Trait: kidney cancer

Trait Information
Identifier MONDO_0002367
Description Primary or metastatic malignant neoplasm involving the kidney. [NCIT: C7548]
Trait category
Cancer
Synonyms 13 synonyms
  • cancer of kidney
  • kidney cancer
  • malignant kidney neoplasm
  • malignant kidney tumor
  • malignant neoplasm of kidney
  • malignant neoplasm of kidney except pelvis
  • malignant neoplasm of the kidney
  • malignant renal neoplasm
  • malignant renal tumor
  • malignant tumor of kidney
  • malignant tumor of the kidney
  • malignant tumour of kidney
  • renal cancer
Mapped term(s) 7 mapped terms
  • DOID:263
  • ICD10:C64
  • ICD9:189.0
  • MESH:D007680
  • NCIT:C7548
  • SCTID:363518003
  • UMLS:CN881103
Child trait(s) 2 child traits

Associated Polygenic Score(s)

Note: This table shows all PGS for "kidney cancer" and any child terms of this trait in the EFO hierarchy by default.
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
PGS000605 PRSWEB_PHECODE189.11_GWAS-Catalog-r2019-05-03-X189.11_P_5e-08_UKB_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Malignant neoplasm of kidney, except pelvis kidney cancer 12 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000605/ScoringFiles/PGS000605.txt.gz
PGS000606 PRSWEB_PHECODE189.11_GWAS-Catalog-r2019-05-03-X189.11_PT_UKB_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Malignant neoplasm of kidney, except pelvis kidney cancer 12 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000606/ScoringFiles/PGS000606.txt.gz

PGS Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

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
PPM001290 PGS000605 (PRSWEB_PHECODE189.11_GWAS-Catalog-r2019-05-03-X189.11_P_5e-08_UKB_20200608) PSS000575 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Malignant neoplasm of kidney, except pelvis OR: 1.154 [1.062, 1.254]
β: 0.143 (0.0426)
AUROC: 0.517 [0.492, 0.54] Nagelkerke's Pseudo-R²: 0.00398
Brier score: 0.0825
Odds Ratio (OR, top 1% vs. Rest): 2.17 [1.13, 4.14]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE189.11_GWAS-Catalog-r2019-05-03-X189.11_P_5e-08_UKB_20200608
PPM001291 PGS000606 (PRSWEB_PHECODE189.11_GWAS-Catalog-r2019-05-03-X189.11_PT_UKB_20200608) PSS000575 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Malignant neoplasm of kidney, except pelvis OR: 1.154 [1.062, 1.254]
β: 0.143 (0.0426)
AUROC: 0.517 [0.492, 0.54] Nagelkerke's Pseudo-R²: 0.00398
Brier score: 0.0825
Odds Ratio (OR, top 1% vs. Rest): 2.17 [1.13, 4.14]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE189.11_GWAS-Catalog-r2019-05-03-X189.11_PT_UKB_20200608

Evaluated Samples

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
[
  • 453 cases
  • , 0 controls
]
Mean = 62.0 years
Sd = 12.0 years
European TCGA
PSS000281
[
  • 0 cases
  • , 13,427 controls
]
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
[
  • 1,341 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000575 PheCode:189.11; ICD9:189.0; ICD10:C64
[
  • 529 cases
  • , 5,289 controls
]
European UKB