Trait: renal cell carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000681
Description A carcinoma that arises from glandular epithelial cells of the kidney [MONDO: DesignPattern]
Trait category
Cancer
Synonyms 7 synonyms
  • RCC
  • hypernephroma
  • kidney adenocarcinoma
  • kidney adenocarcinoma
  • renal cell adenocarcinoma
  • renal cell carcinoma
  • renal cell carcinoma (disease)
Mapped terms 20 mapped terms
  • DOID:4450
  • EFO:0000681
  • GARD:0013215
  • GARD:13215
  • HP:0005584
  • ICD9:189.0
  • MEDGEN:766
  • MESH:D002292
  • MONDO:0005086
  • MedDRA:10020681
  • MedDRA:10067946
  • NANDO:2200045
  • NCIT:C9385
  • NORD:1657
  • OMIM:144700
  • OMIM:300854
  • ONCOTREE:RCC
  • Orphanet:217071
  • SCTID:702391001
  • UMLS:C0007134

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
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 cancer renal cell carcinoma 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000076/ScoringFiles/PGS000076.txt.gz
PGS000787
(CC_Kidney_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Kidney cancer renal cell carcinoma 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000787/ScoringFiles/PGS000787.txt.gz
PGS004245
(PRS12_kidney)
 PGP000542 |
Kim ES et al. NPJ Precis Oncol (2023)
 Kidney cancer renal cell carcinoma 12
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004245/ScoringFiles/PGS004245.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. Nat Commun (2021)
 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
PPM002042 PGS000076
(CC_Kidney)
 PSS001015|
European Ancestry|
391,610 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident kidney cancer HR: 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. former vs. current), cigarette pack-years, ever diagnosed with hypertension C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017169 PGS000076
(CC_Kidney)
 PSS010145|
European Ancestry|
547 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Kidney cancer HR: 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 covariates —
PPM002058 PGS000787
(CC_Kidney_IV)
 PSS001015|
European Ancestry|
391,610 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident kidney cancer HR: 1.15 [1.07, 1.24] AUROC: 0.722
C-index: 0.723 (0.011)		 R²: 0.366 Age at assessment, sex, genotyping array, PCs(1-15), body mass index, smoking status (never vs. former vs. current), cigarette pack-years, ever diagnosed with hypertension C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM020302 PGS004245
(PRS12_kidney)
 PSS011328|
European Ancestry|
133,830 individuals
 PGP000542 |
Kim ES et al. NPJ Precis Oncol (2023)
 Reported Trait: Kidney cancer HR: 1.22 [1.02, 1.45] — — first 10 genetic principal components —
PPM020310 PGS004245
(PRS12_kidney)
 PSS011329|
European Ancestry|
115,207 individuals
 PGP000542 |
Kim ES et al. NPJ Precis Oncol (2023)
 Reported Trait: Kidney cancer HR: 1.25 [1.1, 1.41] — — first 10 genetic principal components —

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
PSS011328 — — 133,830 individuals,
0.0 % Male samples
 — European
(British)		 — UKB —
PSS011329 — — 115,207 individuals,
100.0 % Male samples
 — European
(British)		 — UKB —
PSS010145 — —
[
  • 28 cases
  • , 519 controls
]
 — European — UKB —
PSS001015 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 612 cases
  • , 390,998 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 —