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 Catalog: July 1, 2020

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:
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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

PGS Developed By This Publication

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

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
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
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