Polygenic Score (PGS) ID: PGS000820

Predicted Trait
Reported Trait Hypothyroidism (self-reported)
Mapped Trait(s) hypothyroidism (EFO_0004705)
Released in PGS Catalog: July 29, 2021
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Score Details

Score Construction
PGS Name PRS_hypothyroidism
Variants
Original Genome Build NR
Number of Variants 890,908
Development Method
Name LDpred
Parameters NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000204
Citation (link to publication) Luo J et al. Clin Cancer Res (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
459,318 individuals (100%)
PGS Evaluation
European: 50%
Multi-ancestry (including European): 50%
  • European
  • African
  • Additional Asian Ancestries
  • Hispanic or Latin American
  • Not Reported
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
Europe PMC: 29892013
[
  • 22,500 cases
  • , 436,818 controls
]
European

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
PPM002193 PSS001068|
European Ancestry|
51,070 individuals
PGP000204 |
Luo J et al. Clin Cancer Res (2021)
Reported Trait: Spontaneous hypothyroidism OR: 1.33 [1.29, 1.37] AUROC: 0.6 Age, sex, PCs(1-10)
PPM002195 PSS001070|
Multi-ancestry (including European)|
744 individuals
PGP000204 |
Luo J et al. Clin Cancer Res (2021)
Reported Trait: Immune checkpoint inhibitor therapy induced immune-related thyroid dysfunction in individuals with non-small cell lung cancer HR: 1.34 [1.08, 1.66] AUROC: 0.6 Age, sex, PCs(1-10)
PPM002197 PSS001070|
Multi-ancestry (including European)|
744 individuals
PGP000204 |
Luo J et al. Clin Cancer Res (2021)
Reported Trait: Anti-PD-(L)1 monotherapy induced immune-related thyroid dysfunction in individuals with non-small cell lung cancer HR: 1.34 [1.07, 1.69] Age, sex, PCs(1-10)
PPM002199 PSS001069|
Multi-ancestry (including European)|
561 individuals
PGP000204 |
Luo J et al. Clin Cancer Res (2021)
Reported Trait: Immune checkpoint inhibitor therapy induced immune-related thyroid dysfunction in individuals with non-small cell lung cancer HR: 1.39 [1.07, 1.82] AUROC: 0.64 Age, sex, PCs(1-10)
PPM002198 PSS001071|
European Ancestry|
634 individuals
PGP000204 |
Luo J et al. Clin Cancer Res (2021)
Reported Trait: Immune checkpoint inhibitor therapy induced immune-related thyroid dysfunction in individuals with non-small cell lung cancer HR: 1.27 [1.02, 1.59] Age, sex

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
PSS001068 Spontaneous hypothyroidism cases and controls were defined using phecodes, which aggregate similar ICD-9-CM and ICD-10-CM. Individuals must have had at least 2 ICD codes for hypothyroidism to be assigned a phecode, and individuals with other thyroid diseases were excluded from the control set. 51,070 individuals European BioVu
PSS001069 All individuals had non-small cell lung cancer (NSCLC) and were receiving immune checkpoint inhibitor (CPI) therapy. Cases were individuals who had experienced immune-related thyroid dysfunction following CPI therapy. A thyroid event after the start of CPI therapy was defined as either (1) incident hypothyroidism or (2) transient incident hyperthyroidism followed by incident hypothyroidism. Incident hypothyroidism was defined as (a) a TSH of ≥ 10 mU/L or (b) TSH of ≥ 5 mU/L with a new prescription of levothyroxine ≥ 50 mcg. Incident hyperthyroidism was defined as TSH < 0.05 mU/L. Median = 12.0 months
[
  • 42 cases
  • , 519 controls
]
,
44.0 % Male samples
Median = 67.0 years
Iqr = [60.0, 74.0] years
European, African unspecified, Asian unspecified, Hispanic or Latin American, NR European = 506, African unspecified = 22, Asian unspecified = 17, Not reported = 6, Hispanic or Latin American = 10 Cases and controls were obtained from the Dana-Farber Cancer Institute (DFCI)
PSS001070 All individuals had non-small cell lung cancer (NSCLC) and were receiving immune checkpoint inhibitor (CPI) therapy. of the 744 individuals receiving CPI therapy, 659 were being treated with Anti-PD-(L)1 monotherapy whilst 85 were being treated with Anti-PD-(L)1+CTLA-4 combination therapy. Cases were individuals who had experienced immune-related thyroid dysfunction following CPI therapy. A thyroid event after the start of CPI therapy was defined as either (1) incident hypothyroidism or (2) transient incident hyperthyroidism followed by incident hypothyroidism. Incident hypothyroidism was defined as (a) a TSH of ≥ 10 mU/L or (b) TSH of ≥ 5 mU/L with a new prescription of levothyroxine ≥ 50 mcg. Incident hyperthyroidism was defined as TSH < 0.05 mU/L.
[
  • 95 cases
  • , 649 controls
]
,
50.94 % Male samples
European, African unspecified, Asian unspecified, Hispanic or Latin American, NR European = 634, African unspecified = 50, Asian unspecified = 36, Not reported = 4, Hispanic or Latin American = 20 MSKCC Additional cases and controls were obtained from the Vanderbilt University Medical Centre (VUMC)
PSS001071 All individuals had non-small cell lung cancer (NSCLC) and were receiving immune checkpoint inhibitor (CPI) therapy. Cases were individuals who had experienced immune-related thyroid dysfunction following CPI therapy. A thyroid event after the start of CPI therapy was defined as either (1) incident hypothyroidism or (2) transient incident hyperthyroidism followed by incident hypothyroidism. Incident hypothyroidism was defined as (a) a TSH of ≥ 10 mU/L or (b) TSH of ≥ 5 mU/L with a new prescription of levothyroxine ≥ 50 mcg. Incident hyperthyroidism was defined as TSH < 0.05 mU/L. 634 individuals European MSKCC Additional cases and controls were obtained from the Vanderbilt University Medical Centre (VUMC)