Trait: Hashimoto thyroiditis

Trait Information
Identifier MONDO_0007699
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 categories
Immune system disorder
Other disease
Synonyms 28 synonyms
  • HT
  • 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
  • chronic lymphocytic thyroiditides
  • chronic lymphocytic thyroiditis
  • disease, Hashimoto
  • disease, Hashimoto's
  • hypothyroidism, autoimmune thyroid autoantibodies, included
  • lymphocytic thyroiditides, chronic
  • lymphocytic thyroiditis
  • lymphocytic thyroiditis, chronic
  • syndrome, Hashimoto's
  • syndromes, Hashimoto's
  • 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 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 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 thyroiditis 1,085,142
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005272/ScoringFiles/PGS005272.txt.gz
PGS018695
(TPMI_245.2_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic thyroiditis Hashimoto thyroiditis 171
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018695/ScoringFiles/PGS018695.txt.gz
PGS018696
(TPMI_245.2_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic thyroiditis Hashimoto thyroiditis 939,816
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018696/ScoringFiles/PGS018696.txt.gz
PGS018697
(TPMI_245.2_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic thyroiditis Hashimoto thyroiditis 392,668
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018697/ScoringFiles/PGS018697.txt.gz
PGS018698
(TPMI_245.2_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic thyroiditis Hashimoto thyroiditis 983,771
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018698/ScoringFiles/PGS018698.txt.gz
PGS018699
(TPMI_245.2_PRSmix+)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic thyroiditis Hashimoto thyroiditis 1,071,404
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018699/ScoringFiles/PGS018699.txt.gz
PGS018700
(TPMI_245.2_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic thyroiditis Hashimoto thyroiditis 979,446
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018700/ScoringFiles/PGS018700.txt.gz
PGS018701
(TPMI_245.21_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic lymphocytic thyroiditis Hashimoto thyroiditis 190
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018701/ScoringFiles/PGS018701.txt.gz
PGS018702
(TPMI_245.21_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic lymphocytic thyroiditis Hashimoto thyroiditis 318,664
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018702/ScoringFiles/PGS018702.txt.gz
PGS018703
(TPMI_245.21_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic lymphocytic thyroiditis Hashimoto thyroiditis 394,827
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018703/ScoringFiles/PGS018703.txt.gz
PGS018704
(TPMI_245.21_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic lymphocytic thyroiditis Hashimoto thyroiditis 983,771
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018704/ScoringFiles/PGS018704.txt.gz
PGS018705
(TPMI_245.21_PRSmix+)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic lymphocytic thyroiditis Hashimoto thyroiditis 1,071,405
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018705/ScoringFiles/PGS018705.txt.gz
PGS018706
(TPMI_245.21_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Chronic lymphocytic thyroiditis Hashimoto thyroiditis 1,005,256
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018706/ScoringFiles/PGS018706.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 — — —
PPM036877 PGS018695
(TPMI_245.2_Lassosum2)
 PSS012598|
East Asian Ancestry|
17,340 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic thyroiditis — AUROC: 0.80731 R²: 0.04802 sex, age, array, PCs 1-10 —
PPM036878 PGS018696
(TPMI_245.2_LDpred2)
 PSS012597|
East Asian Ancestry|
17,340 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic thyroiditis — AUROC: 0.81251 R²: 0.04969 sex, age, array, PCs 1-10 —
PPM036879 PGS018697
(TPMI_245.2_MegaPRS)
 PSS012599|
East Asian Ancestry|
17,340 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic thyroiditis — AUROC: 0.80531 R²: 0.04823 sex, age, array, PCs 1-10 —
PPM036880 PGS018698
(TPMI_245.2_PRS-CS)
 PSS012600|
East Asian Ancestry|
17,340 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic thyroiditis — AUROC: 0.81019 R²: 0.04915 sex, age, array, PCs 1-10 —
PPM036881 PGS018699
(TPMI_245.2_PRSmix+)
 PSS012601|
East Asian Ancestry|
17,340 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic thyroiditis — AUROC: 0.81625 R²: 0.05203 sex, age, array, PCs 1-10 —
PPM036882 PGS018700
(TPMI_245.2_SBayesR)
 PSS012602|
East Asian Ancestry|
17,340 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic thyroiditis — AUROC: 0.80447 R²: 0.04689 sex, age, array, PCs 1-10 —
PPM036883 PGS018701
(TPMI_245.21_Lassosum2)
 PSS012592|
East Asian Ancestry|
17,333 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic lymphocytic thyroiditis — AUROC: 0.8083 R²: 0.04684 sex, age, array, PCs 1-10 —
PPM036884 PGS018702
(TPMI_245.21_LDpred2)
 PSS012591|
East Asian Ancestry|
17,333 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic lymphocytic thyroiditis — AUROC: 0.81429 R²: 0.04859 sex, age, array, PCs 1-10 —
PPM036885 PGS018703
(TPMI_245.21_MegaPRS)
 PSS012593|
East Asian Ancestry|
17,333 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic lymphocytic thyroiditis — AUROC: 0.80609 R²: 0.04681 sex, age, array, PCs 1-10 —
PPM036886 PGS018704
(TPMI_245.21_PRS-CS)
 PSS012594|
East Asian Ancestry|
17,333 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic lymphocytic thyroiditis — AUROC: 0.80804 R²: 0.04631 sex, age, array, PCs 1-10 —
PPM036887 PGS018705
(TPMI_245.21_PRSmix+)
 PSS012595|
East Asian Ancestry|
17,333 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic lymphocytic thyroiditis — AUROC: 0.81711 R²: 0.05007 sex, age, array, PCs 1-10 —
PPM036888 PGS018706
(TPMI_245.21_SBayesR)
 PSS012596|
East Asian Ancestry|
17,333 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Chronic lymphocytic thyroiditis — AUROC: 0.8053 R²: 0.04581 sex, age, array, 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
PSS012596 245.2,E06.3 —
[
  • 253 cases
  • , 17,080 controls
]
,
49.3 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012591 245.2,E06.3 —
[
  • 253 cases
  • , 17,080 controls
]
,
49.3 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012592 245.2,E06.3 —
[
  • 253 cases
  • , 17,080 controls
]
,
49.3 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
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 —
PSS012593 245.2,E06.3 —
[
  • 253 cases
  • , 17,080 controls
]
,
49.3 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012594 245.2,E06.3 —
[
  • 253 cases
  • , 17,080 controls
]
,
49.3 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012595 245.2,E06.3 —
[
  • 253 cases
  • , 17,080 controls
]
,
49.3 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012597 245.2, 245.3, 245.8,E06.2, E06.3, E06.5 —
[
  • 260 cases
  • , 17,080 controls
]
,
49.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012598 245.2, 245.3, 245.8,E06.2, E06.3, E06.5 —
[
  • 260 cases
  • , 17,080 controls
]
,
49.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012599 245.2, 245.3, 245.8,E06.2, E06.3, E06.5 —
[
  • 260 cases
  • , 17,080 controls
]
,
49.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012600 245.2, 245.3, 245.8,E06.2, E06.3, E06.5 —
[
  • 260 cases
  • , 17,080 controls
]
,
49.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012601 245.2, 245.3, 245.8,E06.2, E06.3, E06.5 —
[
  • 260 cases
  • , 17,080 controls
]
,
49.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012602 245.2, 245.3, 245.8,E06.2, E06.3, E06.5 —
[
  • 260 cases
  • , 17,080 controls
]
,
49.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —