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Ideozu JE, Liu M, Riley-Gillis BM, Paladugu SR, Rahimov F, Krishnan P, Tripathi R, Dorr P, Levy H, Singh A, Waring JF, Vasanthakumar A. Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences. Genome Med 2024; 16:43. [PMID: 38515211 PMCID: PMC10956269 DOI: 10.1186/s13073-024-01316-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Limited understanding of the diversity of variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene across ancestries hampers efforts to advance molecular diagnosis of cystic fibrosis (CF). The consequences pose a risk of delayed diagnoses and subsequently worsened health outcomes for patients. Therefore, characterizing the spectrum of CFTR variants across ancestries is critical for revolutionizing molecular diagnoses of CF. METHODS We analyzed 454,727 UK Biobank (UKBB) whole-exome sequences to characterize the diversity of CFTR variants across ancestries. Using the PanUKBB classification, the participants were assigned into six major groups: African (AFR), American/American Admixed (AMR), Central South Asia (CSA), East Asian (EAS), European (EUR), and Middle East (MID). We segregated ancestry-specific CFTR variants, including those that are CF-causing or clinically relevant. The ages of certain CF-causing variants were determined and analyzed for selective pressure effects, and curated phenotype analysis was performed for participants with clinically relevant CFTR genotypes. RESULTS We detected over 4000 CFTR variants, including novel ancestry-specific variants, across six ancestries. Europeans had the most unique CFTR variants [n = 2212], while the American group had the least unique variants [n = 23]. F508del was the most prevalent CF-causing variant found in all ancestries, except in EAS, where V520F was the most prevalent. Common EAS variants such as 3600G > A, V456A, and V520, which appeared approximately 270, 215, and 338 generations ago, respectively, did not show evidence of selective pressure. Sixteen participants had two CF-causing variants, with two being diagnosed with CF. We found 154 participants harboring a CF-causing and varying clinical consequences (VCC) variant. Phenotype analysis performed for participants with multiple clinically relevant variants returned significant associations with CF and its pulmonary phenotypes [Bonferroni-adjusted p < 0.05]. CONCLUSIONS We leveraged the UKBB database to comprehensively characterize the broad spectrum of CFTR variants across ancestries. The detection of over 4000 CFTR variants, including several ancestry-specific and uncharacterized CFTR variants, warrants the need for further characterization of their functional and clinical relevance. Overall, the presentation of classical CF phenotypes seen in non-CF diagnosed participants with more than one CF-causing variant indicates that they may benefit from current CFTR modulator therapies.
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Affiliation(s)
- Justin E Ideozu
- Genomic Medicine, Genomics Research Center, AbbVie, Chicago, IL, USA.
| | - Mengzhen Liu
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | | | - Sri R Paladugu
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | - Fedik Rahimov
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
| | | | | | | | - Hara Levy
- Department of Pediatrics, Division of Pulmonology and Sleep Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Jeffrey F Waring
- Genomic Medicine, Genomics Research Center, AbbVie, Chicago, IL, USA
- Human Genetics, Genomics Research Center, AbbVie, Chicago, IL, USA
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Yang B, Lei C, Yang D, Tan Z, Guo T, Luo H. Whole-Exome Sequencing Identified CFTR Variants in Two Consanguineous Families in China. Front Genet 2021; 12:631221. [PMID: 34276759 PMCID: PMC8283821 DOI: 10.3389/fgene.2021.631221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/12/2021] [Indexed: 11/18/2022] Open
Abstract
Background Cystic fibrosis (CF) is an autosomal recessive disease caused by genetic variants of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. It is a common hereditary disease in Caucasians while rare in the Chinese. Until now, only 87 Chinese patients have been reported with molecular confirmations. The variant spectrum and clinical features of Chinese CF patients are obviously different from those of Caucasians. Materials and Methods Whole-exome sequencing was applied to analyze the exome of three individuals who have only the typical CF phenotype in the respiratory system from two consanguineous families. The protein domain and structure analysis were applied to predict the impact of the variants. Sanger sequencing was applied to validate the candidate variants. Results A previously reported homozygous variant in CFTR (NM_000492.4: c.1000C > T, p.R334W) was identified in proband I. A novel homozygous variant in a polymorphic position (NM_000492.4: c.1409T > A, p.V470E) was identified in two individuals in the family II. The novel CFTR variant predicted to be disease-causing is the first, to the best of our knowledge, to be reported in CFTR. However, in vitro validation is still needed. Conclusion Our finding expands the variant spectrum of CFTR, reveals clearer clinical phenotype distinction and variant spectrum distinction between Chinese and Caucasian CF patients, and contributes to a more rapid genetic diagnosis and future genetic counseling.
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Affiliation(s)
- Binyi Yang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Respiratory Disease, Central South University, Changsha, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Cheng Lei
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Respiratory Disease, Central South University, Changsha, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Danhui Yang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Respiratory Disease, Central South University, Changsha, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Zhiping Tan
- Department of Cardiovascular Surgery, Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ting Guo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Respiratory Disease, Central South University, Changsha, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Respiratory Disease, Central South University, Changsha, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
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