Polygenic Score (PGS) ID: PGS000159

Predicted Trait
Reported Trait Pancreatic cancer
Mapped Trait(s) pancreatic carcinoma (EFO_0002618)
Released in PGS Catalog: April 29, 2020
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Terms and Licenses
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Score Details

Score Construction
PGS Name cGRS_Pancreatic
Development Method
Name Pruning and Thresholding (P+T)
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.
Variants
Original Genome Build NR
Number of Variants 9
Effect Weight Type Odds Ratio over expected risk
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 72.5%
Not Reported: 23.7%
Multi-ancestry (excluding European): 2.1%
  • Not Reported
  • Hispanic or Latin American
  • African
  • Additional Asian Ancestries
Additional Diverse Ancestries: 1.2%
East Asian: 0.4%
29,698 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002991
Europe PMC: 26098869
 636 individuals NR, Hispanic or Latin American, African unspecified, Asian unspecified NR
GWAS Catalog: GCST000574
Europe PMC: 20101243
 126 individuals East Asian NR
GWAS Catalog: GCST000574
Europe PMC: 20101243
 7,416 individuals European NR
GWAS Catalog: GCST000574
Europe PMC: 20101243
 369 individuals Other NR
GWAS Catalog: GCST002553
Europe PMC: 25086665
 6,785 individuals European 16 cohorts
  • AHS
  • ,ATBC
  • ,CPSII
  • ,DFCI-GCC
  • ,EPIC
  • ,HPFS
  • ,MCCS
  • ,MEC
  • ,NHS
  • ,PANDoRA
  • ,PANKRAS-II
  • ,PHS
  • ,PLCO
  • ,SELECT
  • ,VITAL
  • ,WHI
GWAS Catalog: GCST002991
Europe PMC: 26098869
 7,046 individuals NR 9 cohorts
  • IARC
  • ,JHH
  • ,MAYO
  • ,MDACCS
  • ,MSKCC
  • ,QIMR
  • ,Toronto
  • ,UCSF
  • ,Yale
GWAS Catalog: GCST002991
Europe PMC: 26098869
 7,320 individuals European 9 cohorts
  • IARC
  • ,JHH
  • ,MAYO
  • ,MDACCS
  • ,MSKCC
  • ,QIMR
  • ,Toronto
  • ,UCSF
  • ,Yale

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) 		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
PPM000490 PSS000279|
European Ancestry|
13,590 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Pancreatic cancer — — Odds Ratio (OR; high vs. average risk groups): 1.67 [1.1, 2.53] — —
PPM000479 PSS000279|
European Ancestry|
13,590 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Pancreatic cancer — — Mean realative risk: 1.13 [1.07, 1.18]
Wilcoxon test (case vs. control) p-value: 0.00015		 — —

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
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 —