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]Show more
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 13 mapped terms
  • DOID:14146
  • ICD10:N21
  • ICD9:592.1
  • MEDGEN:21775
  • MESH:D053039
  • MONDO:0007009
  • MeSH:D053039
  • 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
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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)
PGS001250
(GBE_HC1304)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Calculus of kidney and ureter (time-to-event)nephrolithiasis,
ureterolithiasis		341
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001250/ScoringFiles/PGS001250.txt.gz
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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
PPM008759PGS001250
(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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008760PGS001250
(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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008761PGS001250
(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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008762PGS001250
(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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008763PGS001250
(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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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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
PSS004253——
[
  • 56 cases
  • , 6,441 controls
]
—African unspecified—UKB—
PSS004254——
[
  • 25 cases
  • , 1,679 controls
]
—East Asian—UKB—
PSS004255——
[
  • 384 cases
  • , 24,521 controls
]
—Europeannon-white British ancestryUKB—
PSS004256——
[
  • 146 cases
  • , 7,685 controls
]
—South Asian—UKB—
PSS004257——
[
  • 989 cases
  • , 66,436 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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