Polygenic Score (PGS) ID: PGS002023

Predicted Trait
Reported Trait Thyrotoxicosis with or without goiter
Mapped Trait(s) Thyrotoxicosis (EFO_0009190)
Additional Trait Information endocrine/metabolic
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_242
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 279,385
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: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
PPM011058 PSS009285|
European Ancestry|
19,108 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyrotoxicosis with or without goiter — — Partial Correlation (partial-r): 0.0199 [0.0057, 0.034] sex, age, birth date, deprivation index, 16 PCs —
PPM011059 PSS009059|
European Ancestry|
3,938 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyrotoxicosis with or without goiter — — Partial Correlation (partial-r): 0.0345 [0.0032, 0.0658] sex, age, birth date, deprivation index, 16 PCs —
PPM011060 PSS008613|
European Ancestry|
6,381 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyrotoxicosis with or without goiter — — Partial Correlation (partial-r): 0.0195 [-0.0051, 0.044] sex, age, birth date, deprivation index, 16 PCs —
PPM011061 PSS008389|
Greater Middle Eastern Ancestry|
1,143 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyrotoxicosis with or without goiter — — Partial Correlation (partial-r): -0.0281 [-0.0864, 0.0305] sex, age, birth date, deprivation index, 16 PCs —
PPM011062 PSS008167|
South Asian Ancestry|
5,954 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyrotoxicosis with or without goiter — — Partial Correlation (partial-r): 0.0457 [0.0203, 0.0711] sex, age, birth date, deprivation index, 16 PCs —
PPM011063 PSS007954|
East Asian Ancestry|
1,754 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyrotoxicosis with or without goiter — — Partial Correlation (partial-r): 0.039 [-0.0081, 0.0859] sex, age, birth date, deprivation index, 16 PCs —
PPM011064 PSS007735|
African Ancestry|
2,410 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyrotoxicosis with or without goiter — — Partial Correlation (partial-r): 0.0027 [-0.0374, 0.0428] sex, age, birth date, deprivation index, 16 PCs —
PPM011065 PSS008838|
African Ancestry|
3,836 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyrotoxicosis with or without goiter — — Partial Correlation (partial-r): 0.0172 [-0.0146, 0.0489] 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
PSS009285 — — 19,108 individuals — European UK (+ Ireland) UKB —
PSS008613 — — 6,381 individuals — European Italy (South Europe) UKB —
PSS008167 — — 5,954 individuals — South Asian India (South Asia) UKB —
PSS008389 — — 1,143 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008838 — — 3,836 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007954 — — 1,754 individuals — East Asian China (East Asia) UKB —
PSS007735 — — 2,410 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009059 — — 3,938 individuals — European Poland (NE Europe) UKB —