CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis
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 dise...
Ausführliche Beschreibung
Autor*in: |
Angélica Martínez-Hernández [verfasserIn] Elvia C. Mendoza-Caamal [verfasserIn] Namibia G. Mendiola-Vidal [verfasserIn] Francisco Barajas-Olmos [verfasserIn] José Rafael Villafan-Bernal [verfasserIn] Juan Luis Jiménez-Ruiz [verfasserIn] Tulia Monge-Cazares [verfasserIn] Humberto García-Ortiz [verfasserIn] Cecilia Contreras- Cubas [verfasserIn] Federico Centeno-Cruz [verfasserIn] Carmen Alaez-Verson [verfasserIn] Soraya Ortega-Torres [verfasserIn] Adriana del C. Luna-Castañeda [verfasserIn] Vicente Baca [verfasserIn] José Luis Lezana [verfasserIn] Lorena Orozco [verfasserIn] |
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Format: |
E-Artikel |
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Sprache: |
Englisch |
Erschienen: |
2024 |
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Schlagwörter: |
Next-generation sequencing (NGS) |
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Übergeordnetes Werk: |
In: Heliyon - Elsevier, 2016, 10(2024), 7, Seite e28984- |
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Übergeordnetes Werk: |
volume:10 ; year:2024 ; number:7 ; pages:e28984- |
Links: |
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DOI / URN: |
10.1016/j.heliyon.2024.e28984 |
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Katalog-ID: |
DOAJ095890793 |
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520 | |a 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. | ||
650 | 4 | |a Pathogenic variants | |
650 | 4 | |a Mexican populations | |
650 | 4 | |a Next-generation sequencing (NGS) | |
650 | 4 | |a Three-dimensional protein structure | |
650 | 4 | |a Novel variants | |
650 | 4 | |a Complex allele | |
653 | 0 | |a Science (General) | |
653 | 0 | |a Social sciences (General) | |
700 | 0 | |a Elvia C. Mendoza-Caamal |e verfasserin |4 aut | |
700 | 0 | |a Namibia G. Mendiola-Vidal |e verfasserin |4 aut | |
700 | 0 | |a Francisco Barajas-Olmos |e verfasserin |4 aut | |
700 | 0 | |a José Rafael Villafan-Bernal |e verfasserin |4 aut | |
700 | 0 | |a Juan Luis Jiménez-Ruiz |e verfasserin |4 aut | |
700 | 0 | |a Tulia Monge-Cazares |e verfasserin |4 aut | |
700 | 0 | |a Humberto García-Ortiz |e verfasserin |4 aut | |
700 | 0 | |a Cecilia Contreras- Cubas |e verfasserin |4 aut | |
700 | 0 | |a Federico Centeno-Cruz |e verfasserin |4 aut | |
700 | 0 | |a Carmen Alaez-Verson |e verfasserin |4 aut | |
700 | 0 | |a Soraya Ortega-Torres |e verfasserin |4 aut | |
700 | 0 | |a Adriana del C. Luna-Castañeda |e verfasserin |4 aut | |
700 | 0 | |a Vicente Baca |e verfasserin |4 aut | |
700 | 0 | |a José Luis Lezana |e verfasserin |4 aut | |
700 | 0 | |a Lorena Orozco |e verfasserin |4 aut | |
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10.1016/j.heliyon.2024.e28984 doi (DE-627)DOAJ095890793 (DE-599)DOAJce4c8142ceb54ebeaeeec00442c786a9 DE-627 ger DE-627 rakwb eng Q1-390 H1-99 Angélica Martínez-Hernández verfasserin aut CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Pathogenic variants Mexican populations Next-generation sequencing (NGS) Three-dimensional protein structure Novel variants Complex allele Science (General) Social sciences (General) Elvia C. Mendoza-Caamal verfasserin aut Namibia G. Mendiola-Vidal verfasserin aut Francisco Barajas-Olmos verfasserin aut José Rafael Villafan-Bernal verfasserin aut Juan Luis Jiménez-Ruiz verfasserin aut Tulia Monge-Cazares verfasserin aut Humberto García-Ortiz verfasserin aut Cecilia Contreras- Cubas verfasserin aut Federico Centeno-Cruz verfasserin