Polygenic Score (PGS) ID: PGS000159

Predicted Trait
Reported Trait Pancreatic cancer
Mapped Trait(s) pancreatic carcinoma (EFO_0002618)
Released in PGS: April 29, 2020

Score Details

Score Construction
PGS Name cGRS_Pancreatic
Variants
Original Genome Build NR
Number of Variants 9
Development Method
Name Pruning + Thresholding
Parameters GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2.
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002991
EuropePMC: 26098869
7,046 individuals NR
GWAS Catalog: GCST002991
EuropePMC: 26098869
636 individuals NR, Hispanic or Latin American, African unspecified, Asian unspecified
GWAS Catalog: GCST002991
EuropePMC: 26098869
7,320 individuals European
GWAS Catalog: GCST002553
EuropePMC: 25086665
6,785 individuals European
GWAS Catalog: GCST000574
EuropePMC: 20101243
126 individuals East Asian
GWAS Catalog: GCST000574
EuropePMC: 20101243
7,416 individuals European
GWAS Catalog: GCST000574
EuropePMC: 20101243
369 individuals Other

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)
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
PPM000479 PSS000279 PGP000075
Shi Z et al. (2019)
Reported Trait: Pancreatic cancer Mean realative risk: 1.13[1.07, 1.18]
Wilcoxon test (case vs. control) p-value: 0.000145
PPM000490 PSS000279 PGP000075
Shi Z et al. (2019)
Reported Trait: Pancreatic cancer Odds Ratio (OR; high vs. average risk groups): 1.67[1.1, 2.53]

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
PSS000279 Primary tumor samples from TCGA
[
  • 163 cases
  • , 0 controls
]
Mean = 66.0 years
Sd = 11.0 years
European TCGA
PSS000279
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE