Polygenic Score (PGS) ID: PGS000083

Predicted Trait
Reported Trait Pancreatic cancer
Mapped Trait(s) pancreatic carcinoma (EFO_0002618)
Released in PGS Catalog: Feb. 12, 2020
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name CC_Pancreas
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 22
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
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%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
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
GWAS Catalog: GCST005434
Europe PMC: 29422604
 21,536 individuals European 28 cohorts
  • AHS
  • ,ATBC
  • ,CLUEII
  • ,CPSII
  • ,DFCI-GCC
  • ,EPIC
  • ,HPFS
  • ,IARC
  • ,JHH
  • ,MAYO
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MSKCC
  • ,NHS
  • ,NYU-WHS
  • ,PANDoRA
  • ,PANKRAS-II
  • ,PHS
  • ,PLCO
  • ,QIMR
  • ,SELECT
  • ,SMWHS
  • ,UCSF
  • ,VITAL
  • ,WHI
  • ,WHS
  • ,Yale
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
 636 individuals NR, Hispanic or Latin American, African unspecified, Asian unspecified NR

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
PPM000203 PSS000122|
European Ancestry|
411,019 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Reported Trait: Pancreatic cancer OR: 1.44 [1.33, 1.55] — — Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM002049 PSS001022|
European Ancestry|
391,491 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident pancreatic cancer HR: 1.49 [1.36, 1.62] AUROC: 0.745
C-index: 0.742 (0.012)		 — 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.
PPM017171 PSS010154|
European Ancestry|
451 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Pancreatic cancer HR: 1.51 [1.38, 1.66] — — age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates —

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
PSS000122 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 21100 —
[
  • 665 cases
  • , 410,354 controls
]
,
46.0 % Male samples
 Mean = 58.0 years European — GERA, UKB —
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 —
PSS010154 — —
[
  • 57 cases
  • , 394 controls
]
 — European — UKB —