PGS Publication: PGP000085

Publication Information (EuropePMC)
Title Assessing thyroid cancer risk using polygenic risk scores.
PubMed ID 32132206(Europe PMC)
doi 10.1073/pnas.1919976117
Publication Date March 4, 2020
Journal Proc Natl Acad Sci U S A
Author(s) Liyanarachchi S, Gudmundsson J, Ferkingstad E, He H, Jonasson JG, Tragante V, Asselbergs FW, Xu L, Kiemeney LA, Netea-Maier RT, Mayordomo JI, Plantinga TS, Hjartarson H, Hrafnkelsson J, Sturgis EM, Brock P, Nabhan F, Thorleifsson G, Ringel MD, Stefansson K, de la Chapelle A.
Released in PGS: July 1, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

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

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
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)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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