Trait: thyroid carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0002892
Description A carcinoma arising from the thyroid gland. It is usually an adenocarcinoma and includes the following main subtypes: follicular, papillary, medullary, poorly differentiated, and anaplastic. [NCIT: C4815]
Trait category
Cancer
Synonyms 12 synonyms
  • Thyroid Gland Carcinoma
  • cancer of the thyroid
  • cancer of thyroid
  • carcinoma of the thyroid
  • carcinoma of the thyroid gland
  • carcinoma of thyroid
  • carcinoma of thyroid gland
  • head and neck cancer, thyroid
  • thyroid cancer
  • thyroid carcinoma
  • thyroid gland cancer
  • thyroid gland carcinoma
Mapped term(s) 10 mapped terms
  • DOID:3963
  • EFO:1000586
  • HP:0002890
  • ICD10:C73
  • MedDRA:10007476
  • NCIT:C4815
  • NCIt:C4815
  • Orphanet:100088
  • SCTID:448216007
  • UMLS:C0549473

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 PGS Scoring File (FTP Link)
PGS000087
(CC_Thyroid)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Thyroid cancer thyroid carcinoma 12
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000087/ScoringFiles/PGS000087.txt.gz
PGS000162
(cGRS_Thyroid)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Thyroid cancer thyroid carcinoma 6
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000162/ScoringFiles/PGS000162.txt.gz
PGS000207
(TC10_Ohio)
PGP000085 |
Liyanarachchi S et al. Proc Natl Acad Sci U S A (2020)
Thyroid cancer thyroid carcinoma 10
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000207/ScoringFiles/PGS000207.txt.gz
PGS000208
(TC10_Iceland)
PGP000085 |
Liyanarachchi S et al. Proc Natl Acad Sci U S A (2020)
Thyroid cancer thyroid carcinoma 10
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000208/ScoringFiles/PGS000208.txt.gz
PGS000209
(TC10_UKB)
PGP000085 |
Liyanarachchi S et al. Proc Natl Acad Sci U S A (2020)
Thyroid cancer thyroid carcinoma 10
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000209/ScoringFiles/PGS000209.txt.gz
PGS000626
(PRSWEB_PHECODE193_20001-1065_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 8
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000626/ScoringFiles/PGS000626.txt.gz
PGS000627
(PRSWEB_PHECODE193_C3-THYROID-GLAND_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 11
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000627/ScoringFiles/PGS000627.txt.gz
PGS000628
(PRSWEB_PHECODE193_C3-THYROID-GLAND_LASSOSUM_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 656
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000628/ScoringFiles/PGS000628.txt.gz
PGS000629
(PRSWEB_PHECODE193_C73_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 8
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000629/ScoringFiles/PGS000629.txt.gz
PGS000630
(PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_P_5e-08_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 10
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000630/ScoringFiles/PGS000630.txt.gz
PGS000631
(PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_P_5e-08_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 10
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000631/ScoringFiles/PGS000631.txt.gz
PGS000632
(PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 8
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000632/ScoringFiles/PGS000632.txt.gz
PGS000633
(PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_PT_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 5
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000633/ScoringFiles/PGS000633.txt.gz
PGS000634
(PRSWEB_PHECODE193_UKBB-SAIGE-HRC-X193_PRS-CS_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 1,119,238
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000634/ScoringFiles/PGS000634.txt.gz
PGS000635
(PRSWEB_PHECODE193_UKBB-SAIGE-HRC-X193_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 5
