Trait: Hashimoto's thyroiditis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003779
Description An autoimmune disorder caused by the production of autoantibodies against thyroid tissue. There is progressive destruction of the thyroid follicles leading to hypothyroidism. [NCIT: C27191]
Trait category
Immune system disorder
Synonyms 41 synonyms
  • HT
  • Hashimoto Thyroiditis
  • Hashimoto disease
  • Hashimoto hypothyroidism
  • Hashimoto struma
  • Hashimoto syndrome
  • Hashimoto thyroiditides
  • Hashimoto thyroiditis
  • Hashimoto's disease
  • Hashimoto's struma
  • Hashimoto's syndrome
  • Hashimoto's syndromes
  • Hashimoto's thyroiditis
  • Hashimotos disease
  • Hashimotos syndrome
  • Ht
  • Lymphocytic Thyroiditides
  • Lymphocytic Thyroiditis
  • Lymphomatous Thyroiditides
  • Thyroiditides, Lymphocytic
  • Thyroiditides, Lymphomatous
  • Thyroiditis, Lymphocytic
  • Thyroiditis, Lymphomatous
  • autoimmune thyroiditis
  • autoimmune thyroiditis
  • chronic lymphocytic thyroiditides
  • chronic lymphocytic thyroiditis
  • disease, Hashimoto
  • disease, Hashimoto's
  • hypothyroidism, autoimmune
  • hypothyroidism, autoimmune thyroid autoantibodies, included
  • lymphocytic thyroiditides, chronic
  • lymphocytic thyroiditis
  • lymphocytic thyroiditis, chronic
  • syndrome, Hashimoto's
  • syndromes, Hashimoto's
  • thyroid autoantibodies
  • thyroiditides, Hashimoto
  • thyroiditides, chronic lymphocytic
  • thyroiditis, Hashimoto
  • thyroiditis, chronic lymphocytic

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:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
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)
PGS005270
(lymphocytic_thyroiditis_mixed_pt)
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Lymphocytic thyroiditis Hashimoto's thyroiditis 55
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005270/ScoringFiles/PGS005270.txt.gz
PGS005271
(lymphocytic_thyroiditis_mixed_prscs)
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Lymphocytic thyroiditis Hashimoto's thyroiditis 1,085,156
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005271/ScoringFiles/PGS005271.txt.gz
PGS005272
(lymphocytic_thyroiditis_eur_prscs)
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Lymphocytic thyroiditis Hashimoto's thyroiditis 1,085,142
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005272/ScoringFiles/PGS005272.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
PPM022753 PGS005270
(lymphocytic_thyroiditis_mixed_pt)
 PSS012069|
Multi-ancestry (including European)|
94,651 individuals
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Reported Trait: lymphocytic thyroiditis OR: 1.037
β: 0.037		 AUROC: 0.63868 — — —
PPM022754 PGS005271
(lymphocytic_thyroiditis_mixed_prscs)
 PSS012069|
Multi-ancestry (including European)|
94,651 individuals
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Reported Trait: lymphocytic thyroiditis OR: 1.54908
β: 0.43766		 AUROC: 0.62973 — — —
PPM022755 PGS005272
(lymphocytic_thyroiditis_eur_prscs)
 PSS012069|
Multi-ancestry (including European)|
94,651 individuals
 PGP000748 |
White SL et al. medRxiv (2025)
|Pre		 Reported Trait: lymphocytic thyroiditis OR: 1.41698
β: 0.34853		 AUROC: 0.60542 — — —

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
PSS012069 Cases - ICD-9-CM codes: 193, V10.87, ICD-10-CM billing codes: C73, Z85.850, ICD-9 codes: 193, V10.87, ICD-10 codes: C73, SNOMED: 92767001 Carcinoma in situ of thyroid gland, 363478007 Malignant tumor of thyroid gland, 255028004 Follicular thyroid carcinoma, 423158009 Hurthle cell carcinoma of thyroid, 772992009 Primary differentiated carcinoma of thyroid gland. Controls - ICD-9-CM codes: 241 Nontoxic nodular goiter, 241.0 Nontoxic uninodular goiter, 241.1 Nontoxic multinodular goiter, 241.9 Unspecified nontoxic nodular goiter ICD-10-CM billing codes: E01.1 Iodine-deficiency related multinodular (endemic) goiter, E04.1 Nontoxic single thyroid nodule, E04.2 Nontoxic multinodular goiter, E04.8 Other specified nontoxic goiter, E04.9 Nontoxic goiter, unspecified, ICD-9-CM codes: 241 Nontoxic nodular goiter, 241.0 Nontoxic uninodular goiter, 241.1 Nontoxic multinodular goiter, 241.9 Unspecified nontoxic nodular goiter, ICD-10 codes: E01.1 Iodine-deficiency related multinodular (endemic) goiter, E04.1 Nontoxic single thyroid nodule, E04.2 Nontoxic multinodular goiter, E04.8 Other specified nontoxic goiter, E04.9 Nontoxic goiter, unspecified, SNOMED: 419153005 Nodular goiter, 190236006 Non-toxic nodular goiter, 66392007 Substernal goiter, 60968001 Adenomatous goiter — 94,651 individuals — African American or Afro-Caribbean, Hispanic or Latin American, European — CCPM —