| Predicted Trait | |
| Reported Trait | Colorectal cancer |
| Mapped Trait(s) | colorectal cancer (EFO_0005842) |
| Score Construction | |
| PGS Name | cGRS_Colorectal |
| Variants | |
| Original Genome Build | NR |
| Number of Variants | 30 |
| Development Method | |
| Name | Pruning + Thresholding |
| Parameters | GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2. |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000075 |
| Citation (link to publication) | Shi Z et al. Cancer Med (2019) |
| Study Identifiers | Sample Numbers | Sample Ancestry |
|---|---|---|
| GWAS Catalog: GCST006131 EuropePMC: 29917119 |
6,597 individuals | African American or Afro-Caribbean |
| GWAS Catalog: GCST006131 EuropePMC: 29917119 |
67,812 individuals | European |
| GWAS Catalog: GCST000843 EuropePMC: 2097244 |
30,420 individuals | European |
| GWAS Catalog: GCST000843 EuropePMC: 2097244 |
7,962 individuals | European |
| GWAS Catalog: GCST001787 EuropePMC: 23266556 |
27,809 individuals | European |
| GWAS Catalog: GCST001544 EuropePMC: 22634755 |
17,780 individuals | European |
| GWAS Catalog: GCST000169 EuropePMC: 18372905 |
1,849 individuals | European |
| GWAS Catalog: GCST000053 EuropePMC: 17618284 |
1,890 individuals | European |
| GWAS Catalog: GCST000168 EuropePMC: 18372901 |
1,983 individuals | European (U.K.) |
| GWAS Catalog: GCST003017 EuropePMC: 26151821 |
37,955 individuals | European |
| GWAS Catalog: GCST001161 EuropePMC: 21761138 |
6,322 individuals | European |
|
PGS Performance Metric ID (PPM ID) |
PGS Sample Set ID (PSS ID) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
PGS Classification Metrics | Other Metrics | Covariates Included in the Model | PGS Performance: Other Relevant Information |
|---|---|---|---|---|---|---|---|---|
| PPM000474 | PSS000274 | PGP000075 Shi Z et al. (2019) |
Reported Trait: Colorectal cancer | — | — | Mean realative risk: 1.08[1.04, 1.12] Wilcoxon test (case vs. control) p-value: 8.29e-06 |
— | — |
| PPM000485 | PSS000274 | PGP000075 Shi Z et al. (2019) |
Reported Trait: Colorectal cancer | — | — | Odds Ratio (OR; high vs. average risk groups): 1.18[0.87, 1.61] | — | — |
|
PGS Sample Set ID (PSS ID) |
Detailed Phenotype Description | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
|---|---|---|---|---|---|---|---|---|
| PSS000274 | Primary tumor samples from TCGA | — | [
|
Mean = 68.0 years Sd = 13.0 years |
European | — | TCGA | — |
| PSS000274 | — | — | [
|
— | European | — | eMERGE | — |