Trait: number of cancers, self-reported

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009800
Description Number of cancer occurrences in an individual, as reported by the individual.
Trait category
Other trait

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 Scoring File (FTP Link)
PGS001005
(GBE_INI134)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Number of self reported cancers number of cancers, self-reported 526
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001005/ScoringFiles/PGS001005.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
PPM007788 PGS001005
(GBE_INI134)
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 PGS001005
(GBE_INI134)
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 PGS001005
(GBE_INI134)
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 PGS001005
(GBE_INI134)
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 PGS001005
(GBE_INI134)
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