PGS Catalog - hypothyroidism [EFO:0004705] (Polygenic Trait)

Trait: hypothyroidism

Experimental Factor Ontology (EFO) Information
Identifier	EFO_0004705
Description	Abnormally low levels of thyroid hormone. [NCIT: P378]
Trait category	Other disease
Synonyms	5 synonyms hypothyroid hypothyroidism thyroid deficiency thyroid insufficiency underactive thyroid
Mapped terms	15 mapped terms DOID:1459 ICD10:E03 ICD9:244.9 MEDGEN:6991 MESH:D007037 MONDO:0005420 MeSH:D007037 MedDRA:10021114 NANDO:2100120 NCIT:C26800 NCIt:C26800 SCTID:40930008 SNOMEDCT:40930008 UMLS:C0020676 icd11.foundation:1722092627
Child trait(s)	myxedema

Associated Polygenic Score(s)

Note: This table shows all PGS for "hypothyroidism" and any child terms of this trait in the EFO hierarchy by default. Include PGS Score(s) for child traits

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
PGS000820 (PRS_hypothyroidism)	PGP000204 \| Luo J et al. Clin Cancer Res (2021)	Hypothyroidism (self-reported)	hypothyroidism	890,908	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000820/ScoringFiles/PGS000820.txt.gz
PGS000965 (GBE_HC219)	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Hypothyroidism/myxoedema	hypothyroidism, myxedema	4,535	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000965/ScoringFiles/PGS000965.txt.gz
PGS001181 (GBE_HC643)	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Other hypothyroidism (time-to-event)	hypothyroidism	4,739	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001181/ScoringFiles/PGS001181.txt.gz
PGS001816 (portability-PLR_244)	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Hypothyroidism	hypothyroidism	11,130	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001816/ScoringFiles/PGS001816.txt.gz
PGS002024 (portability-ldpred2_244)	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Hypothyroidism	hypothyroidism	632,597	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002024/ScoringFiles/PGS002024.txt.gz
PGS002336 (disease_HYPOTHYROIDISM_SELF_REP.BOLT-LMM)	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Hypothyroidism	hypothyroidism	1,109,311	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002336/ScoringFiles/PGS002336.txt.gz
PGS002408 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.0001)	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Hypothyroidism	hypothyroidism	4,815	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002408/ScoringFiles/PGS002408.txt.gz
PGS002457 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.001)	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Hypothyroidism	hypothyroidism	17,519	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002457/ScoringFiles/PGS002457.txt.gz
PGS002506 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.01)	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Hypothyroidism	hypothyroidism	97,010	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002506/ScoringFiles/PGS002506.txt.gz
PGS002555 (disease_HYPOTHYROIDISM_SELF_REP.P+T.1e-06)	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Hypothyroidism	hypothyroidism	986	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002555/ScoringFiles/PGS002555.txt.gz
PGS002604 (disease_HYPOTHYROIDISM_SELF_REP.P+T.5e-08)	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Hypothyroidism	hypothyroidism	550	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002604/ScoringFiles/PGS002604.txt.gz
PGS002653 (disease_HYPOTHYROIDISM_SELF_REP.PolyFun-pred)	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Hypothyroidism	hypothyroidism	197,450	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002653/ScoringFiles/PGS002653.txt.gz
PGS002702 (disease_HYPOTHYROIDISM_SELF_REP.SBayesR)	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Hypothyroidism	hypothyroidism	889,041	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002702/ScoringFiles/PGS002702.txt.gz
PGS002766 (Hypothyroidism_prscs)	PGP000364 \| Mars N et al. Am J Hum Genet (2022)	Hypothyroidism	hypothyroidism	1,092,122	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002766/ScoringFiles/PGS002766.txt.gz
PGS004446 (disease.E03.score)	PGP000561 \| Jung H et al. Commun Biol (2024)	E03 (Other hypothyroidism)	hypothyroidism	1,059,939	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004446/ScoringFiles/PGS004446.txt.gz
PGS004516 (meta.E03.score)	PGP000561 \| Jung H et al. Commun Biol (2024)	E03 (Other hypothyroidism)	hypothyroidism	1,059,939	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004516/ScoringFiles/PGS004516.txt.gz
PGS004789 (hypothyroid_PRSmix_eur)	PGP000604 \| Truong B et al. Cell Genom (2024)	Hypothyroidism	hypothyroidism	1,109,333	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004789/ScoringFiles/PGS004789.txt.gz
