Journal Article

Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences

Rahimov, Fedik, Vasanthakumar, Aparna, Krishnan, Preethi, Dorr, Patrick, Ideozu, Justin E., Liu, Mengzhen, Paladugu, Sri R., Riley-Gillis, Bridget M., Levy, Hara, Tripathi, Rakesh, Singh, Ashvani, Waring, Jeffrey F.

2024

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Age / Analysis / Biobanks / Bioinformatics / Biological Specimen Banks / Biomedical and Life Sciences / Biomedicine / Cancer Research / CFTR / Classification / Cystic fibrosis / Cystic Fibrosis - genetics / Cystic Fibrosis Transmembrane Conductance Regulator - genetics / Ethnicity / Exome / Genetic testing / Genomes / Genotypes / Health aspects / Human Genetics / Humans / Medicine/Public Health / Metabolomics / Mutation / Patients / Phenotypes / Systems Biology / UK Biobank / Whole exome sequencing