y Genómica Humana, Instituto Nacional de Perinatología, Ciudad de Mexico, México ,grid.413678.fPresent Address: Centro Médico ABC, Campus Santa Fe, Ciudad de Mexico, México
| | - Dora Gilda Mayen
- Unidad de Genética Aplicada. Hospital Ángeles Lomas, Huixquilucan, Edo. de México México
| | - Camilo Villarroel
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Esther Lieberman
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Emiy Yokoyama
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Victoria Del Castillo
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Leda Torres
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Sara Frias
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México ,grid.9486.30000 0001 2159 0001Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
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