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000635/ScoringFiles/PGS000635.txt.gz
PGS000636
(PRSWEB_PHECODE193_UKBB-SAIGE-HRC-X193_LASSOSUM_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Thyroid cancer thyroid carcinoma 954
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000636/ScoringFiles/PGS000636.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
PPM000207 PGS000087
(CC_Thyroid)
PSS000126|
European Ancestry|
411,118 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Thyroid cancer OR: 1.55 [1.44, 1.67] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000493 PGS000162
(cGRS_Thyroid)
PSS000282|
European Ancestry|
13,814 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Thyroid cancer Odds Ratio (OR; high vs. average risk groups): 1.7 [1.29, 2.25]
PPM000482 PGS000162
(cGRS_Thyroid)
PSS000282|
European Ancestry|
13,814 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Thyroid cancer Mean realative risk: 1.09 [1.04, 1.15]
Wilcoxon test (case vs. control) p-value: 4e-05
PPM001314 PGS000629
(PRSWEB_PHECODE193_C73_PT_MGI_20200608)
PSS000558|
European Ancestry|
4,270 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer β: 0.114 (0.0517)
OR: 1.121 [1.013, 1.24]
AUROC: 0.52 [0.488, 0.55] Nagelkerke's Pseudo-R²: 0.00247
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 2.15 [1.01, 4.59]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_C73_PT_MGI_20200608
PPM001317 PGS000632
(PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_PT_MGI_20200608)
PSS000558|
European Ancestry|
4,270 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer OR: 1.568 [1.412, 1.74]
β: 0.45 (0.0532)
AUROC: 0.618 [0.587, 0.647] Nagelkerke's Pseudo-R²: 0.0365
Brier score: 0.0812
Odds Ratio (OR, top 1% vs. Rest): 5.14 [2.94, 8.99]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_PT_MGI_20200608
PPM001320 PGS000635
(PRSWEB_PHECODE193_UKBB-SAIGE-HRC-X193_PT_MGI_20200608)
PSS000558|
European Ancestry|
4,270 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer OR: 1.315 [1.194, 1.448]
β: 0.274 (0.0492)
AUROC: 0.569 [0.538, 0.598] Nagelkerke's Pseudo-R²: 0.0151
Brier score: 0.0822
Odds Ratio (OR, top 1% vs. Rest): 1.65 [0.708, 3.83]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_UKBB-SAIGE-HRC-X193_PT_MGI_20200608
PPM001311 PGS000626
(PRSWEB_PHECODE193_20001-1065_PT_MGI_20200608)
PSS000558|
European Ancestry|
4,270 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer OR: 1.161 [1.048, 1.285]
β: 0.149 (0.052)
AUROC: 0.529 [0.496, 0.559] Nagelkerke's Pseudo-R²: 0.0041
Brier score: 0.0826
Odds Ratio (OR, top 1% vs. Rest): 2.44 [1.18, 5.02]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_20001-1065_PT_MGI_20200608
PPM001312 PGS000627
(PRSWEB_PHECODE193_C3-THYROID-GLAND_PT_MGI_20200608)
PSS000558|
European Ancestry|
4,270 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer OR: 1.27 [1.148, 1.405]
β: 0.239 (0.0515)
AUROC: 0.56 [0.53, 0.59] Nagelkerke's Pseudo-R²: 0.0107
Brier score: 0.0824
Odds Ratio (OR, top 1% vs. Rest): 2.42 [1.17, 4.98]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_C3-THYROID-GLAND_PT_MGI_20200608
PPM001313 PGS000628
(PRSWEB_PHECODE193_C3-THYROID-GLAND_LASSOSUM_MGI_20200608)
PSS000558|
European Ancestry|
4,270 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer OR: 1.276 [1.155, 1.41]
β: 0.244 (0.0509)
AUROC: 0.565 [0.535, 0.595] Nagelkerke's Pseudo-R²: 0.0114
Brier score: 0.0823
Odds Ratio (OR, top 1% vs. Rest): 1.91 [0.861, 4.22]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_C3-THYROID-GLAND_LASSOSUM_MGI_20200608
PPM001315 PGS000630
(PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_P_5e-08_MGI_20200608)
PSS000558|
European Ancestry|
4,270 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer OR: 1.598 [1.439, 1.775]
β: 0.469 (0.0536)
AUROC: 0.626 [0.597, 0.655] Nagelkerke's Pseudo-R²: 0.0393
Brier score: 0.0811
Odds Ratio (OR, top 1% vs. Rest): 3.53 [1.87, 6.66]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_P_5e-08_MGI_20200608