aut Carmen Alaez-Verson verfasserin aut Soraya Ortega-Torres verfasserin aut Adriana del C. Luna-Castañeda verfasserin aut Vicente Baca verfasserin aut José Luis Lezana verfasserin aut Lorena Orozco verfasserin aut In Heliyon Elsevier, 2016 10(2024), 7, Seite e28984- (DE-627)835893197 (DE-600)2835763-2 24058440 nnns volume:10 year:2024 number:7 pages:e28984- https://doi.org/10.1016/j.heliyon.2024.e28984 kostenfrei https://doaj.org/article/ce4c8142ceb54ebeaeeec00442c786a9 kostenfrei http://www.sciencedirect.com/science/article/pii/S2405844024050151 kostenfrei https://doaj.org/toc/2405-8440 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 10 2024 7 e28984- |
spelling |
10.1016/j.heliyon.2024.e28984 doi (DE-627)DOAJ095890793 (DE-599)DOAJce4c8142ceb54ebeaeeec00442c786a9 DE-627 ger DE-627 rakwb eng Q1-390 H1-99 Angélica Martínez-Hernández verfasserin aut CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Pathogenic variants Mexican populations Next-generation sequencing (NGS) Three-dimensional protein structure Novel variants Complex allele Science (General) Social sciences (General) Elvia C. Mendoza-Caamal verfasserin aut Namibia G. Mendiola-Vidal verfasserin aut Francisco Barajas-Olmos verfasserin aut José Rafael Villafan-Bernal verfasserin aut Juan Luis Jiménez-Ruiz verfasserin aut Tulia Monge-Cazares verfasserin aut Humberto García-Ortiz verfasserin aut Cecilia Contreras- Cubas verfasserin aut Federico Centeno-Cruz verfasserin aut Carmen Alaez-Verson verfasserin aut Soraya Ortega-Torres verfasserin aut Adriana del C. Luna-Castañeda verfasserin aut Vicente Baca verfasserin aut José Luis Lezana verfasserin aut Lorena Orozco verfasserin aut In Heliyon Elsevier, 2016 10(2024), 7, Seite e28984- (DE-627)835893197 (DE-600)2835763-2 24058440 nnns volume:10 year:2024 number:7 pages:e28984- https://doi.org/10.1016/j.heliyon.2024.e28984 kostenfrei https://doaj.org/article/ce4c8142ceb54ebeaeeec00442c786a9 kostenfrei http://www.sciencedirect.com/science/article/pii/S2405844024050151 kostenfrei https://doaj.org/toc/2405-8440 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 10 2024 7 e28984- |
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10.1016/j.heliyon.2024.e28984 doi (DE-627)DOAJ095890793 (DE-599)DOAJce4c8142ceb54ebeaeeec00442c786a9 DE-627 ger DE-627 rakwb eng Q1-390 H1-99 Angélica Martínez-Hernández verfasserin aut CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Pathogenic variants Mexican populations Next-generation sequencing (NGS) Three-dimensional protein structure Novel variants Complex allele Science (General) Social sciences (General) Elvia C. Mendoza-Caamal verfasserin aut Namibia G. Mendiola-Vidal verfasserin aut Francisco Barajas-Olmos verfasserin aut José Rafael Villafan-Bernal verfasserin aut Juan Luis Jiménez-Ruiz verfasserin aut Tulia Monge-Cazares verfasserin aut Humberto García-Ortiz verfasserin aut Cecilia Contreras- Cubas verfasserin aut Federico Centeno-Cruz verfasserin aut Carmen Alaez-Verson verfasserin aut Soraya Ortega-Torres verfasserin aut Adriana del C. Luna-Castañeda verfasserin aut Vicente Baca verfasserin aut José Luis Lezana verfasserin aut Lorena Orozco verfasserin aut In Heliyon Elsevier, 2016 10(2024), 7, Seite e28984- (DE-627)835893197 (DE-600)2835763-2 24058440 nnns volume:10 year:2024 number:7 pages:e28984- https://doi.org/10.1016/j.heliyon.2024.e28984 kostenfrei https://doaj.org/article/ce4c8142ceb54ebeaeeec00442c786a9 kostenfrei http://www.sciencedirect.com/science/article/pii/S2405844024050151 kostenfrei https://doaj.org/toc/2405-8440 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 10 2024 7 e28984- |
allfieldsGer |
