Polygenic Score (PGS) ID: PGS000794

Predicted Trait
Reported Trait Pancreatic cancer
Mapped Trait(s) pancreatic carcinoma (EFO_0002618)
Released in PGS Catalog: May 28, 2021
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Score Details

Score Construction
PGS Name CC_Pancreas_IV
Development Method
Name 22 variants from Graff et al (PGS000083) with inverse variant weights
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 22
Effect Weight Type Inverse-variance weighting
PGS Source
PGS Catalog Publication (PGP) ID PGP000186
Citation (link to publication) Kachuri L et al. Nat Commun (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 86.6%
Not Reported: 12.3%
Multi-ancestry (excluding European): 1.1%
  • Not Reported
  • Hispanic or Latin American
  • African
  • Additional Asian Ancestries
57,275 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 9 cohorts
  • IARC
  • ,JHH
  • ,MAYO
  • ,MDACCS
  • ,MSKCC
  • ,QIMR
  • ,Toronto
  • ,UCSF
  • ,Yale
GWAS Catalog: GCST005434
Europe PMC: 29422604
 21,536 individuals European PANSCAN
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: GCST003758
Europe PMC: 27579533
 13,952 individuals European 28 cohorts
  • AHS
  • ,ATBC
  • ,CLUEII
  • ,CPSII
  • ,DFCI-GCC
  • ,EPIC
  • ,HPFS
  • ,Iowa-Mayo
  • ,JHH
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MSKCC
  • ,NHS
  • ,NYU-WHS
  • ,PACIFIC
  • ,PANDoRA
  • ,PANKRAS-II
  • ,PHS
  • ,PLCO
  • ,SELECT
  • ,SMWHS
  • ,Toronto
  • ,UCSF
  • ,VITAL
  • ,WHI
  • ,WHS
  • ,Yale
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
PPM002065 PSS001022|
European Ancestry|
391,491 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident pancreatic cancer HR: 1.49 [1.37, 1.63] AUROC: 0.745
C-index: 0.743 (0.012)		 R²: 0.439 Age at assessment, sex, genotyping array, PCs(1-15), family history of cancer (prostate, breast, lung, bowel), body mass index, cigarette pack-years, smoking status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
PSS001022 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 493 cases
  • , 390,998 controls
]
 — European — UKB —