Polygenic Score (PGS) ID: PGS002022

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

Score Construction
PGS Name portability-ldpred2_241.2
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 375,470
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
PPM011050 PSS009284|
European Ancestry|
19,043 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nontoxic multinodular goiter — — Partial Correlation (partial-r): 0.024 [0.0098, 0.0382] sex, age, birth date, deprivation index, 16 PCs —
PPM011051 PSS009058|
European Ancestry|
3,930 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nontoxic multinodular goiter — — Partial Correlation (partial-r): 0.0213 [-0.01, 0.0527] sex, age, birth date, deprivation index, 16 PCs —
PPM011052 PSS008612|
European Ancestry|
6,363 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nontoxic multinodular goiter — — Partial Correlation (partial-r): 0.019 [-0.0056, 0.0436] sex, age, birth date, deprivation index, 16 PCs —
PPM011053 PSS008388|
Greater Middle Eastern Ancestry|
1,140 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nontoxic multinodular goiter — — Partial Correlation (partial-r): 0.0214 [-0.0372, 0.0799] sex, age, birth date, deprivation index, 16 PCs —
PPM011054 PSS008166|
South Asian Ancestry|
5,927 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nontoxic multinodular goiter — — Partial Correlation (partial-r): 0.0677 [0.0423, 0.0931] sex, age, birth date, deprivation index, 16 PCs —
PPM011055 PSS007953|
East Asian Ancestry|
1,744 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nontoxic multinodular goiter — — Partial Correlation (partial-r): 0.0096 [-0.0376, 0.0568] sex, age, birth date, deprivation index, 16 PCs —
PPM011056 PSS007734|
African Ancestry|
2,378 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nontoxic multinodular goiter — — Partial Correlation (partial-r): 0.0282 [-0.0122, 0.0685] sex, age, birth date, deprivation index, 16 PCs —
PPM011057 PSS008837|
African Ancestry|
3,830 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nontoxic multinodular goiter — — Partial Correlation (partial-r): 0.0496 [0.0179, 0.0813] 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
PSS009284 — — 19,043 individuals — European UK (+ Ireland) UKB —
PSS008388 — — 1,140 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008166 — — 5,927 individuals — South Asian India (South Asia) UKB —
PSS008612 — — 6,363 individuals — European Italy (South Europe) UKB —
PSS008837 — — 3,830 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007953 — — 1,744 individuals — East Asian China (East Asia) UKB —
PSS007734 — — 2,378 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009058 — — 3,930 individuals — European Poland (NE Europe) UKB —