PGS Publication: PGP000164

Publication Information (EuropePMC)
Title Genetic variation associated with thyroid autoimmunity shapes the systemic immune response to PD-1 checkpoint blockade.
PubMed ID 34099659(Europe PMC)
doi 10.1038/s41467-021-23661-4
Publication Date June 7, 2021
Journal Nat Commun
Author(s) Khan Z, Hammer C, Carroll J, Di Nucci F, Acosta SL, Maiya V, Bhangale T, Hunkapiller J, Mellman I, Albert ML, McCarthy MI, Chandler GS.
Released in PGS Catalog: June 11, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000759
(hypoT)
 PGP000164 |
Khan Z et al. Nat Commun (2021)
 Hypothyroidism hypothyroidism 140
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000759/ScoringFiles/PGS000759.txt.gz
PGS000761
(LDpred2_hypoT_PRS)
 PGP000164 |
Khan Z et al. Nat Commun (2021)
 Hypothyroidism hypothyroidism 1,099,649
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000761/ScoringFiles/PGS000761.txt.gz
PGS000760
(VIT)
 PGP000164 |
Khan Z et al. Nat Commun (2021)
 Vitiligo Vitiligo 42
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000760/ScoringFiles/PGS000760.txt.gz

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) 		Evaluated Score 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
PPM001934 PGS000759
(hypoT)
 PSS000970|
European Ancestry|
1,584 individuals
 PGP000164 |
Khan Z et al. Nat Commun (2021)
 Reported Trait: anti-PD-L1 induced hypothyroidism in cancer patients HR: 1.52 [1.31, 1.74] — meta-analysis p-value: 7.52e-09 5 genotype PCs —
PPM001935 PGS000760
(VIT)
 PSS000970|
European Ancestry|
1,584 individuals
 PGP000164 |
Khan Z et al. Nat Commun (2021)
 Reported Trait: anti-PD-L1 induced hypothyroidism in cancer patients HR: 1.41 [1.22, 1.61] — meta-analysis p-value: 1.10e-06 5 genotype PCs —
PPM001936 PGS000761
(LDpred2_hypoT_PRS)
 PSS000970|
European Ancestry|
1,584 individuals
 PGP000164 |
Khan Z et al. Nat Commun (2021)
 Reported Trait: anti-PD-L1 induced hypothyroidism in cancer patients HR: 1.49 [1.3, 1.71] — meta-analysis p-value: 5.49e-09 5 genotype 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
PSS000970 — Median = 400.0 days 1,584 individuals — European — GNEHGI2020Q2 —