PGS Publication: PGP000251

Publication Information (EuropePMC)
Title Polygenic Risk Score Improves Risk Stratification and Prediction of Subsequent Thyroid Cancer after Childhood Cancer.
PubMed ID 34465587(Europe PMC)
doi 10.1158/1055-9965.epi-21-0448
Publication Date Aug. 31, 2021
Journal Cancer Epidemiol Biomarkers Prev
Author(s) Song N, Liu Q, Wilson CL, Sapkota Y, Ehrhardt MJ, Gibson TM, Morton LM, Chanock SJ, Neglia JP, Arnold MA, Michael JR, Gout AM, Mulder HL, Easton J, Bhatia S, Armstrong GT, Zhang J, Delaney A, Hudson MM, Robison LL, Yasui Y, Wang Z.
Released in PGS Catalog: Nov. 4, 2021

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Additional Asian Ancestries
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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 Scoring File (FTP Link)
PGS001354
(PRS12_TC)
PGP000251 |
Song N et al. Cancer Epidemiol Biomarkers Prev (2021)
Thyroid cancer thyroid carcinoma 12
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001354/ScoringFiles/PGS001354.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
PPM005178 PGS001354
(PRS12_TC)
PSS003603|
European Ancestry|
2,370 individuals
PGP000251 |
Song N et al. Cancer Epidemiol Biomarkers Prev (2021)
Reported Trait: Subsequent thyroid cancer in childhood cancer survivors Relative Rate (RR): 1.57 [1.24, 1.98] Attained age modeled by restricted cubic splines
PPM005179 PGS001354
(PRS12_TC)
PSS003603|
European Ancestry|
2,370 individuals
PGP000251 |
Song N et al. Cancer Epidemiol Biomarkers Prev (2021)
Reported Trait: Subsequent thyroid cancer in childhood cancer survivors who had received neck radiotherapy Relative Rate (RR): 1.68 [1.29, 2.18] Attained age modeled by restricted cubic splines
PPM005180 PGS001354
(PRS12_TC)
PSS003602|
European Ancestry|
6,416 individuals
PGP000251 |
Song N et al. Cancer Epidemiol Biomarkers Prev (2021)
Reported Trait: Subsequent thyroid cancer in childhood cancer survivors Relative Rate (RR): 1.52 [1.25, 1.83] Attained age modeled by restricted cubic splines
PPM005181 PGS001354
(PRS12_TC)
PSS003602|
European Ancestry|
6,416 individuals
PGP000251 |
Song N et al. Cancer Epidemiol Biomarkers Prev (2021)
Reported Trait: Subsequent thyroid cancer in childhood cancer survivors who had received neck radiotherapy Relative Rate (RR): 1.42 [1.09, 1.85] Attained age modeled by restricted cubic splines
PPM005182 PGS001354
(PRS12_TC)
PSS003602|
European Ancestry|
6,416 individuals
PGP000251 |
Song N et al. Cancer Epidemiol Biomarkers Prev (2021)
Reported Trait: Subsequent thyroid cancer in childhood cancer survivors who had not received neck radiotherapy Relative Rate (RR): 1.66 [1.26, 2.2] Attained age modeled by restricted cubic splines
PPM005183 PGS001354
(PRS12_TC)
PSS003603|
European Ancestry|
2,370 individuals
PGP000251 |
Song N et al. Cancer Epidemiol Biomarkers Prev (2021)
Reported Trait: Subsequent thyroid cancer in childhood cancer survivors aged 40 AUROC: 0.83
C-index: 0.842
Clincial model (age at diagnosis, attained age modeled by restricted cubic splines, sex, combined treatment group)
PPM005184 PGS001354
(PRS12_TC)
PSS003602|
European Ancestry|
6,416 individuals
PGP000251 |
Song N et al. Cancer Epidemiol Biomarkers Prev (2021)
Reported Trait: Subsequent thyroid cancer in childhood cancer survivors aged 40 AUROC: 0.73
C-index: 0.73
Clincial model (age at diagnosis, attained age modeled by restricted cubic splines, sex, combined treatment group)
PPM005185 PGS001354
(PRS12_TC)
PSS003603|
European Ancestry|
2,370 individuals
PGP000251 |
Song N et al. Cancer Epidemiol Biomarkers Prev (2021)
Reported Trait: Subsequent thyroid cancer in childhood cancer survivors aged 50 AUROC: 0.82
C-index: 0.834
Clincial model (age at diagnosis, attained age modeled by restricted cubic splines, sex, combined treatment group)
PPM005186 PGS001354
(PRS12_TC)
PSS003602|
European Ancestry|
6,416 individuals
PGP000251 |
Song N et al. Cancer Epidemiol Biomarkers Prev (2021)
Reported Trait: Subsequent thyroid cancer in childhood cancer survivors aged 50 AUROC: 0.72
C-index: 0.727
Clincial model (age at diagnosis, attained age modeled by restricted cubic splines, sex, combined treatment group)

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
PSS003602 All individuals were childhood cancer survivors. Of the 6,414 childhood cancer survivors, 1,374 had received neck radiotherapy (neck-RT) as a form of treatment. Cases were individuals who developed subsequent thyroid cancer (STC). Cases of STC were ascertained by self-report questionnaires and subsequently confirmed by pathology reports. 73 of the 121 STC cases had received neck-RT as a form of childhood cancer treatment, whilst 48 had not. Of the controls, 1,301 had received neck-RT as a form of childhood cancer treatment. Median = 36.5 years
[
  • 121 cases
  • , 6,295 controls
]
,
47.7 % Male samples
European NR
PSS003603 All individuals were childhood cancer survivors. Of the 2,370 childhood cancer survivors, 476 had received neck radiotherapy (neck-RT) as a form of treatment. Cases were individuals who developed subsequent thyroid cancer (STC). Cases of STC were clinically ascertained. 47 of the 65 STC cases had received neck-RT as a form of childhood cancer treatment, whilst 18 had not. Median = 36.6 years
IQR = [30.3, 44.1] years
[
  • 65 cases
  • , 2,305 controls
]
,
53.4 % Male samples
European SJCRH