Polygenic Score (PGS) ID: PGS001005

Predicted Trait
Reported Trait Number of self reported cancers
Mapped Trait(s) number of cancers, self-reported (EFO_0009800)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI134
Released in PGS Catalog: Oct. 21, 2021
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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 GBE_INI134
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 526
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
269,672 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
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
269,672 individuals European white British ancestry UKB

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
PPM007788 PSS004826|
African Ancestry|
6,483 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: # of self-reported cancers : 0.01182 [0.00659, 0.01704]
Incremental R2 (full-covars): -0.00015
PGS R2 (no covariates): 0.00029 [-0.00054, 0.00112]
age, sex, UKB array type, Genotype PCs
PPM007789 PSS004827|
East Asian Ancestry|
1,702 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: # of self-reported cancers : 0.02753 [0.01224, 0.04282]
Incremental R2 (full-covars): -0.00083
PGS R2 (no covariates): 0.00016 [-0.00104, 0.00136]
age, sex, UKB array type, Genotype PCs
PPM007790 PSS004828|
European Ancestry|
24,894 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: # of self-reported cancers : 0.02065 [0.01715, 0.02414]
Incremental R2 (full-covars): 0.00068
PGS R2 (no covariates): 0.00081 [0.00011, 0.00152]
age, sex, UKB array type, Genotype PCs
PPM007791 PSS004829|
South Asian Ancestry|
7,812 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: # of self-reported cancers : 0.00918 [0.00497, 0.01338]
Incremental R2 (full-covars): -0.00087
PGS R2 (no covariates): 0.00012 [-0.00037, 0.00062]
age, sex, UKB array type, Genotype PCs
PPM007792 PSS004830|
European Ancestry|
67,419 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: # of self-reported cancers : 0.01676 [0.01484, 0.01868]
Incremental R2 (full-covars): 0.00083
PGS R2 (no covariates): 0.00079 [0.00036, 0.00121]
age, sex, UKB array type, Genotype 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
PSS004828 24,894 individuals European non-white British ancestry UKB
PSS004829 7,812 individuals South Asian UKB
PSS004830 67,419 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS004826 6,483 individuals African unspecified UKB
PSS004827 1,702 individuals East Asian UKB