Trait: Thyroid preparation use measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009933
Description Quantification of some aspect of the use of thyroid preparations.
Trait category
Other measurement
Mapped term(s) PMID:31015401

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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Multi-ancestry (excluding European)
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Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000821
(PRS_hypomed)
PGP000204 |
Luo J et al. Clin Cancer Res (2021)
Thyroid medication use Thyroid preparation use measurement 872,391
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000821/ScoringFiles/PGS000821.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
PPM002194 PGS000821
(PRS_hypomed)
PSS001068|
European Ancestry|
51,070 individuals
PGP000204 |
Luo J et al. Clin Cancer Res (2021)
Reported Trait: Spontaneous hypothyroidism AUROC: 0.6 Age, sex, PCs(1-10)
PPM002196 PGS000821
(PRS_hypomed)
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: 1.32 [1.07, 1.63] Age, sex, PCs(1-10)
PPM002200 PGS000821
(PRS_hypomed)
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 AUROC: 0.7 Age, sex, PCs(1-10)

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
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)