1 / 7

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

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

clea
Download Presentation

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

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related