PGS004790 (hypothyroid_PRSmixPlus_eur)	PGP000604 \| Truong B et al. Cell Genom (2024)	Hypothyroidism	hypothyroidism	1,841,655	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004790/ScoringFiles/PGS004790.txt.gz
PGS004935 (hypothyroidism_snpnet_combined)	PGP000665 \| Moreno-Grau S et al. Human Genomics (2024)	Hypothyroidism	hypothyroidism	6,127	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004935/ScoringFiles/PGS004935.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	—
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	—
PPM002193	PGS000820 (PRS_hypothyroidism)	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	PGS000820 (PRS_hypothyroidism)	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	PGS000820 (PRS_hypothyroidism)	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	PGS000820 (PRS_hypothyroidism)	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	PGS000820 (PRS_hypothyroidism)	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	—
PPM007649	PGS000965 (GBE_HC219)	PSS004354\| African Ancestry\| 6,497 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Hypothyroidism/myxoedema	—	AUROC: 0.70914 [0.67391, 0.74437]	R²: 0.06732 Incremental AUROC (full-covars): 0.00847 PGS R2 (no covariates): 0.01005 PGS AUROC (no covariates): 0.58277 [0.54281, 0.62272]	age, sex, UKB array type, Genotype PCs	Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007650	PGS000965 (GBE_HC219)	PSS004355\| East Asian Ancestry\| 1,704 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Hypothyroidism/myxoedema	—	AUROC: 0.68903 [0.61236, 0.7657]	R²: 0.05952 Incremental AUROC (full-covars): 0.01842 PGS R2 (no covariates): 0.01318 PGS AUROC (no covariates): 0.58777 [0.50589, 0.66966]	age, sex, UKB array type, Genotype PCs	Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007651	PGS000965 (GBE_HC219)	PSS004356\| European Ancestry\| 24,905 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Hypothyroidism/myxoedema	—	AUROC: 0.76462 [0.75294, 0.7763]	R²: 0.14559 Incremental AUROC (full-covars): 0.06544 PGS R2 (no covariates): 0.06844 PGS AUROC (no covariates): 0.68233 [0.66882, 0.69583]	age, sex, UKB array type, Genotype PCs	Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007652	PGS000965 (GBE_HC219)	PSS004357\| South Asian Ancestry\| 7,831 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Hypothyroidism/myxoedema	—	AUROC: 0.74628 [0.72661, 0.76594]	R²: 0.13858 Incremental AUROC (full-covars): 0.03694 PGS R2 (no covariates): 0.04737 PGS AUROC (no covariates): 0.64507 [0.62236, 0.66778]	age, sex, UKB array type, Genotype PCs	Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007653	PGS000965 (GBE_HC219)	PSS004358\| European Ancestry\| 67,425 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Hypothyroidism/myxoedema	—	AUROC: 0.76828 [0.76142, 0.77515]	R²: 0.14978 Incremental AUROC (full-covars): 0.07249 PGS R2 (no covariates): 0.07271 PGS AUROC (no covariates): 0.68907 [0.68098, 0.69716]	age, sex, UKB array type, Genotype PCs	Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008594	PGS001181 (GBE_HC643)	PSS004555\| African Ancestry\| 6,497 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: TTE other hypothyroidism	—	AUROC: 0.70862 [0.67381, 0.74343]	R²: 0.06703 Incremental AUROC (full-covars): 0.01118 PGS R2 (no covariates): 0.01121 PGS AUROC (no covariates): 0.58683 [0.5475, 0.62616]	age, sex, UKB array type, Genotype PCs	Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008595	PGS001181 (GBE_HC643)	PSS004556\| East Asian Ancestry\| 1,704 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: TTE other hypothyroidism	—	AUROC: 0.71469 [0.64687, 0.78251]	R²: 0.07343 Incremental AUROC (full-covars): 0.03489 PGS R2 (no covariates): 0.01956 PGS AUROC (no covariates): 0.60912 [0.53836, 0.67988]	age, sex, UKB array type, Genotype PCs	Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008596	PGS001181 (GBE_HC643)	PSS004557\| European Ancestry\| 24,905 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: TTE other hypothyroidism	—	AUROC: 0.76338 [0.75207, 0.77469]	R²: 0.14671 Incremental AUROC (full-covars): 0.06656 PGS R2 (no covariates): 0.06971 PGS AUROC (no covariates): 0.68243 [0.66936, 0.69549]	age, sex, UKB array type, Genotype PCs	Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008597	PGS001181 (GBE_HC643)	PSS004558\| South Asian Ancestry\| 7,831 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: TTE other hypothyroidism	—	AUROC: 0.74011 [0.72045, 0.75977]	R²: 0.1348 Incremental AUROC (full-covars): 0.03883 PGS R2 (no covariates): 0.04904 PGS AUROC (no covariates): 0.6475 [0.62543, 0.66957]	age, sex, UKB array type, Genotype PCs	Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008598	PGS001181 (GBE_HC643)	PSS004559\| European Ancestry\| 67,425 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: TTE other hypothyroidism	—	AUROC: 0.76691 [0.7602, 0.77362]	R²: 0.15134 Incremental AUROC (full-covars): 