OncoArray chip

This is the latest project in a partnership with other international cancer consortia. The OncoArray is a custom SNP genotyping array specifically designed to evaluate genetic variants for association with the risk of breast, ovarian, prostate, colorectal and lung cancer. The OncoArray contains ~600k SNPs with a genome-wide backbone. Additional SNPs include genetic variants associated with the 5 cancers plus SNPs covering ancestry, quantitative traits, pharmacogenetics, and fine-mapping of common cancer susceptibility loci.

The goal of the project is to genotype this array in ~ 500k samples from large case-control studies in disease-based consortia: BCAC/DRIVE (breast cancer), CIMBA (BRCA1 and BRCA2 carriers), CORECT (colorectal cancer), OCAC/FOCI (ovarian cancer), PRACTICAL/ELLIPSE (prostate cancer), and TRICL (lung cancer).

The NCI is providing approximately half of the funding for the project under its Genetic Associations and Mechanisms of Oncology (GAME-ON) initiative. Other funding sources include Genome Canada, Genome Quebec, and Cancer Research UK. Particularly for the prostate component, the NCI is providing funding for the majority of the project.

For more information, visit the OncoArray Network at the NCI. A general description can be found in the following article “Consortium launches genotyping effort”, Cancer Discov. 2013 Dec;3(12):1321-2.

This YouTube video explains the OncoArray effort: OncoArray – An International Collaboration to Discover Cancer Genetic Risk Factors.

PRACTICAL in OncoArray:

PRACTICAL contributed with ~110 samples from European, Asian, African American and Latino populations.

PRACTICAL OncoArray has contributed to the identification of ~60 new prostate cancer susceptibility loci, which makes a total of ~100 known PrCa SNPs. Two papers, one covering the European/Asian analysis and the other the African American /Latino, have been submitted and are expected to be published earlier 2017.

Further papers will be published with data generated from PRACTICAL OncoArray from ~150 proposals of analysis which are currently being undertaken. For the most up to date published papers, please visit the Publications link.

Phenotypic data has been collected for the samples included in this project in following categories:

  1. Core data = ID, Ethnicity, Age, PrCa Fam. Hist.
  2. Survival = Follow Up, Death
  3. Clinical/Pathological = Blood Draw, Gleason, Cancer Stage, PSA, Symptom score, Method detection, Treatment, TMPRSS2-ERG fusion status, BRCA mutation, MMR mutation,
  4. Epidemiological = Country origin, Education, Marital status, Occupational history, Physical activity, Smoking , Caffeine consumption, Alcohol intake, Acne, Vasectomy, Baldness, BrCa Fam. Hist., Barium, X-ray history, Hypertension, Heart disease, Diabetes , Prostatitis, Benign Prostatic Hyperplasia, Sexual activity, BMI, Hand pattern, Medication