Polygenic Score (PGS) ID: PGS002089

Predicted Trait
Reported Trait Ankylosing spondylitis
Mapped Trait(s) ankylosing spondylitis (EFO_0003898)
Additional Trait Information musculoskeletal
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_715.2
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 22,026
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 60%
Greater Middle Eastern: 20%
South Asian: 20%
5 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011572 PSS009353|
European Ancestry|
18,262 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ankylosing spondylitis — — Partial Correlation (partial-r): 0.0919 [0.0775, 0.1063] sex, age, birth date, deprivation index, 16 PCs —
PPM011573 PSS009127|
European Ancestry|
3,854 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ankylosing spondylitis — — Partial Correlation (partial-r): 0.0476 [0.016, 0.0791] sex, age, birth date, deprivation index, 16 PCs —
PPM011574 PSS008681|
European Ancestry|
6,216 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ankylosing spondylitis — — Partial Correlation (partial-r): 0.0596 [0.0348, 0.0844] sex, age, birth date, deprivation index, 16 PCs —
PPM011576 PSS008235|
South Asian Ancestry|
5,671 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ankylosing spondylitis — — Partial Correlation (partial-r): 0.0424 [0.0163, 0.0684] sex, age, birth date, deprivation index, 16 PCs —
PPM011575 PSS008455|
Greater Middle Eastern Ancestry|
1,124 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ankylosing spondylitis — — Partial Correlation (partial-r): 0.1631 [0.1051, 0.22] 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
PSS008455 — — 1,124 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009127 — — 3,854 individuals — European Poland (NE Europe) UKB —
PSS008681 — — 6,216 individuals — European Italy (South Europe) UKB —
PSS009353 — — 18,262 individuals — European UK (+ Ireland) UKB —
PSS008235 — — 5,671 individuals — South Asian India (South Asia) UKB —