0.0729 PGS R2 (no covariates): 0.07419 PGS AUROC (no covariates): 0.68962 [0.68178, 0.69747]	age, sex, UKB array type, Genotype PCs	Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009430	PGS001816 (portability-PLR_244)	PSS008614\| European Ancestry\| 6,601 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.1003 [0.0763, 0.1241]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009428	PGS001816 (portability-PLR_244)	PSS009286\| European Ancestry\| 19,852 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.1192 [0.1054, 0.1329]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009429	PGS001816 (portability-PLR_244)	PSS009060\| European Ancestry\| 4,100 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.1349 [0.1047, 0.1649]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009431	PGS001816 (portability-PLR_244)	PSS008390\| Greater Middle Eastern Ancestry\| 1,186 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.1247 [0.0677, 0.1808]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009432	PGS001816 (portability-PLR_244)	PSS008168\| South Asian Ancestry\| 6,272 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.11 [0.0854, 0.1344]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009433	PGS001816 (portability-PLR_244)	PSS007955\| East Asian Ancestry\| 1,782 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.044 [-0.0027, 0.0905]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009434	PGS001816 (portability-PLR_244)	PSS007736\| African Ancestry\| 2,434 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.0033 [-0.0366, 0.0432]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009435	PGS001816 (portability-PLR_244)	PSS008839\| African Ancestry\| 3,876 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.0419 [0.0104, 0.0734]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011066	PGS002024 (portability-ldpred2_244)	PSS009286\| European Ancestry\| 19,852 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.122 [0.1083, 0.1357]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011067	PGS002024 (portability-ldpred2_244)	PSS009060\| European Ancestry\| 4,100 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.143 [0.1128, 0.1729]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011068	PGS002024 (portability-ldpred2_244)	PSS008614\| European Ancestry\| 6,601 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.1035 [0.0795, 0.1273]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011069	PGS002024 (portability-ldpred2_244)	PSS008390\| Greater Middle Eastern Ancestry\| 1,186 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.133 [0.0762, 0.189]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011070	PGS002024 (portability-ldpred2_244)	PSS008168\| South Asian Ancestry\| 6,272 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.1186 [0.094, 0.1429]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011071	PGS002024 (portability-ldpred2_244)	PSS007955\| East Asian Ancestry\| 1,782 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.047	sex, age, birth date, deprivation index, 16 PCs	—
PPM011072	PGS002024 (portability-ldpred2_244)	PSS007736\| African Ancestry\| 2,434 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.0093 [-0.0306, 0.0492]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011073	PGS002024 (portability-ldpred2_244)	PSS008839\| African Ancestry\| 3,876 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	—	—	Partial Correlation (partial-r): 0.0396 [0.0081, 0.0711]	sex, age, birth date, deprivation index, 16 PCs	—
PPM013101	PGS002336 (disease_HYPOTHYROIDISM_SELF_REP.BOLT-LMM)	PSS009787\| African Ancestry\| 6,503 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0045	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013150	PGS002336 (disease_HYPOTHYROIDISM_SELF_REP.BOLT-LMM)	PSS009788\| East Asian Ancestry\| 922 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0111	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013248	PGS002336 (disease_HYPOTHYROIDISM_SELF_REP.BOLT-LMM)	PSS009790\| South Asian Ancestry\| 8,098 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0173	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013199	PGS002336 (disease_HYPOTHYROIDISM_SELF_REP.BOLT-LMM)	PSS009789\| European Ancestry\| 43,505 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0247	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013389	PGS002408 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.0001)	PSS009787\| African Ancestry\| 6,503 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0002	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013438	PGS002408 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.0001)	PSS009788\| East Asian Ancestry\| 922 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013487	PGS002408 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.0001)	