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Integrating OMIM Mendelian database to SPOKE Xiaoming (Sherman) Jia, MD MEng Baranzini Lab

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Integrating OMIM Mendelian database to SPOKE Xiaoming (Sherman) Jia, MD MEng Baranzini Lab. Data sources. Disease ontology Disease characteristics. OMIM Gene-disease relationships. Processed OMIM

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Integrating OMIM Mendelian database to SPOKE Xiaoming (Sherman) Jia, MD MEng Baranzini Lab

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  1. Integrating OMIM Mendelian database to SPOKEXiaoming (Sherman) Jia, MD MEngBaranzini Lab Genetics and SPOKE

  2. Data sources Disease ontology Disease characteristics OMIM Gene-disease relationships Processed OMIM Extract relationships with highest level of evidence (phenotype mapping key = 3), inheritance patter (Mendelian or other), and modifiers Processed Disease ontology Extract OMIM ID to DOID mappings Integrate GENE-DOID mappings into SPOKE Genetics and SPOKE

  3. OMIM raw data requires some text parsing Genetics and SPOKE

  4. Disease-gene relationships from OMIM: keep bolded Genetics and SPOKE

  5. Edits to raw OMIM data • Encode modifiers if disease name contains: • “susceptibility for” (299) • “modifier of” (27) • “protection against” (30) • “resistance to” (25) • “reduced risk of” (6) • Add to inheritance patterns if disease name contains : • “somatic” or “somatic mosaic” (212) • “digenic” (19) • “autosomal recessive” (19) • “autosomal dominant” (15) • “X-linked” (9) • “Y-linked” (1) Genetics and SPOKE

  6. Formatted OMIM data (ready for integration) Total: 3,858 mappable gene-disease relationships Genetics and SPOKE

  7. Recommended filtering after integration • High-confidence Mendelian relationships (3,220): • Keep Mendelian inheritance: autosomal dominant (AD), autosomal recessive (AR), X-linked dominant (XLD), X-linked recessive (XLR), X-linked (XL), Mitochondrial (MT), Digenic recessive (DR), or Y-linked (YL). May include Mendelian AND SOMATIC (hereditary cancer syndromes). • Exclude relationships with modifiers (i.e. susceptibility = “-”) • Moderate-confidence Mendelian relationships (137): • Mendelian relationships that have modifiers: susceptibility for (SUSCEPTIBILITY), modifier of (MODIFIES), protection against (PROTECTIVE), resistance to (RESISTANCE), reduced risk of (REDUCED). • Low-confidence relationships (335): • Relationships that don’t have a Mendelian inheritance (i.e. inheritance = “-”) • Somatic (166): • Inheritance = “SOMATIC” (i.e. not Mendelian and not unknown) Genetics and SPOKE

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