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Martínez-Hernández A, Mendoza-Caamal EC, Mendiola-Vidal NG, Barajas-Olmos F, Villafan-Bernal JR, Jiménez-Ruiz JL, Monge-Cazares T, García-Ortiz H, Cubas CC, Centeno-Cruz F, Alaez-Verson C, Ortega-Torres S, Luna-Castañeda ADC, Baca V, Lezana JL, Orozco L. CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis. Heliyon 2024; 10:e28984. [PMID: 38601560 PMCID: PMC11004572 DOI: 10.1016/j.heliyon.2024.e28984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Background Molecular diagnosis of cystic fibrosis (CF) is challenging in Mexico due to the population's high genetic heterogeneity. To date, 46 pathogenic variants (PVs) have been reported, yielding a detection rate of 77%. We updated the spectrum and frequency of PVs responsible for this disease in mexican patients. Methods We extracted genomic DNA from peripheral blood lymphocytes obtained from 297 CF patients and their parents. First, we analyzed the five most frequent PVs in the Mexican population using PCR-mediated site-directed mutagenesis. In patients with at least one identified allele, CFTR sequencing was performed using next-generation sequencing tools and multiplex ligation-dependent probe amplification. For variants not previously classified as pathogenic, we used a combination of in silico prediction, CFTR modeling, and clinical characteristics to determine a genotype-phenotype correlation. Results We identified 95 PVs, increasing the detection rate to 87.04%. The most frequent variants were p.(PheF508del) (42.7%), followed by p.(Gly542*) (5.6%), p.(Ser945Leu) (2.9%), p.(Trp1204*) and p.(Ser549Asn) (2.5%), and CFTRdel25-26 and p.(Asn386Ilefs*3) (2.3%). The remaining variants had frequencies of <2.0%, and some were exclusive to one family. We identified 10 novel PVs localized in different exons (frequency range: 0.1-0.8%), all of which produced structural changes, deletions, or duplications in different domains of the protein, resulting in dysfunctional ion flow. The use of different in silico software and American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) criteria allowed us to assume that all of these PVs were pathogenic, causing a severe phenotype. Conclusions In a highly heterogeneous population, combinations of different tools are needed to identify the variants responsible for CF and enable the establishment of appropriate strategies for CF diagnosis, prevention, and treatment.
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Affiliation(s)
- Angélica Martínez-Hernández
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Elvia C. Mendoza-Caamal
- Clinical Area, Instituto Nacional de Medicina Genómica, SS, Tlalpan, 14610, CDMX, Mexico City, Mexico
| | - Namibia G. Mendiola-Vidal
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
- Maestría en Ciencias Médicas. PMDCMOS. Sede: HGGEA, UNAM. Coyoacan, 04510, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - José Rafael Villafan-Bernal
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
- Investigador por Mexico, Consejo Nacional de Humanidades, Ciencia y Tecnología (CONAHCYT), Benito Juarez, 03940, Mexico City, Mexico
| | - Juan Luis Jiménez-Ruiz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Tulia Monge-Cazares
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Cecilia Contreras- Cubas
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Federico Centeno-Cruz
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
| | - Carmen Alaez-Verson
- Genomic Diagnostic Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, CDMX, Mexico City, Mexico
| | - Soraya Ortega-Torres
- Curso de Alta Especialidad en Medicina Genómica, Instituto Nacional de Medicina Genomica, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Coyoacan, 04510, Mexico City, Mexico
| | | | - Vicente Baca
- Rheumatology Department, Hospital de Pediatría, CMN Siglo XXI IMSS, Cuauhtemoc, 06720, Mexico City, Mexico
| | - José Luis Lezana
- Cystic Fibrosis Clinic and Pulmonary Physiology Laboratory. Hospital Infantil de Mexico Federico Gómez, SS, Cuauhtemoc, 06720, Mexico City, Mexico
- Asociacion Mexicana de Fibrosis Quistica, A.C. Benito Juarez, 03700, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Genomica, SS, Tlalpan, 14610, Mexico City, Mexico
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