Polygenic Score (PGS) ID: PGS003568

Predicted Trait
Reported Trait Sensitive stomach
Mapped Trait(s) health trait (EFO_0007652)
Released in PGS Catalog: April 12, 2023
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 cont-decay-sensitive_stomach
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
122,312 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 Sample Sets

Development Samples

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
— 122,312 individuals,
0.44 % Male samples
 European UKB — Mean = 56.2 years
Sd = 7.6 years		 — white British —

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
PPM017496 PSS010935|
European Ancestry|
6,703 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sensitive stomach — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM017580 PSS010851|
European Ancestry|
1,216 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sensitive stomach — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM017664 PSS010683|
European Ancestry|
2,159 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sensitive stomach — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM017748 PSS010599|
Greater Middle Eastern Ancestry|
196 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sensitive stomach — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM017832 PSS010263|
European Ancestry|
976 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sensitive stomach — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM017916 PSS010515|
South Asian Ancestry|
840 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sensitive stomach — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM018000 PSS010431|
East Asian Ancestry|
413 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sensitive stomach — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM018084 PSS010347|
African Ancestry|
355 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sensitive stomach — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM018168 PSS010767|
African Ancestry|
478 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sensitive stomach — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —

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
PSS010263 — — 976 individuals,
43.0 % Male samples
 Mean = 57.5 years
Sd = 6.9 years		 European Ashkenazi UKB —
PSS010431 — — 413 individuals,
25.0 % Male samples
 Mean = 52.5 years
Sd = 7.2 years		 East Asian Chinese UKB —
PSS010851 — — 1,216 individuals,
34.0 % Male samples
 Mean = 54.1 years
Sd = 7.3 years		 European Polish UKB —
PSS010599 — — 196 individuals,
59.0 % Male samples
 Mean = 54.1 years
Sd = 7.5 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010347 — — 355 individuals,
33.0 % Male samples
 Mean = 50.7 years
Sd = 7.0 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010767 — — 478 individuals,
46.0 % Male samples
 Mean = 50.7 years
Sd = 7.0 years		 African unspecified Nigerian UKB —
PSS010515 — — 840 individuals,
55.0 % Male samples
 Mean = 52.5 years
Sd = 8.3 years		 South Asian Indian UKB —
PSS010935 — — 6,703 individuals,
45.0 % Male samples
 Mean = 56.2 years
Sd = 7.6 years		 European white British UKB —
PSS010683 — — 2,159 individuals,
42.0 % Male samples
 Mean = 54.1 years
Sd = 8.1 years		 European Italian UKB —