Polygenic Score (PGS) ID: PGS002018

Predicted Trait
Reported Trait Thyroid cancer
Mapped Trait(s) thyroid carcinoma (EFO_0002892)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_193
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 311,520
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
PPM011018 PSS009279|
European Ancestry|
19,923 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyroid cancer — — Partial Correlation (partial-r): 0.0295 [0.0157, 0.0434] sex, age, birth date, deprivation index, 16 PCs —
PPM011019 PSS009053|
European Ancestry|
4,120 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyroid cancer — — Partial Correlation (partial-r): -0.0056 [-0.0362, 0.0251] sex, age, birth date, deprivation index, 16 PCs —
PPM011020 PSS008607|
European Ancestry|
6,640 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyroid cancer — — Partial Correlation (partial-r): 0.0208 [-0.0033, 0.0448] sex, age, birth date, deprivation index, 16 PCs —
PPM011021 PSS008383|
Greater Middle Eastern Ancestry|
1,197 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyroid cancer — — Partial Correlation (partial-r): -0.0107 [-0.0677, 0.0465] sex, age, birth date, deprivation index, 16 PCs —
PPM011022 PSS008161|
South Asian Ancestry|
6,305 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyroid cancer — — Partial Correlation (partial-r): 0.0149 [-0.0098, 0.0396] sex, age, birth date, deprivation index, 16 PCs —
PPM011023 PSS007948|
East Asian Ancestry|
1,801 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyroid cancer — — Partial Correlation (partial-r): -0.004 [-0.0505, 0.0424] sex, age, birth date, deprivation index, 16 PCs —
PPM011024 PSS007730|
African Ancestry|
2,453 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyroid cancer — — Partial Correlation (partial-r): 0.0184 [-0.0213, 0.0581] sex, age, birth date, deprivation index, 16 PCs —
PPM011025 PSS008833|
African Ancestry|
3,896 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Thyroid cancer — — Partial Correlation (partial-r): 0.0029 [-0.0286, 0.0343] 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
PSS008833 — — 3,896 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007948 — — 1,801 individuals — East Asian China (East Asia) UKB —
PSS007730 — — 2,453 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008383 — — 1,197 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008607 — — 6,640 individuals — European Italy (South Europe) UKB —
PSS009053 — — 4,120 individuals — European Poland (NE Europe) UKB —
PSS009279 — — 19,923 individuals — European UK (+ Ireland) UKB —
PSS008161 — — 6,305 individuals — South Asian India (South Asia) UKB —