Trait: kidney cancer

Trait Information
Identifier MONDO_0002367
Description Primary or metastatic malignant neoplasm involving the kidney. [NCIT: C7548]
Trait category
Cancer
Synonyms 15 synonyms
  • cancer of kidney
  • kidney cancer
  • malignant kidney neoplasm
  • malignant kidney tumor
  • malignant kidney tumour
  • malignant neoplasm of kidney
  • malignant neoplasm of kidney except pelvis
  • malignant neoplasm of the kidney
  • malignant renal neoplasm
  • malignant renal tumor
  • malignant renal tumour
  • malignant tumor of kidney
  • malignant tumor of the kidney
  • malignant tumour of kidney
  • malignant tumour of the kidney
Mapped terms 7 mapped terms
  • DOID:263
  • ICD9:189.0
  • MEDGEN:149263
  • MESH:D007680
  • NCIT:C7548
  • SCTID:363518003
  • UMLS:C0740457
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.
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Polygenic Score ID & Name
PGS Publication ID (PGP)
Reported Trait
Mapped Trait(s) (Ontology)
Number of Variants
Ancestry distribution
GWAS
Dev
Eval
Scoring File (FTP Link)
PGS000076
(CC_Kidney)
PGP000050 |
Graff RE et al. Nat Commun (2021)
Kidney cancerrenal cell carcinoma19
G
-
E
 https://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 cancerrenal carcinoma10
G
-
E
 https://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 pelviskidney cancer12
G
D
E
 https://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 pelviskidney cancer12
G
D
E
 https://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 cancerrenal carcinoma15
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000722/ScoringFiles/PGS000722.txt.gz
PGS000787
(CC_Kidney_IV)
PGP000186 |
Kachuri L et al. Nat Commun (2020)
Kidney cancerrenal cell carcinoma19
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000787/ScoringFiles/PGS000787.txt.gz
PGS003744
(PRS14_RC)
PGP000470 |
Xin J et al. EBioMedicine (2023)
Renal cancerrenal carcinoma14
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003744/ScoringFiles/PGS003744.txt.gz
PGS004245
(PRS12_kidney)
PGP000542 |
Kim ES et al. NPJ Precis Oncol (2023)
Kidney cancerrenal cell carcinoma12
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004245/ScoringFiles/PGS004245.txt.gz
PGS004690
(kidney_cancer)
PGP000596 |
Hu J et al. JNCI Cancer Spectr (2024)
Kidney cancerrenal carcinoma6,351,669
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004690/ScoringFiles/PGS004690.txt.gz
PGS004908
(PRS107_KC)
PGP000640 |
Purdue MP et al. Nat Genet (2024)
Kidney cancerrenal carcinoma107
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004908/ScoringFiles/PGS004908.txt.gz
Showing 1 to 10 of 10 rows

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.

