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- W4210771138 abstract "<ns3:p><ns3:bold>Background:</ns3:bold> Low frequency mutations within the filaggrin (<ns3:italic>FLG</ns3:italic>) gene are established genetic risk factors for atopic dermatitis. Studies of<ns3:italic> FLG</ns3:italic> have typically used sequencing or bespoke genotyping. Large-scale population cohorts with genome-wide imputed data offer powerful genetic analysis opportunities, but bespoke <ns3:italic>FLG </ns3:italic>genotyping is often not feasible in such studies. Therefore, we aimed to determine the quality of selected <ns3:italic>FLG</ns3:italic> null genotype data extracted from genome-wide imputed sources, focussing on UK population data.</ns3:p><ns3:p> <ns3:bold>Methods:</ns3:bold> We compared the allele frequencies of three <ns3:italic>FLG</ns3:italic> null mutations (R501X, R2447X and S3247X) in directly genotyped and genome-wide imputed data in the ALSPAC cohort. Logistic regression analysis was used to test the association of atopic dermatitis with imputed and genotyped <ns3:italic>FLG</ns3:italic> null mutations in ALSPAC and UK Biobank to investigate the usefulness of imputed <ns3:italic>FLG</ns3:italic> data.</ns3:p><ns3:p> <ns3:bold>Results:</ns3:bold> The three <ns3:italic>FLG</ns3:italic> null mutations appear to be well imputed in datasets that use the Haplotype Reference Consortium (HRC) for imputation (0.3% discordance compared with directly genotyped data). However, a greater proportion of null alleles failed imputation compared to wild-type alleles. Despite the calling of <ns3:italic>FLG</ns3:italic> mutations in imputed data being imperfect, they are still strongly associated with atopic dermatitis (p-values between 7x10<ns3:sup>-10</ns3:sup> and 5x10<ns3:sup>-75</ns3:sup> in UK Biobank).</ns3:p><ns3:p> <ns3:bold>Conclusions:</ns3:bold> HRC imputed data appears to be adequate for UK population-based genetic analysis of selected <ns3:italic>FLG</ns3:italic> null mutations.</ns3:p>" @default.
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- W4210771138 date "2022-02-01" @default.
- W4210771138 modified "2023-09-26" @default.
- W4210771138 title "Imputation provides an opportunity to study filaggrin (FLG) null mutations in large population cohorts that lack bespoke genotyping" @default.
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- W4210771138 doi "https://doi.org/10.12688/wellcomeopenres.17657.1" @default.
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