PPM001316 PGS000631
(PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_P_5e-08_UKB_20200608)
PSS000579|
European Ancestry|
1,778 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer OR: 1.651 [1.41, 1.934]
β: 0.501 (0.0806)
AUROC: 0.636 [0.589, 0.682] Nagelkerke's Pseudo-R²: 0.0478
Brier score: 0.0803
Odds Ratio (OR, top 1% vs. Rest): 4.4 [1.81, 10.7]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_P_5e-08_UKB_20200608
PPM001318 PGS000633
(PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_PT_UKB_20200608)
PSS000579|
European Ancestry|
1,778 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer OR: 1.609 [1.38, 1.876]
β: 0.476 (0.0783)
AUROC: 0.628 [0.582, 0.675] Nagelkerke's Pseudo-R²: 0.0447
Brier score: 0.0804
Odds Ratio (OR, top 1% vs. Rest): 4.41 [1.81, 10.7]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_PT_UKB_20200608
PPM001319 PGS000634
(PRSWEB_PHECODE193_UKBB-SAIGE-HRC-X193_PRS-CS_MGI_20200608)
PSS000558|
European Ancestry|
4,270 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer OR: 1.119 [1.008, 1.241]
β: 0.112 (0.053)
AUROC: 0.535 [0.504, 0.567] Nagelkerke's Pseudo-R²: 0.00228
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 1.39 [0.562, 3.45]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_UKBB-SAIGE-HRC-X193_PRS-CS_MGI_20200608
PPM001321 PGS000636
(PRSWEB_PHECODE193_UKBB-SAIGE-HRC-X193_LASSOSUM_MGI_20200608)
PSS000558|
European Ancestry|
4,270 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Thyroid cancer OR: 1.385 [1.254, 1.529]
β: 0.325 (0.0507)
AUROC: 0.578 [0.548, 0.607] Nagelkerke's Pseudo-R²: 0.0205
Brier score: 0.0819
Odds Ratio (OR, top 1% vs. Rest): 3.21 [1.67, 6.15]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_UKBB-SAIGE-HRC-X193_LASSOSUM_MGI_20200608
PPM000633 PGS000209
(TC10_UKB)
PSS000343|
European Ancestry|
408,479 individuals
PGP000085 |
Liyanarachchi S et al. Proc Natl Acad Sci U S A (2020)
Reported Trait: Thyroid cancer AUROC: 0.694 [0.673, 0.716] gender, birth year AUROC (Clinical factors alone) = 0.629 [0.606 - 0.651]
PPM000632 PGS000208
(TC10_Iceland)
PSS000341|
European Ancestry|
130,279 individuals
PGP000085 |
Liyanarachchi S et al. Proc Natl Acad Sci U S A (2020)
Reported Trait: Thyroid cancer AUROC: 0.751 [0.736, 0.768] gender, birth year, family history of disease (1st or 2nd degree relative) AUROC (Clinical factors alone) = 0.697 [0.680 - 0.714]
PPM000631 PGS000207
(TC10_Ohio)
PSS000342|
European Ancestry|
3,137 individuals
PGP000085 |
Liyanarachchi S et al. Proc Natl Acad Sci U S A (2020)
Reported Trait: Thyroid cancer AUROC: 0.692 [0.673, 0.71] gender, birth year, family history of disease (1st or 2nd degree relative) AUROC (Clinical factors alone) = 0.585 [0.565 - 0.605]

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
PSS000282 Primary tumor samples from TCGA
[
  • 387 cases
  • , 0 controls
]
Mean = 49.0 years
Sd = 16.0 years
European TCGA
PSS000282
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE
PSS000558 PheCode:193; ICD9CM:193, V10.87; ICD10CM:C73
[
  • 389 cases
  • , 3,881 controls
]
European MGI
PSS000126 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 32010
[
  • 764 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000341 Cases were ascertained using ICD-10 C73 (PTC, FTC, cancer/carcinoma, and rare nonmedullary)
[
  • 723 cases
  • , 129,556 controls
]
,
46.41 % Male samples
European deCODE
PSS000342 Histologically confirmed papillary or follicular thyroid carcinoma (PTC) patients (including traditional PTC and follicular variant PTC)
[
  • 1,544 cases
  • , 1,593 controls
]
,
26.08 % Male samples
European
PSS000343 Cases were ascertained using ICD-10 C73 (PTC, FTC, cancer/carcinoma, and rare nonmedullary)
[
  • 534 cases
  • , 407,945 controls
]
,
45.97 % Male samples
European UKB
PSS000579 PheCode:193; ICD9:193; ICD10:C73
[
  • 161 cases
  • , 1,617 controls
]
European UKB