Polygenic Score (PGS) ID: PGS000356

Predicted Trait
Reported Trait Any cancer
Mapped Trait(s) cancer (MONDO_0004992)
Released in PGS Catalog: Dec. 15, 2020
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name PRSWEB_PHECODE10001_UKBB-SAIGE-HRC-X10001_LASSOSUM_MGI_20200608
Development Method
Name lassosum
Parameters s=0.2;Lambda=0.008859
Variants
Original Genome Build GRCh37
Number of Variants 179
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
371,216 individuals (100%)
Score Development/Training
European: 100%
15,157 individuals (100%)
PGS Evaluation
European: 60%
African: 40%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 32424355
[
  • 69,190 cases
  • , 302,026 controls
]
 European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 32991828
[
  • 10,357 cases
  • , 4,800 controls
]
 European MGI PheCode:10001; ICD9CM:; ICD10CM: — — — —

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) 		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
PPM001041 PSS000533|
European Ancestry|
15,286 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Any Cancer OR: 1.106 [1.065, 1.148]
β: 0.101 (0.0192)		 AUROC: 0.523 [0.512, 0.535] Nagelkerke's Pseudo-R²: 0.00294
Brier score: 0.182
Odds Ratio (OR, top 1% vs. Rest): 1.61 [1.14, 2.27]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE10001_UKBB-SAIGE-HRC-X10001_LASSOSUM_MGI_20200608
PPM021339 PSS011694|
European Ancestry|
4,322 individuals
 PGP000635 |
Im C et al. J Clin Oncol (2023)
|Ext.		 Reported Trait: Subsequent malignant neoplasm in nonirridated childhood cancer survivors HR: 1.28 [1.13, 1.45] — — Sex, age at diagnosis, 5 PCs, study cohort, treatment, and doses of alkylating agents, anthracyclines, epipodophyllotoxins, and platinums —
PPM021337 PSS011696|
European Ancestry|
9,895 individuals
 PGP000635 |
Im C et al. J Clin Oncol (2023)
|Ext.		 Reported Trait: Subsequent malignant neoplasm in childhood cancer survivors HR: 1.11 [1.05, 1.17] — — Sex, age at diagnosis, 5 PCs, radiation therapy and chemotherapy dosages, cohort/batch effects —
PPM021338 PSS011695|
African Ancestry|
718 individuals
 PGP000635 |
Im C et al. J Clin Oncol (2023)
|Ext.		 Reported Trait: Subsequent malignant neoplasm in childhood cancer survivors HR: 1.01 [0.66, 1.55] — — Sex, age at diagnosis, 5 PCs, radiation therapy and chemotherapy dosages, cohort/batch effects —
PPM021340 PSS011693|
African Ancestry|
414 individuals
 PGP000635 |
Im C et al. J Clin Oncol (2023)
|Ext.		 Reported Trait: Subsequent malignant neoplasm in nonirridated childhood cancer survivors HR: 0.86 [0.35, 2.13] — — Sex, age at diagnosis, 5 PCs, study cohort, treatment, and doses of alkylating agents, anthracyclines, epipodophyllotoxins, and platinums —

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
PSS011693 — —
[
  • 9 cases
  • , 405 controls
]
 — African unspecified — CCSS, SJLIFE —
PSS011694 — —
[
  • 259 cases
  • , 4,063 controls
]
 — European — CCSS, SJLIFE —
PSS011695 — — 718 individuals,
49.4 % Male samples
 — African unspecified — CCSS, SJLIFE —
PSS011696 — — 9,895 individuals,
49.8 % Male samples
 — European — CCSS, SJLIFE —
PSS000533 Any Cancer PheCode —
[
  • 10,394 cases
  • , 4,892 controls
]
 — European — MGI —