Trait: hypothyroidism

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004705
Description Abnormally low levels of thyroid hormone. [NCIT: P378]
Trait category
Other disease
Synonyms 4 synonyms
  • hypothyroidism
  • thyroid deficiency
  • thyroid insufficiency
  • underactive thyroid
Mapped terms 11 mapped terms
  • DOID:1459
  • ICD10:E03
  • ICD9:244.9
  • MESH:D007037
  • MONDO:0005420
  • MeSH:D007037
  • MedDRA:10021114
  • NCIT:C26800
  • NCIt:C26800
  • SCTID:40930008
  • SNOMEDCT:40930008
Child trait(s) myxedema

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
Note: This table shows all PGS for "hypothyroidism" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution 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
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

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] : 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] : 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] : 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] : 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] : 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] : 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] : 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] : 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] : 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] : 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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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‚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

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
[
  • 196 cases
  • , 6,301 controls
]
African unspecified UKB
PSS004556
[
  • 61 cases
  • , 1,643 controls
]
East Asian UKB
PSS004557
[
  • 1,684 cases
  • , 23,221 controls
]
European non-white British ancestry UKB
PSS004558
[
  • 653 cases
  • , 7,178 controls
]
South Asian UKB
PSS004559
[
  • 4,577 cases
  • , 62,848 controls
]
European white British ancestry UKB Testing cohort (heldout set)
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
[
  • 194 cases
  • , 6,303 controls
]
African unspecified UKB
PSS004355
[
  • 53 cases
  • , 1,651 controls
]
East Asian UKB
PSS004356
[
  • 1,582 cases
  • , 23,323 controls
]
European non-white British ancestry UKB
PSS004357
[
  • 624 cases
  • , 7,207 controls
]
South Asian UKB
PSS004358
[
  • 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
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
[
  • 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.
[
  • 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)