Trait: Simple Cyst of Kidney

Experimental Factor Ontology (EFO) Information
Identifier EFO_0008619
Description A homogenous cyst located in the kidney. [ NCI NICHD ]
Trait category
Other trait

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)
PGS019453
(TPMI_586.2_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cyst of kidney acquired Simple Cyst of Kidney 2
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019453/ScoringFiles/PGS019453.txt.gz
PGS019454
(TPMI_586.2_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cyst of kidney acquired Simple Cyst of Kidney 268,992
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019454/ScoringFiles/PGS019454.txt.gz
PGS019455
(TPMI_586.2_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cyst of kidney acquired Simple Cyst of Kidney 548,639
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019455/ScoringFiles/PGS019455.txt.gz
PGS019456
(TPMI_586.2_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cyst of kidney acquired Simple Cyst of Kidney 983,813
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019456/ScoringFiles/PGS019456.txt.gz
PGS019457
(TPMI_586.2_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cyst of kidney acquired Simple Cyst of Kidney 1,004,389
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019457/ScoringFiles/PGS019457.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
PPM037635 PGS019453
(TPMI_586.2_Lassosum2)
 PSS013351|
East Asian Ancestry|
16,706 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cyst of kidney acquired — AUROC: 0.61942 R²: 0.00333 sex, age, array, PCs 1-10 —
PPM037636 PGS019454
(TPMI_586.2_LDpred2)
 PSS013350|
East Asian Ancestry|
16,706 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cyst of kidney acquired — AUROC: 0.6205 R²: 0.00345 sex, age, array, PCs 1-10 —
PPM037637 PGS019455
(TPMI_586.2_MegaPRS)
 PSS013352|
East Asian Ancestry|
16,706 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cyst of kidney acquired — AUROC: 0.61672 R²: 0.00299 sex, age, array, PCs 1-10 —
PPM037638 PGS019456
(TPMI_586.2_PRS-CS)
 PSS013353|
East Asian Ancestry|
16,706 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cyst of kidney acquired — AUROC: 0.61949 R²: 0.00324 sex, age, array, PCs 1-10 —
PPM037639 PGS019457
(TPMI_586.2_SBayesR)
 PSS013354|
East Asian Ancestry|
16,706 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cyst of kidney acquired — AUROC: 0.6192 R²: 0.0031 sex, age, array, PCs 1-10 —

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
PSS013350 593.2,N28.1 —
[
  • 123 cases
  • , 16,583 controls
]
,
44.24 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013351 593.2,N28.1 —
[
  • 123 cases
  • , 16,583 controls
]
,
44.24 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013352 593.2,N28.1 —
[
  • 123 cases
  • , 16,583 controls
]
,
44.24 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013353 593.2,N28.1 —
[
  • 123 cases
  • , 16,583 controls
]
,
44.24 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013354 593.2,N28.1 —
[
  • 123 cases
  • , 16,583 controls
]
,
44.24 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —