PGS Publication: PGP000293

Publication Information (EuropePMC)
Title Predicting Pancreatic Cancer in the UK Biobank Cohort Using Polygenic Risk Scores and Diabetes Mellitus.
PubMed ID 35065983(Europe PMC)
doi 10.1053/j.gastro.2022.01.016
Publication Date Jan. 21, 2022
Journal Gastroenterology
Author(s) Sharma S, Tapper WJ, Collins A, Hamady ZZR.
Released in PGS Catalog: March 16, 2022

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
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 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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS002264
(PRS_Combined)
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Pancreatic ductal adenocarcinoma pancreatic ductal adenocarcinoma 49
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002264/ScoringFiles/PGS002264.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
PPM012888 PGS002264
(PRS_Combined)
 PSS009595|
Ancestry Not Reported|
11,462 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma — AUROC: 0.605 [0.587, 0.623] Positive predictive values (PPV highest quintile): 14.4 [13, 15.9] — —
PPM012894 PGS002264
(PRS_Combined)
 PSS009600|
Ancestry Not Reported|
206 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma (with long-standing diabetes mellitus) — — Positive predictive values (PPV highest quintile): 0.239 [0.181, 0.303] — —
PPM012892 PGS002264
(PRS_Combined)
 PSS009598|
Ancestry Not Reported|
10,259 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma (without diabetes mellitus) — AUROC: 0.594 [0.573, 0.614] Positive predictive values (PPV highest quintile): 0.119 [0.105, 0.134] — —
PPM012895 PGS002264
(PRS_Combined)
 PSS009600|
Ancestry Not Reported|
206 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma (with long-standing diabetes mellitus) OR: 1.873 [1.53, 2.292] — — principal components (PC 1-10) —
PPM012896 PGS002264
(PRS_Combined)
 PSS009601|
Ancestry Not Reported|
998 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma (with new onset diabetes mellitus) — — Positive predictive values (PPV highest quintile): 0.867 [0.732, 0.949] — —
PPM012897 PGS002264
(PRS_Combined)
 PSS009601|
Ancestry Not Reported|
998 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma (with new onset diabetes mellitus) OR: 1.885 [1.279, 2.778] — — principal components (PC 1-10) —
PPM012898 PGS002264
(PRS_Combined)
 PSS009596|
Ancestry Not Reported|
1,203 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma (with diabetes mellitus) OR: 1.674 [1.443, 1.942] — — principal components (PC 1-10) —
PPM012899 PGS002264
(PRS_Combined)
 PSS009596|
Ancestry Not Reported|
1,203 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma (with diabetes mellitus) — AUROC: 0.645 — — —
PPM012900 PGS002264
(PRS_Combined)
 PSS009597|
Ancestry Not Reported|
242 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma (< 60 years) OR: 1.633 [1.292, 2.064] — — principal components (PC 1-10) —
PPM012901 PGS002264
(PRS_Combined)
 PSS009599|
Ancestry Not Reported|
274 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma (60 years) OR: 1.538 [1.287, 1.837] — — principal components (PC 1-10) —
PPM012893 PGS002264
(PRS_Combined)
 PSS009598|
Ancestry Not Reported|
10,259 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma (without diabetes mellitus) OR: 1.386 [1.288, 1.492] — — principal components (PC 1-10) —
PPM012889 PGS002264
(PRS_Combined)
 PSS009595|
Ancestry Not Reported|
11,462 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma — — HR (highest vs lowest quintile): 2.738 [2.227, 3.365] Smoking (never, current and previous), waist circumference (cm), DM onset (No DM, NODM, LSDM) and first-degree family history of digestive cancer (yes/no) —
PPM012890 PGS002264
(PRS_Combined)
 PSS009595|
Ancestry Not Reported|
11,462 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma — AUROC: 0.83 [0.8, 0.86] — Age of participants at recruitment, age when DM diagnosed, DM onset (No DM, NODM, LSDM), waist circumference (cm), and first-degree family history of digestive cancer (yes/no)., clinical risk —
PPM012891 PGS002264
(PRS_Combined)
 PSS009595|
Ancestry Not Reported|
11,462 individuals
 PGP000293 |
Sharma S et al. Gastroenterology (2022)
 Reported Trait: Incident pancreatic ductal adenocarcinoma OR: 1.43 — — principal components (PC 1-10) —

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
PSS009595 PDAC cases were considered incident if diagnosed after study entry or without a date of diagnosis if identified by mortality alone. Median = 109.0 months
[
  • 1,042 cases
  • , 10,420 controls
]
,
52.0 % Male samples
 Mean = 61.3 years Not reported European, African American or Afro-Caribbean, South Asian, East Asian, African unspecified UKB —
PSS009596 PDAC cases were considered incident if diagnosed after study entry or without a date of diagnosis if identified by mortality alone. —
[
  • 251 cases
  • , 952 controls
]
 — Not reported European, African American or Afro-Caribbean, South Asian, East Asian, African unspecified UKB —
PSS009597 PDAC cases were considered incident if diagnosed after study entry or without a date of diagnosis if identified by mortality alone. —
[
  • 37 cases
  • , 205 controls
]
 Not reported European, African American or Afro-Caribbean, South Asian, East Asian, African unspecified UKB —
PSS009598 PDAC cases were considered incident if diagnosed after study entry or without a date of diagnosis if identified by mortality alone. —
[
  • 791 cases
  • , 9,468 controls
]
 — Not reported European, African American or Afro-Caribbean, South Asian, East Asian, African unspecified UKB —
PSS009599 PDAC cases were considered incident if diagnosed after study entry or without a date of diagnosis if identified by mortality alone. —
[
  • 55 cases
  • , 219 controls
]
 Not reported European, African American or Afro-Caribbean, South Asian, East Asian, African unspecified UKB —
PSS009600 PDAC cases were considered incident if diagnosed after study entry or without a date of diagnosis if identified by mortality alone. LSDM is defined in cases as type 2 diabetes diagnosed more than 24 months before PDAC diagnosis. Defined in controls as type 2 diabetes diagnosed more than 24 months before date of death or date of last follow up. —
[
  • 135 cases
  • , 70 controls
]
 — Not reported European, African American or Afro-Caribbean, South Asian, East Asian, African unspecified UKB —
PSS009601 PDAC cases were considered incident if diagnosed after study entry or without a date of diagnosis if identified by mortality alone. NODM is defined in cases as type 2 diabetes diagnosed within 24 months before or after diagnosis of PDAC. Defined in controls as type 2 diabetes diagnosed 24 months before death or last follow up. —
[
  • 116 cases
  • , 882 controls
]
 — Not reported European, African American or Afro-Caribbean, South Asian, East Asian, African unspecified UKB —