Abstract
BackgroundOnline Mendelian Inheritance in Man (OMIM) is a computerized database of information about genes and heritable traits in human populations, based on information reported in the scientific literature. Our objective was to establish an automated text-mining system for OMIM that will identify genetically-related cancers and cancer-related genes. We developed the computer program CGMIM to search for entries in OMIM that are related to one or more cancer types. We performed manual searches of OMIM to verify the program results.ResultsIn the OMIM database on September 30, 2004, CGMIM identified 1943 genes related to cancer. BRCA2 (OMIM *164757), BRAF (OMIM *164757) and CDKN2A (OMIM *600160) were each related to 14 types of cancer. There were 45 genes related to cancer of the esophagus, 121 genes related to cancer of the stomach, and 21 genes related to both. Analysis of CGMIM results indicate that fewer than three gene entries in OMIM should mention both, and the more than seven-fold discrepancy suggests cancers of the esophagus and stomach are more genetically related than current literature suggests.ConclusionCGMIM identifies genetically-related cancers and cancer-related genes. In several ways, cancers with shared genetic etiology are anticipated to lead to further etiologic hypotheses and advances regarding environmental agents. CGMIM results are posted monthly and the source code can be obtained free of charge from the BC Cancer Research Centre website .
Highlights
Online Mendelian Inheritance in Man (OMIM) is a computerized database of information about genes and heritable traits in human populations, based on information reported in the scientific literature
We reviewed the entries to identify sentences that referred to cancer, but for which evidence indicated there was no association. (E.g., "An early study showed the gene was not related to breast cancer.") While an OMIM entry might include a sentence of that sort, another sentence in the entry might cite evidence supporting the association. (E.g., "A subsequent study showed the gene was related to breast cancer.") Despite the negative statement, this example OMIM entry mentions evidence supporting the association and would be included when tallying entries associated with the cancer
CGMIM uses an expert database of genetic information to determine a summary of gene and cancer associations
Summary
Online Mendelian Inheritance in Man (OMIM) is a computerized database of information about genes and heritable traits in human populations, based on information reported in the scientific literature. We developed the computer program CGMIM to search for entries in OMIM that are related to one or more cancer types. Cancers are complex diseases with multiple genetic and environmental factors contributing to their development. The most prominent success stories in cancer genetics to date have involved genes that produce a recognizable pattern of disease within certain rare families. Most cancers are sporadic and appear in people who do not have a clear family history of the disease. These cancers are currently being studied in epidemiological investigations that examine genetics, environmental exposures or both. Number of Genes Related to Both Observed (O) Expected (E).
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