10.1016/j.heliyon.2024.e28984 doi (DE-627)DOAJ095890793 (DE-599)DOAJce4c8142ceb54ebeaeeec00442c786a9 DE-627 ger DE-627 rakwb eng Q1-390 H1-99 Angélica Martínez-Hernández verfasserin aut CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Pathogenic variants Mexican populations Next-generation sequencing (NGS) Three-dimensional protein structure Novel variants Complex allele Science (General) Social sciences (General) Elvia C. Mendoza-Caamal verfasserin aut Namibia G. Mendiola-Vidal verfasserin aut Francisco Barajas-Olmos verfasserin aut José Rafael Villafan-Bernal verfasserin aut Juan Luis Jiménez-Ruiz verfasserin aut Tulia Monge-Cazares verfasserin aut Humberto García-Ortiz verfasserin aut Cecilia Contreras- Cubas verfasserin aut Federico Centeno-Cruz verfasserin aut Carmen Alaez-Verson verfasserin aut Soraya Ortega-Torres verfasserin aut Adriana del C. Luna-Castañeda verfasserin aut Vicente Baca verfasserin aut José Luis Lezana verfasserin aut Lorena Orozco verfasserin aut In Heliyon Elsevier, 2016 10(2024), 7, Seite e28984- (DE-627)835893197 (DE-600)2835763-2 24058440 nnns volume:10 year:2024 number:7 pages:e28984- https://doi.org/10.1016/j.heliyon.2024.e28984 kostenfrei https://doaj.org/article/ce4c8142ceb54ebeaeeec00442c786a9 kostenfrei http://www.sciencedirect.com/science/article/pii/S2405844024050151 kostenfrei https://doaj.org/toc/2405-8440 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 10 2024 7 e28984- |
allfieldsSound |
10.1016/j.heliyon.2024.e28984 doi (DE-627)DOAJ095890793 (DE-599)DOAJce4c8142ceb54ebeaeeec00442c786a9 DE-627 ger DE-627 rakwb eng Q1-390 H1-99 Angélica Martínez-Hernández verfasserin aut CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Pathogenic variants Mexican populations Next-generation sequencing (NGS) Three-dimensional protein structure Novel variants Complex allele Science (General) Social sciences (General) Elvia C. Mendoza-Caamal verfasserin aut Namibia G. Mendiola-Vidal verfasserin aut Francisco Barajas-Olmos verfasserin aut José Rafael Villafan-Bernal verfasserin aut Juan Luis Jiménez-Ruiz verfasserin aut Tulia Monge-Cazares verfasserin aut Humberto García-Ortiz verfasserin aut Cecilia Contreras- Cubas verfasserin aut Federico Centeno-Cruz verfasserin aut Carmen Alaez-Verson verfasserin aut Soraya Ortega-Torres verfasserin aut Adriana del C. Luna-Castañeda verfasserin aut Vicente Baca verfasserin aut José Luis Lezana verfasserin aut Lorena Orozco verfasserin aut In Heliyon Elsevier, 2016 10(2024), 7, Seite e28984- (DE-627)835893197 (DE-600)2835763-2 24058440 nnns volume:10 year:2024 number:7 pages:e28984- https://doi.org/10.1016/j.heliyon.2024.e28984 kostenfrei https://doaj.org/article/ce4c8142ceb54ebeaeeec00442c786a9 kostenfrei http://www.sciencedirect.com/science/article/pii/S2405844024050151 kostenfrei https://doaj.org/toc/2405-8440 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 10 2024 7 e28984- |
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Angélica Martínez-Hernández @@aut@@ Elvia C. Mendoza-Caamal @@aut@@ Namibia G. Mendiola-Vidal @@aut@@ Francisco Barajas-Olmos @@aut@@ José Rafael Villafan-Bernal @@aut@@ Juan Luis Jiménez-Ruiz @@aut@@ Tulia Monge-Cazares @@aut@@ Humberto García-Ortiz @@aut@@ Cecilia Contreras- Cubas @@aut@@ Federico Centeno-Cruz @@aut@@ Carmen Alaez-Verson @@aut@@ Soraya Ortega-Torres @@aut@@ Adriana del C. Luna-Castañeda @@aut@@ Vicente Baca @@aut@@ José Luis Lezana @@aut@@ Lorena Orozco @@aut@@ |
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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%. 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Angélica Martínez-Hernández |
