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CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes

Chris D Bajdik1*, Byron Kuo1, Shawn Rusaw2, Steven Jones2 and Angela Brooks-Wilson12

Author Affiliations

1 Cancer Control Research Program, BC Cancer Agency, 600 West 10th Avenue, Vancouver BC, V5Z 4E6, Canada

2 Genome Sciences Centre, BC Cancer Agency, 600 West 10th Avenue, Vancouver BC, V5Z 4E6, Canada

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BMC Bioinformatics 2005, 6:78  doi:10.1186/1471-2105-6-78

Published: 29 March 2005

Abstract

Background

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. 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.

Results

In 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.

Conclusion

CGMIM 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 http://www.bccrc.ca/ccr/CGMIM webcite.