This set of code is to perform a PHEWAS of multiple genes and phenotypes. The phenotypes are based of the Human Phenotype Ontology (HPO) terms mapped to ICD10 code and a number of physical measurement and biological sample from the UK-Biobank.
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HPO terms extraction: In this step, we first extract the HPO term of the target syndromic diseases of interest from https://hpo.jax.org/app/. The HPO term were then matched to ICD10 code and others biobank phenotypes using SORTA https://molgenis19.gcc.rug.nl/.
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Quality control of the phenotype matching and extrcation of the most accurate phenotype matching
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Extract the varaints related to the genes of interested
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Perform the analysis at the SNP levels then at the genes levels
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Organize the results with tables and figures