Polygenic Score (PGS) ID: PGS002024

Predicted Trait
Reported Trait Hypothyroidism
Mapped Trait(s) hypothyroidism (EFO_0004705)
Additional Trait Information endocrine/metabolic
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_244
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 632,597
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
PPM011066 PSS009286|
European Ancestry|
19,852 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hypothyroidism — — Partial Correlation (partial-r): 0.122 [0.1083, 0.1357] sex, age, birth date, deprivation index, 16 PCs —
PPM011067 PSS009060|
European Ancestry|
4,100 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hypothyroidism — — Partial Correlation (partial-r): 0.143 [0.1128, 0.1729] sex, age, birth date, deprivation index, 16 PCs —
PPM011068 PSS008614|
European Ancestry|
6,601 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hypothyroidism — — Partial Correlation (partial-r): 0.1035 [0.0795, 0.1273] sex, age, birth date, deprivation index, 16 PCs —
PPM011069 PSS008390|
Greater Middle Eastern Ancestry|
1,186 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hypothyroidism — — Partial Correlation (partial-r): 0.133 [0.0762, 0.189] sex, age, birth date, deprivation index, 16 PCs —
PPM011070 PSS008168|
South Asian Ancestry|
6,272 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hypothyroidism — — Partial Correlation (partial-r): 0.1186 [0.094, 0.1429] sex, age, birth date, deprivation index, 16 PCs —
PPM011071 PSS007955|
East Asian Ancestry|
1,782 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hypothyroidism — — Partial Correlation (partial-r): 0.047 sex, age, birth date, deprivation index, 16 PCs —
PPM011072 PSS007736|
African Ancestry|
2,434 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hypothyroidism — — Partial Correlation (partial-r): 0.0093 [-0.0306, 0.0492] sex, age, birth date, deprivation index, 16 PCs —
PPM011073 PSS008839|
African Ancestry|
3,876 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hypothyroidism — — Partial Correlation (partial-r): 0.0396 [0.0081, 0.0711] 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
PSS009060 — — 4,100 individuals — European Poland (NE Europe) UKB —
PSS008614 — — 6,601 individuals — European Italy (South Europe) UKB —
PSS009286 — — 19,852 individuals — European UK (+ Ireland) UKB —
PSS008390 — — 1,186 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008168 — — 6,272 individuals — South Asian India (South Asia) UKB —
PSS008839 — — 3,876 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007955 — — 1,782 individuals — East Asian China (East Asia) UKB —
PSS007736 — — 2,434 individuals — African American or Afro-Caribbean Carribean UKB —