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)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Note: This table shows all PGS for "kidney cancer" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution 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
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

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)
Evaluated Score PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000196 PGS000076
(CC_Kidney)
PSS000115|
European Ancestry|
411,695 individuals
PGP000050 |
Graff RE et al. bioRxiv (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|
European Ancestry|
13,880 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Renal cancer Odds Ratio (OR; high vs. average risk groups): 1.58 [1.14, 2.18]
PPM000481 PGS000161
(cGRS_Renal)
PSS000281|
European Ancestry|
13,880 individuals
PGP000075 |
Shi Z et al. Cancer Med (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|
European Ancestry|
5,818 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
5,818 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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
PPM001652 PGS000722
(PRS_Kidney)
PSS000856|
European Ancestry|
400,812 individuals
PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
Reported Trait: Incident kidney cancer AUROC: 0.567 [0.543, 0.591] Genotyping array

Evaluated Samples

PGS Sample Set ID
(PSS)
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
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
[
  • 545 cases
  • , 400,267 controls
]
,
46.5 % Male samples
European UKB
PSS000575 PheCode:189.11; ICD9:189.0; ICD10:C64
[
  • 529 cases
  • , 5,289 controls
]
European UKB
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