OMIM.org: leveraging knowledge across phenotype–gene relationships

Abstract

For over 50 years Mendelian Inheritance in Man has chronicled the collective knowledge of the field of medical genetics. It initially cataloged the known X-linked, autosomal recessive and autosomal dominant inherited disorders, but grew to be the primary repository of curated information on both genes and genetic phenotypes and the relationships between them. Each phenotype and gene is given a separate entry assigned a stable, unique identifier. The entries contain structured summaries of new and important information based on expert review of the biomedical literature. OMIM.org provides interactive access to the knowledge repository, including genomic coordinate searches of the gene map, views of genetic heterogeneity of phenotypes in Phenotypic Series, and side-by-side comparisons of clinical synopses. OMIM.org also supports computational queries via a robust API. All entries have extensive targeted links to other genomic resources and additional references. Updates to OMIM can be found on the update list or followed through the MIMmatch service. Updated user guides and tutorials are available on the website. As of September 2018, OMIM had over 24,600 entries, and the OMIM Morbid Map Scorecard had 6,259 molecularized phenotypes connected to 3,961 genes.

Making sense out of missense mutations: Mechanistic dissection of Notch receptors through structure‐function studies inDrosophila

“…Similar late truncating and missense GOF mutations in NOTCH1 and NOTCH2 are also frequently found in B-cell chronic lymphocytic leukemia (B-CLL) (Fabbri et al, 2011;Puente et al, 2011;Sportoletti et al, 2010) and splenic marginal zone lymphoma (Kiel et al, 2012;Rossi et al, 2012), respectively. This table was assembled based on information gathered through Online Mendelian Inheritance in Man (OMIM, https ://www.omim.org/) (Amberger, Bocchini, Scott, & Hamosh, 2019), MARRVEL (http://marrv el.org/) (Wang et al, 2017;Wang, Mao, et al, 2019b) and PubMed (https ://www.ncbi.nlm. This table was assembled based on information gathered through Online Mendelian Inheritance in Man (OMIM, https ://www.omim.org/) (Amberger, Bocchini, Scott, & Hamosh, 2019), MARRVEL (http://marrv el.org/) (Wang et al, 2017;Wang, Mao, et al, 2019b) and PubMed (https ://www.ncbi.nlm.…”

“…On the contrary, LOF mutations in NOTCH genes are frequently found in chronic myelomonocytic leukemia (Klinakis et al, 2011), bladder transitional cell carcinoma (Rampias et al, 2014), TA B L E 1 Human NOTCH receptor genes and their links to rare and common diseases. This table was assembled based on information gathered through Online Mendelian Inheritance in Man (OMIM, https ://www.omim.org/) (Amberger, Bocchini, Scott, & Hamosh, 2019), MARRVEL (http://marrv el.org/) (Wang et al, 2017;Wang, Mao, et al, 2019b) and PubMed (https ://www.ncbi.nlm. nih.gov/pubmed).…”

The Clinical Genome and Ancestry Report: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition

“…To identify genes associated with user‐defined phenotypes, we used FindZebra—a database of genotype and phenotype associations based on machine‐learning of literature (Dragusin et al, ). FindZebra uses a text search engine to retrieve and rank genes according to gene‐specific scores for phenotype based on various sources of curated documents such as Online Mendelian Inheritance in Men (OMIM; Amberger et al, ) or Genetic and Rare Diseases Information Center (GARD, https://rarediseases.info.nih.gov/). From the ranked list of genes, CGAR selects the genes with top scores within a user‐specified threshold.…”

Large-scale transgenicDrosophilaresource collections for loss- and gain-of-function studies

“…To identify the set of fly genes orthologous to genes known or suspected to be associated with human diseases, we selected 4,850 human disease genes described in the Online Mendelian Inheritance in Man (OMIM) database (Amberger et al 2015;Amberger et al 2019) as "with known sequence and phenotype" (omim.org/statistics/geneMap). We then mapped the human genes to fly genes using version 3 of our DIOPT tool (Hu et al, 2011) and selected those with DIOPT scores >=2 (best score, forward or reverse search) or DIOPT score >=4, identifying 3,017 genes (10 was the max score for DIOPT vs3).…”