Trait: ureterolithiasis

Experimental Factor Ontology (EFO) Information
Identifier EFO_1001228
Description The presence of a calculus in the ureter of the kidney; this is most often composed of mineral salts and proteins. [NCIT: P378]
Trait category
Other disease
Synonyms 10 synonyms
  • Ureteric Stone
  • Ureteric calculus
  • Ureteric stone
  • Ureteric stone (disorder)
  • Ureterolithiasis
  • Ureterolithiasis (disorder)
  • calculus of ureter
  • ureteric calculus
  • ureteric stone
  • ureterolithiasis
Mapped terms 12 mapped terms
  • DOID:14146
  • ICD10:N21
  • ICD9:592.1
  • MEDGEN:21775
  • MESH:D053039
  • MONDO:0007009
  • MedDRA:10077989
  • NCIT:C114696
  • NCIt:C114696
  • SCTID:31054009
  • SNOMEDCT:31054009
  • UMLS:C0041952

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)
PGS001250
(GBE_HC1304)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Calculus of kidney and ureter (time-to-event) nephrolithiasis,
ureterolithiasis		 341
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001250/ScoringFiles/PGS001250.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
PPM008759 PGS001250
(GBE_HC1304)
 PSS004253|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.63458 [0.56104, 0.70812] R²: 0.02267
Incremental AUROC (full-covars): -4e-05
PGS R2 (no covariates): 0.00013
PGS AUROC (no covariates): 0.50619 [0.43811, 0.57426]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008760 PGS001250
(GBE_HC1304)
 PSS004254|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.66992 [0.57144, 0.7684] R²: 0.05343
Incremental AUROC (full-covars): 0.02085
PGS R2 (no covariates): 0.01881
PGS AUROC (no covariates): 0.61787 [0.49482, 0.74092]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008761 PGS001250
(GBE_HC1304)
 PSS004255|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.6584 [0.63099, 0.68582] R²: 0.03459
Incremental AUROC (full-covars): 0.00159
PGS R2 (no covariates): 0.00193
PGS AUROC (no covariates): 0.53735 [0.50853, 0.56617]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008762 PGS001250
(GBE_HC1304)
 PSS004256|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.66463 [0.62056, 0.7087] R²: 0.03629
Incremental AUROC (full-covars): 0.01093
PGS R2 (no covariates): 0.0077
PGS AUROC (no covariates): 0.57305 [0.52667, 0.61943]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008763 PGS001250
(GBE_HC1304)
 PSS004257|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE calculus of kidney and ureter — AUROC: 0.66491 [0.64839, 0.68143] R²: 0.03503
Incremental AUROC (full-covars): 0.01494
PGS R2 (no covariates): 0.00592
PGS AUROC (no covariates): 0.56681 [0.54876, 0.58486]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004253 — —
[
  • 56 cases
  • , 6,441 controls
]
 — African unspecified — UKB —
PSS004254 — —
[
  • 25 cases
  • , 1,679 controls
]
 — East Asian — UKB —
PSS004255 — —
[
  • 384 cases
  • , 24,521 controls
]
 — European non-white British ancestry UKB —
PSS004256 — —
[
  • 146 cases
  • , 7,685 controls
]
 — South Asian — UKB —
PSS004257 — —
[
  • 989 cases
  • , 66,436 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)