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J Biomol Tech. 2007 February; 18(1): 7–8.
PMCID: PMC2291937

P20-M NCI CGEMS Data Portal: Sharing Data for Genome-Wide Association Studies


A new NCI initiative, Cancer Genetic Markers of Susceptibility (CGEMS), is a three-year study designed to identify common genetic variations associated with risk for prostate and breast cancer. CGEMS will analyze the entire genome for the most common type of genetic variation, the single-nucleotide polymorphism (SNP). By studying large populations of individuals with and without disease, the CGEMS research can provide powerful indicators as to which SNP variations are associated with each disease. This study design is especially valuable for unraveling the genetic origins of complex diseases such as prostate and breast cancer.

A critical requirement of the CGEMS project is to share raw data and analysis results from the study with the cancer research community. The NCI Center for Bioinformatics (NCICB), in collaboration with other NCI research groups, has built the CGEMS data portal to support data sharing of the CGEMS project (

The first whole genome scan includes approximately 1200 prostate cancer cases and 1200 controls. The datasets available through the portal include:

  • Association test results for over 300,000 SNPs
  • Frequency and descriptive statistics on these 300,000 SNPs
  • Individual phenotypic and genotypic data for the study participants and control samples. Note that these data can be made available only to eligible investigators after a registration process.

CGEMS data portal development has leveraged the caIntegrator application framework, developed at NCICB. It shares a common set of application programming interfaces (APIs) and specification objects that support the clinical genomic analysis services. This allows fast development of Web-based query functionalities on all the data objects from the CGEMS project.

Articles from Journal of Biomolecular Techniques : JBT are provided here courtesy of The Association of Biomolecular Resource Facilities