| Experimental Factor Ontology (EFO) Information | |
| Identifier | EFO_0002890 |
| Description | A carcinoma arising from the epithelium of the renal parenchyma or the renal pelvis. The majority are renal cell carcinomas. Kidney carcinomas usually affect middle aged and elderly adults. Hematuria, abdominal pain, and a palpable mass are common symptoms. [NCIT: C9384] | Trait category |
Cancer
|
| Synonyms |
21 synonyms
|
| Mapped term(s) |
7 mapped terms
|
| Child trait(s) | renal cell carcinoma |
| Polygenic Score (PGS) ID | PGS Name | PGS Publication (PGP) ID | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | PGS Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS000076 | CC_Kidney | PGP000050 Graff RE et al. bioRxiv (2020) Pre | Kidney cancer | renal cell carcinoma | 19 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000076/ScoringFiles/PGS000076.txt.gz |
| PGS000161 | cGRS_Renal | PGP000075 Shi Z et al. Cancer Med (2019) | Renal cancer | renal carcinoma | 10 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000161/ScoringFiles/PGS000161.txt.gz |
| PGS000722 | PRS_Kidney | PGP000135 Jia G et al. JNCI Cancer Spectr (2020) | Kidney cancer | renal carcinoma | 15 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000722/ScoringFiles/PGS000722.txt.gz |
|
PGS Performance Metric ID (PPM ID) |
Evaluated Score |
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000196 | PGS000076 (CC_Kidney) | PSS000115 | PGP000050 Graff RE et al. (2020) Pre | Reported Trait: Kidney cancer | OR: 1.21 [1.14, 1.27] | — | — | Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. | Results from meta-analysis of GERA and UKB |
| PPM000492 | PGS000161 (cGRS_Renal) | PSS000281 | PGP000075 Shi Z et al. (2019) | Reported Trait: Renal cancer | — | — | Odds Ratio (OR; high vs. average risk groups): 1.58 [1.14, 2.18] | — | — |
| PPM000481 | PGS000161 (cGRS_Renal) | PSS000281 | PGP000075 Shi Z et al. (2019) | Reported Trait: Renal cancer | — | — | Mean realative risk: 1.09 [1.06, 1.12] Wilcoxon test (case vs. control) p-value: 8.66e-10 |
— | — |
| PPM001652 | PGS000722 (PRS_Kidney) | PSS000856 | PGP000135 Jia G et al. (2020) | Reported Trait: Incident kidney cancer | — | AUROC: 0.567 [0.543, 0.591] | — | Genotyping array | — |
|
PGS Sample Set ID (PSS ID) |
Phenotype Definitions and Methods | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
|---|---|---|---|---|---|---|---|---|
| PSS000281 | Primary tumor samples from TCGA | — | [
|
Mean = 62.0 years Sd = 12.0 years |
European | — | TCGA | — |
| PSS000281 | — | — | [
|
— | European | — | eMERGE | — |
| PSS000115 | Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 29020 | — | [ ,
46.0 % Male samples |
Mean = 58.0 years | European | — | GERA, UKB | — |
| PSS000856 | Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Kidney Cancer=(ICD-9 = 189.0 or ICD-10 = C64) | Median = 5.8 years | [ ,
46.5 % Male samples |
— | European | — | UKB | — |