Trait: urolithiasis

Trait Information
Identifier MONDO_0024647
Description Stone(s) within the urinary tract. [NCIT: C114688]
Trait category
Other disease
Synonyms 3 synonyms
  • calculus
  • urinary stones
  • urolithiasis
Mapped terms 7 mapped terms
  • DOID:0080653
  • ICD10CM:N20-N23
  • ICD10CM:N21
  • MESH:D052878
  • NCIT:C114688
  • SCTID:95566004
  • UMLS:C0451641
Child trait(s) nephrolithiasis

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 "urolithiasis" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution 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
PGS001864
(portability-PLR_594)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Urinary calculus urolithiasis 5,599
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001864/ScoringFiles/PGS001864.txt.gz
PGS002075
(portability-ldpred2_594)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Urinary calculus urolithiasis 731,196
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002075/ScoringFiles/PGS002075.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] : 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] : 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] : 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] : 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] : 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
PPM009801 PGS001864
(portability-PLR_594)
PSS009339|
European Ancestry|
19,913 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0323 [0.0184, 0.0462] sex, age, birth date, deprivation index, 16 PCs
PPM009802 PGS001864
(portability-PLR_594)
PSS009113|
European Ancestry|
4,121 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0291 [-0.0015, 0.0597] sex, age, birth date, deprivation index, 16 PCs
PPM009803 PGS001864
(portability-PLR_594)
PSS008667|
European Ancestry|
6,632 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0503 [0.0263, 0.0743] sex, age, birth date, deprivation index, 16 PCs
PPM009805 PGS001864
(portability-PLR_594)
PSS008221|
South Asian Ancestry|
6,306 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.033 [0.0082, 0.0576] sex, age, birth date, deprivation index, 16 PCs
PPM009806 PGS001864
(portability-PLR_594)
PSS008002|
East Asian Ancestry|
1,803 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0058 [-0.0406, 0.0522] sex, age, birth date, deprivation index, 16 PCs
PPM009807 PGS001864
(portability-PLR_594)
PSS007786|
African Ancestry|
2,475 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.005 [-0.0345, 0.0446] sex, age, birth date, deprivation index, 16 PCs
PPM009808 PGS001864
(portability-PLR_594)
PSS008890|
African Ancestry|
3,912 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0052 [-0.0262, 0.0366] sex, age, birth date, deprivation index, 16 PCs
PPM009804 PGS001864
(portability-PLR_594)
PSS008441|
Greater Middle Eastern Ancestry|
1,192 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0222 [-0.0352, 0.0793] sex, age, birth date, deprivation index, 16 PCs
PPM011461 PGS002075
(portability-ldpred2_594)
PSS009339|
European Ancestry|
19,913 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0385 [0.0246, 0.0524] sex, age, birth date, deprivation index, 16 PCs
PPM011462 PGS002075
(portability-ldpred2_594)
PSS009113|
European Ancestry|
4,121 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0419 [0.0113, 0.0724] sex, age, birth date, deprivation index, 16 PCs
PPM011463 PGS002075
(portability-ldpred2_594)
PSS008667|
European Ancestry|
6,632 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0543 [0.0303, 0.0783] sex, age, birth date, deprivation index, 16 PCs
PPM011464 PGS002075
(portability-ldpred2_594)
PSS008441|
Greater Middle Eastern Ancestry|
1,192 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0156 [-0.0417, 0.0728] sex, age, birth date, deprivation index, 16 PCs
PPM011465 PGS002075
(portability-ldpred2_594)
PSS008221|
South Asian Ancestry|
6,306 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0401 [0.0154, 0.0648] sex, age, birth date, deprivation index, 16 PCs
PPM011466 PGS002075
(portability-ldpred2_594)
PSS008002|
East Asian Ancestry|
1,803 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0058 [-0.0406, 0.0522] sex, age, birth date, deprivation index, 16 PCs
PPM011468 PGS002075
(portability-ldpred2_594)
PSS008890|
African Ancestry|
3,912 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0125 [-0.0189, 0.0439] sex, age, birth date, deprivation index, 16 PCs
PPM011467 PGS002075
(portability-ldpred2_594)
PSS007786|
African Ancestry|
2,475 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Urinary calculus Partial Correlation (partial-r): 0.0047 [-0.0349, 0.0442] sex, age, birth date, deprivation index, 16 PCs

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)
PSS008667 6,632 individuals European Italy (South Europe) UKB
PSS007786 2,475 individuals African American or Afro-Caribbean Carribean UKB
PSS009113 4,121 individuals European Poland (NE Europe) UKB
PSS008890 3,912 individuals African unspecified Nigeria (West Africa) UKB
PSS009339 19,913 individuals European UK (+ Ireland) UKB
PSS008441 1,192 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008221 6,306 individuals South Asian India (South Asia) UKB
PSS008002 1,803 individuals East Asian China (East Asia) UKB