PSS009789\| European Ancestry\| 43,505 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0003	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013536	PGS002408 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.0001)	PSS009790\| South Asian Ancestry\| 8,098 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013585	PGS002457 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.001)	PSS009787\| African Ancestry\| 6,503 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0001	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013634	PGS002457 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.001)	PSS009788\| East Asian Ancestry\| 922 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013683	PGS002457 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.001)	PSS009789\| European Ancestry\| 43,505 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0001	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013732	PGS002457 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.001)	PSS009790\| South Asian Ancestry\| 8,098 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013781	PGS002506 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.01)	PSS009787\| African Ancestry\| 6,503 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0001	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013830	PGS002506 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.01)	PSS009788\| East Asian Ancestry\| 922 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013879	PGS002506 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.01)	PSS009789\| European Ancestry\| 43,505 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0002	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013928	PGS002506 (disease_HYPOTHYROIDISM_SELF_REP.P+T.0.01)	PSS009790\| South Asian Ancestry\| 8,098 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014026	PGS002555 (disease_HYPOTHYROIDISM_SELF_REP.P+T.1e-06)	PSS009788\| East Asian Ancestry\| 922 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.001	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014075	PGS002555 (disease_HYPOTHYROIDISM_SELF_REP.P+T.1e-06)	PSS009789\| European Ancestry\| 43,505 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0012	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014124	PGS002555 (disease_HYPOTHYROIDISM_SELF_REP.P+T.1e-06)	PSS009790\| South Asian Ancestry\| 8,098 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0001	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013977	PGS002555 (disease_HYPOTHYROIDISM_SELF_REP.P+T.1e-06)	PSS009787\| African Ancestry\| 6,503 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014173	PGS002604 (disease_HYPOTHYROIDISM_SELF_REP.P+T.5e-08)	PSS009787\| African Ancestry\| 6,503 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014222	PGS002604 (disease_HYPOTHYROIDISM_SELF_REP.P+T.5e-08)	PSS009788\| East Asian Ancestry\| 922 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.001	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014271	PGS002604 (disease_HYPOTHYROIDISM_SELF_REP.P+T.5e-08)	PSS009789\| European Ancestry\| 43,505 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0015	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014320	PGS002604 (disease_HYPOTHYROIDISM_SELF_REP.P+T.5e-08)	PSS009790\| South Asian Ancestry\| 8,098 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0001	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014369	PGS002653 (disease_HYPOTHYROIDISM_SELF_REP.PolyFun-pred)	PSS009787\| African Ancestry\| 6,503 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0046	age, sex, age*sex, assessment center, genotyping array, 10 PCs	See disease_HYPOTHYROIDISM_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014418	PGS002653 (disease_HYPOTHYROIDISM_SELF_REP.PolyFun-pred)	PSS009788\| East Asian Ancestry\| 922 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0129	age, sex, age*sex, assessment center, genotyping array, 10 PCs	See disease_HYPOTHYROIDISM_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014467	PGS002653 (disease_HYPOTHYROIDISM_SELF_REP.PolyFun-pred)	PSS009789\| European Ancestry\| 43,505 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0262	age, sex, age*sex, assessment center, genotyping array, 10 PCs	See disease_HYPOTHYROIDISM_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014516	PGS002653 (disease_HYPOTHYROIDISM_SELF_REP.PolyFun-pred)	PSS009790\| South Asian Ancestry\| 8,098 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0183	age, sex, age*sex, assessment center, genotyping array, 10 PCs	See disease_HYPOTHYROIDISM_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014565	PGS002702 (disease_HYPOTHYROIDISM_SELF_REP.SBayesR)	PSS009787\| African Ancestry\| 6,503 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0043	