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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
PPM000196PGS000076
(CC_Kidney)
PSS000115|
European Ancestry|
411,695 individuals
PGP000050 |
Graff RE et al. Nat Commun (2021)
Reported Trait: Kidney cancerOR: 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
PPM000481PGS000161
(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		——
PPM000492PGS000161
(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]——
PPM001290PGS000605
(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 pelvisOR: 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 1-4Cancer PRSweb PheWAS Results: PRSWEB_PHECODE189.11_GWAS-Catalog-r2019-05-03-X189.11_P_5e-08_UKB_20200608
PPM001291PGS000606
(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 pelvisOR: 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 1-4Cancer PRSweb PheWAS Results: PRSWEB_PHECODE189.11_GWAS-Catalog-r2019-05-03-X189.11_PT_UKB_20200608
PPM001652PGS000722
(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—
PPM002042PGS000076
(CC_Kidney)
PSS001015|
European Ancestry|
391,610 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		Reported Trait: Incident kidney cancerHR: 1.16 [1.08, 1.26]AUROC: 0.722
C-index: 0.724 (0.011)		—Age at assessment, sex, genotyping array, PCs(1-15), body mass index, smoking status (never vs. form... er vs. current), cigarette pack-years, ever diagnosed with hypertensionShow moreC-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002058PGS000787
(CC_Kidney_IV)
PSS001015|
European Ancestry|
391,610 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
Reported Trait: Incident kidney cancerHR: 1.15 [1.07, 1.24]AUROC: 0.722
C-index: 0.723 (0.011)		R²: 0.366Age at assessment, sex, genotyping array, PCs(1-15), body mass index, smoking status (never vs. form... er vs. current), cigarette pack-years, ever diagnosed with hypertensionShow moreC-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017169PGS000076
(CC_Kidney)
PSS010145|
European Ancestry|
547 individuals
PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		Reported Trait: Kidney cancerHR: 1.14 [1.05, 1.24]——age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs... ), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariatesShow more—
PPM018500PGS003744
(PRS14_RC)
PSS010994|
European Ancestry|
692 individuals
PGP000470 |
Xin J et al. EBioMedicine (2023)
Reported Trait: Renal cancerOR: 1.24 [1.14, 1.35]————
PPM020302PGS004245
(PRS12_kidney)
PSS011328|
European Ancestry|
133,830 individuals
PGP000542 |
Kim ES et al. NPJ Precis Oncol (2023)
Reported Trait: Kidney cancerHR: 1.22 [1.02, 1.45]——first 10 genetic principal components—
PPM020310PGS004245
(PRS12_kidney)
PSS011329|
European Ancestry|
115,207 individuals
PGP000542 |
Kim ES et al. NPJ Precis Oncol (2023)
Reported Trait: Kidney cancerHR: 1.25 [1.1, 1.41]——first 10 genetic principal components—
PPM020875PGS004690
(kidney_cancer)
PSS011434|
European Ancestry|
40,841 individuals
PGP000596 |
Hu J et al. JNCI Cancer Spectr (2024)
Reported Trait: Kidney cancer—AUROC: 0.5644———
PPM021361PGS004908
(PRS107_KC)
PSS011702|
European Ancestry|
324,805 individuals
PGP000640 |
Purdue MP et al. Nat Genet (2024)
Reported Trait: Kidney cancerOR: 1.5 [1.43, 1.58]AUROC: 0.74 [0.72, 0.75]—Age, sex, PCs, BMI, smoking, hypertension—
PPM021362PGS004908
(PRS107_KC)
PSS011702|
European Ancestry|
324,805 individuals
PGP000640 |
Purdue MP et al. Nat Genet (2024)
Reported Trait: Clear cell renal cell carcinomaOR: 1.69 [1.57, 1.81]AUROC: 0.74 [0.72, 0.76]—Age, sex, PCs, BMI, smoking, hypertension—
Showing 1 to 15 of 15 rows

Evaluated Samples

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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
PSS000115Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 code... s in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 29020Show more—
[
  • 1,341 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 yearsEuropean—GERA, UKB—
PSS000281Primary 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—
PSS000575PheCode:189.11; ICD9:189.0; ICD10:C64—
[
  • 529 cases
  • , 5,289 controls
]
—European—UKB—
PSS000856Data and diagnoses on site-specific incident cancers were provided by the National Health Service In... formation 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)Show moreMedian = 5.8 years
[
  • 545 cases
  • , 400,267 controls
]
,
46.5 % Male samples
—European—UKB—
PSS001015Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant pri... mary cancer were defined as cases.Show more—
[
  • 612 cases
  • , 390,998 controls
]
—European—UKB—
PSS010145——
[
  • 28 cases
  • , 519 controls
]
—European—UKB—
PSS010994——692 individualsMean = 60.99 yearsEuropean—TCGA—
PSS011328——133,830 individuals,
0.0 % Male samples
—European
(British)		—UKB—
PSS011329——115,207 individuals,
100.0 % Male samples
—European
(British)		—UKB—
PSS011434——
[
  • 158 cases
  • , 40,683 controls
]
—European—UKB—
PSS011702——
[
  • 1,696 cases
  • , 323,109 controls
]
—European—UKB—
Showing 1 to 12 of 12 rows
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