GWAS validations and others

Below is the list of past projects (pre 2014) run by the PRACTICAL consortium.

  • PRACTICAL Phase I = CRUK GWAS stage 1 validation
    Validation of the most significant SNPs based on a GWAS that genotyped 541,129 SNPs in 1,854 clinically detected PrCa cases and 1,894 controls from a multicenter UK study (Eeles et al., Nat Genet 2008;40:316–21). The results were evaluated using samples from PRACTICAL. A total of 13 PRACTICAL groups participated in this effort with DNA from 7,370 prostate cancer cases and 5,742 male controls. 7 SNPs were validated as being associated with prostate cancer. This project is described in Kote-Jarai et al, Cancer Epidemiol Biomarkers Prev. 2008;17(8):2052-61.
  • PRACTICAL Phase II = CRUK/AU GWAS stage 2 validation
    Validation of the second stage of the above described GWAS where 43,671 SNPs showing evidence for association in stage 1 were genotyped in 3,650 PrCa cases and 3,940 controls, from UK and Australian studies. A follow up of 12 new association signals was performed through genotyping in 16,229 cases and 14,821 controls from 21 studies in PRACTICAL. 7 new prostate cancer susceptibility loci were identified. The results can be found at
    Eeles et al., Nat Genet. 2009 Oct;41(10):1116-21.
  • PRACTICAL Phase III = Risk modeling
    Based on 25 PrCa SNPs (known to be associated with prostate cancer from previous phases and other GWASes) and ~28,000 cases and ~28,000 controls from 29 studies in PRACTICAL. The results can be found at Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci, CEBP, Apr 2015, Vol 24(7), pg 1121-9 [PMID:25837820]
  • PRACTICAL Phase IV-a – CRUK/AU GWAS stage 3 validation
    Validation of the third stage of the above mentioned UK/AU GWAS stage 2 in which 1,536 SNPs were evaluated in 4,574 individuals with prostate cancer (cases) and 4,164 controls. A follow up of ten new association signals was performed through genotyping in 51,311 samples in 30 studies from PRACTICAL. 9 SNPs were identified. The results can be found at Kote-Jarai et al., Nat Genet. 2011 Jul 10;43(8):785-91
  • PRACTICAL Phase IV-b = BPC3 + CAPS + CGEMS + CRUK Meta-analysis
    Validation of a meta-analysis of four GWAS including 5,953 cases of aggressive PrCa and 11,463 controls (men without PrCa). The follow up of the most significant SNPs was performed by genotyping 49,121 samples in 29 studies from PRACTICAL and BPC3 consortia. The association of a PrCa susceptibility locus, rs11672691 on chromosome 19, could be confirmed and also showed an association with aggressive PrCa. The results can be found at Amin Al Olama et al., Hum Mol Genet, Nov 2012, Vol 22(2), pg 408-15
  • PRACTICAL Phase IV-c = Survival CAPS GWAS
    This analyses followed the combination of two GWAses: CAPS with 1,932 samples (422 PrCa deaths) and CRUK stage 1 with 1,820 samples (206 PrCa deaths). A follow up with 15,282 samples (682 PrCa deaths) from 13 PRACTICAL studies did not validate any hit. A second follow up with 15,483 samples (1,028 PrCa deaths) from the PRACTICAL iCOGS did not show any strong hit.