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014614	PGS002702 (disease_HYPOTHYROIDISM_SELF_REP.SBayesR)	PSS009788\| East Asian Ancestry\| 922 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0117	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014663	PGS002702 (disease_HYPOTHYROIDISM_SELF_REP.SBayesR)	PSS009789\| European Ancestry\| 43,505 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0206	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014712	PGS002702 (disease_HYPOTHYROIDISM_SELF_REP.SBayesR)	PSS009790\| South Asian Ancestry\| 8,098 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (full model vs. covariates alone): 0.0139	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM014966	PGS002766 (Hypothyroidism_prscs)	PSS009939\| European Ancestry\| 39,444 individuals	PGP000364 \| Mars N et al. Am J Hum Genet (2022)	Reported Trait: Hypothyroidism	OR: 1.47 [1.43, 1.52]	—	—	age, sex, 10 PCs, technical covariates	—
PPM020561	PGS004446 (disease.E03.score)	PSS011364\| European Ancestry\| 56,192 individuals	PGP000561 \| Jung H et al. Commun Biol (2024)	Reported Trait: E03 (Other hypothyroidism)	OR: 1.47851	—	—	—	—
PPM020631	PGS004516 (meta.E03.score)	PSS011364\| European Ancestry\| 56,192 individuals	PGP000561 \| Jung H et al. Commun Biol (2024)	Reported Trait: E03 (Other hypothyroidism)	OR: 1.49623	—	—	—	—
PPM021014	PGS004789 (hypothyroid_PRSmix_eur)	PSS011465\| European Ancestry\| 9,462 individuals	PGP000604 \| Truong B et al. Cell Genom (2024)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (Full model versus model with only covariates): 0.041 [0.033, 0.049]	age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10	Incremental R2 (Full model versus model with only covariates)
PPM021015	PGS004790 (hypothyroid_PRSmixPlus_eur)	PSS011465\| European Ancestry\| 9,462 individuals	PGP000604 \| Truong B et al. Cell Genom (2024)	Reported Trait: Hypothyroidism	—	—	Incremental R2 (Full model versus model with only covariates): 0.042 [0.034, 0.05]	age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10	Incremental R2 (Full model versus model with only covariates)
PPM021723	PGS004935 (hypothyroidism_snpnet_combined)	PSS011762\| European Ancestry\| 8,417 individuals	PGP000665 \| Moreno-Grau S et al. Human Genomics (2024)	Reported Trait: Hypothyroidism	OR: 1.5 [1.41, 1.6]	AUROC: 0.7	—	—	—

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
PSS009286	—	—	19,852 individuals	—	European	UK (+ Ireland)	UKB	—
PSS008390	—	—	1,186 individuals	—	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iran (Middle East)	UKB	—
PSS004555	—	—	6,497 individuals [ 196 cases , 6,301 controls ]	—	African unspecified	—	UKB	—
PSS004556	—	—	1,704 individuals [ 61 cases , 1,643 controls ]	—	East Asian	—	UKB	—
PSS004557	—	—	24,905 individuals [ 1,684 cases , 23,221 controls ]	—	European	non-white British ancestry	UKB	—
PSS004558	—	—	7,831 individuals [ 653 cases , 7,178 controls ]	—	South Asian	—	UKB	—
PSS004559	—	—	67,425 individuals [ 4,577 cases , 62,848 controls ]	—	European	white British ancestry	UKB	Testing cohort (heldout set)
PSS011465	—	—	9,462 individuals	—	European	—	AllofUs	—
PSS009060	—	—	4,100 individuals	—	European	Poland (NE Europe)	UKB	—
PSS008168	—	—	6,272 individuals	—	South Asian	India (South Asia)	UKB	—
PSS009787	—	—	6,503 individuals	—	African unspecified	—	UKB	—
PSS009788	—	—	922 individuals	—	East Asian	—	UKB	—
PSS009789	—	—	43,505 individuals	—	European	Non-British European	UKB	—
PSS009790	—	—	8,098 individuals	—	South Asian	—	UKB	—
PSS008839	—	—	3,876 individuals	—	African unspecified	Nigeria (West Africa)	UKB	—
PSS000970	—	Median = 400.0 days	1,584 individuals	—	European	—	GNEHGI2020Q2	—
PSS004354	—	—	6,497 individuals [ 194 cases , 6,303 controls ]	—	African unspecified	—	UKB	—
PSS004355	—	—	1,704 individuals [ 53 cases , 1,651 controls ]	—	East Asian	—	UKB	—
PSS004356	—	—	24,905 individuals [ 1,582 cases , 23,323 controls ]	—	European	non-white British ancestry	UKB	—
PSS004357	—	—	7,831 individuals [ 624 cases , 7,207 controls ]	—	South Asian	—	UKB	—
PSS004358	—	—	67,425 individuals [ 4,298 cases , 63,127 controls ]	—	European	white British ancestry	UKB	Testing cohort (heldout set)
PSS007955	—	—	1,782 individuals	—	East Asian	China (East Asia)	UKB	—
PSS011762	—	—	8,417 individuals	—	European	—	BBofA	—
PSS011364	—	—	56,192 individuals	—	European	—	UKB	—
PSS009939	—	—	39,444 individuals	—	European (Finnish)	—	FinnGen	—
PSS008614	—	—	6,601 individuals	—	European	Italy (South Europe)	UKB	—
PSS007736	—	—	2,434 individuals	—	African American or Afro-Caribbean	Carribean	UKB	—
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	561 individuals [ 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	NR	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.	—	744 individuals [ 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)