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Angélica Martínez-Hernández misc Q1-390 misc H1-99 misc Pathogenic variants misc Mexican populations misc Next-generation sequencing (NGS) misc Three-dimensional protein structure misc Novel variants misc Complex allele misc Science (General) misc Social sciences (General) CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis |
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Q1-390 H1-99 CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis Pathogenic variants Mexican populations Next-generation sequencing (NGS) Three-dimensional protein structure Novel variants Complex allele |
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misc Q1-390 misc H1-99 misc Pathogenic variants misc Mexican populations misc Next-generation sequencing (NGS) misc Three-dimensional protein structure misc Novel variants misc Complex allele misc Science (General) misc Social sciences (General) |
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CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis |
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CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis |
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Angélica Martínez-Hernández |
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Angélica Martínez-Hernández Elvia C. Mendoza-Caamal Namibia G. Mendiola-Vidal Francisco Barajas-Olmos José Rafael Villafan-Bernal Juan Luis Jiménez-Ruiz Tulia Monge-Cazares Humberto García-Ortiz Cecilia Contreras- Cubas Federico Centeno-Cruz Carmen Alaez-Verson Soraya Ortega-Torres Adriana del C. Luna-Castañeda Vicente Baca José Luis Lezana Lorena Orozco |
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10.1016/j.heliyon.2024.e28984 |
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cftr pathogenic variants spectrum in a cohort of mexican patients with cystic fibrosis |
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Q1-390 |
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CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis |
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. |
abstractGer |
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. |
abstract_unstemmed |
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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container_issue |
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title_short |
CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis |
url |
https://doi.org/10.1016/j.heliyon.2024.e28984 https://doaj.org/article/ce4c8142ceb54ebeaeeec00442c786a9 http://www.sciencedirect.com/science/article/pii/S2405844024050151 https://doaj.org/toc/2405-8440 |
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author2 |
Elvia C. Mendoza-Caamal Namibia G. Mendiola-Vidal Francisco Barajas-Olmos José Rafael Villafan-Bernal Juan Luis Jiménez-Ruiz Tulia Monge-Cazares Humberto García-Ortiz Cecilia Contreras- Cubas Federico Centeno-Cruz Carmen Alaez-Verson Soraya Ortega-Torres Adriana del C. Luna-Castañeda Vicente Baca José Luis Lezana Lorena Orozco |
author2Str |
Elvia C. Mendoza-Caamal Namibia G. Mendiola-Vidal Francisco Barajas-Olmos José Rafael Villafan-Bernal Juan Luis Jiménez-Ruiz Tulia Monge-Cazares Humberto García-Ortiz Cecilia Contreras- Cubas Federico Centeno-Cruz Carmen Alaez-Verson Soraya Ortega-Torres Adriana del C. Luna-Castañeda Vicente Baca José Luis Lezana Lorena Orozco |
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10.1016/j.heliyon.2024.e28984 |
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up_date |
2024-07-03T17:12:46.304Z |
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score |
7.4026995 |