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
  • head and neck cancer, thyroid
  • thyroid carcinoma
  • carcinoma of the thyroid gland
  • Thyroid Gland Carcinoma
  • cancer of thyroid
  • carcinoma of the thyroid
  • thyroid gland carcinoma
  • carcinoma of thyroid gland
  • carcinoma of thyroid
  • thyroid cancer
  • cancer of the thyroid
  • thyroid gland cancer
Mapped term(s) 10 mapped terms
  • NCIt:C4815
  • DOID:3963
  • HP:0002890
  • Orphanet:100088
  • EFO:1000586
  • UMLS:C0549473
  • ICD10:C73
  • SCTID:448216007
  • NCIT:C4815
  • MedDRA:10007476

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants 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

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000207 PGS000087 (CC_Thyroid) PSS000126 PGP000050
Graff RE et al. (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
PPM000482 PGS000162 (cGRS_Thyroid) PSS000282 PGP000075
Shi Z et al. (2019)
Reported Trait: Thyroid cancer Mean realative risk: 1.09[1.04, 1.15]
Wilcoxon test (case vs. control) p-value: 4e-05
PPM000493 PGS000162 (cGRS_Thyroid) PSS000282 PGP000075
Shi Z et al. (2019)
Reported Trait: Thyroid cancer Odds Ratio (OR; high vs. average risk groups): 1.7[1.29, 2.25]
PPM000633 PGS000209 (TC10_UKB) PSS000343 PGP000085
Liyanarachchi S et al. (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 PGP000085
Liyanarachchi S et al. (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 PGP000085
Liyanarachchi S et al. (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 ID)
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
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