| Experimental Factor Ontology (EFO) Information | |
| Identifier | EFO_1000218 |
| Description | A malignant neoplasm that arises from the epithelium of any part of the digestive system. Representative examples include colorectal carcinoma, esophageal carcinoma, and pancreatic carcinoma. [NCIT: C96963] | Trait categories |
Cancer
Digestive system disorder
|
| Synonyms |
6 synonyms
|
| Mapped terms |
6 mapped terms
|
| Child trait(s) | 6 child traits |
| Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS000083 (CC_Pancreas) |
PGP000050 | Graff RE et al. Nat Commun (2021) |
Pancreatic cancer | pancreatic carcinoma | 22 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000083/ScoringFiles/PGS000083.txt.gz |
| PGS000159 (cGRS_Pancreatic) |
PGP000075 | Shi Z et al. Cancer Med (2019) |
Pancreatic cancer | pancreatic carcinoma | 9 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000159/ScoringFiles/PGS000159.txt.gz |
| PGS000376 (PRSWEB_PHECODE153.2_C18_PRS-CS_MGI_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Colon cancer | colon carcinoma | 1,111,490 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000376/ScoringFiles/PGS000376.txt.gz | |
| PGS000377 (PRSWEB_PHECODE153.2_C18_LASSOSUM_MGI_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Colon cancer | colon carcinoma | 5,740,814 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000377/ScoringFiles/PGS000377.txt.gz | |
| PGS000378 (PRSWEB_PHECODE153.2_C3-COLON_PRS-CS_MGI_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Colon cancer | colon carcinoma | 1,111,399 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000378/ScoringFiles/PGS000378.txt.gz | |
| PGS000379 (PRSWEB_PHECODE153.2_C3-COLON_LASSOSUM_MGI_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Colon cancer | colon carcinoma | 5,715,093 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000379/ScoringFiles/PGS000379.txt.gz | |
| PGS000380 (PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PRS-CS_MGI_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Colon cancer | colon carcinoma | 1,119,238 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000380/ScoringFiles/PGS000380.txt.gz | |
| PGS000381 (PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PT_MGI_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Colon cancer | colon carcinoma | 12 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000381/ScoringFiles/PGS000381.txt.gz | |
| PGS000382 (PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_LASSOSUM_MGI_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Colon cancer | colon carcinoma | 150 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000382/ScoringFiles/PGS000382.txt.gz | |
| PGS000385 (PRSWEB_PHECODE157_GWAS-Catalog-r2019-05-03-X157_P_5e-08_UKB_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Pancreatic cancer | pancreatic carcinoma | 17 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000385/ScoringFiles/PGS000385.txt.gz | |
| PGS000386 (PRSWEB_PHECODE157_GWAS-Catalog-r2019-05-03-X157_PT_UKB_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Pancreatic cancer | pancreatic carcinoma | 10 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000386/ScoringFiles/PGS000386.txt.gz | |
| PGS000663 (wGRS22) |
PGP000123 | Kim J et al. Cancer Epidemiol Biomarkers Prev (2020) |
Pancreatic cancer | pancreatic carcinoma | 22 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000663/ScoringFiles/PGS000663.txt.gz |
| PGS000725 (PRS_Pancreas) |
PGP000135 | Jia G et al. JNCI Cancer Spectr (2020) |
Pancreatic cancer | pancreatic carcinoma | 22 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000725/ScoringFiles/PGS000725.txt.gz |
| PGS000794 (CC_Pancreas_IV) |
PGP000186 | Kachuri L et al. Nat Commun (2020) |
Pancreatic cancer | pancreatic carcinoma | 22 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000794/ScoringFiles/PGS000794.txt.gz |
| 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 |
| PGS002298 (PRS14_esophageal) |
PGP000328 | Choi J et al. Int J Cancer (2020) |
Esophageal cancer | esophageal carcinoma | 14 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002298/ScoringFiles/PGS002298.txt.gz |
| PGS002740 (PRS22_PC) |
PGP000347 | Yuan C et al. Ann Oncol (2022) |
Pancreatic cancer | pancreatic carcinoma | 22 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002740/ScoringFiles/PGS002740.txt.gz |
| PGS002747 (PRS_GI) |
PGP000359 | Liu Y et al. Cancer Med (2022) |
Gastrointestinal cancer | Digestive System Carcinoma | 106 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002747/ScoringFiles/PGS002747.txt.gz |
| PGS003386 (best_COADREAD) |
PGP000413 | Namba S et al. Cancer Res (2022) |
Colorectal cancer | colorectal carcinoma | 61 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003386/ScoringFiles/PGS003386.txt.gz |
| PGS003387 (best_ESCA_BEEA) |
PGP000413 | Namba S et al. Cancer Res (2022) |
Esophageal adenocarcinoma or Barrett’s esophagus | Barrett's esophagus, esophageal adenocarcinoma |
601,980 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003387/ScoringFiles/PGS003387.txt.gz |
| PGS003388 (best_ESCA_EA) |
PGP000413 | Namba S et al. Cancer Res (2022) |
Esophageal adenocarcinoma | esophageal adenocarcinoma | 356,743 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003388/ScoringFiles/PGS003388.txt.gz |
| PGS003739 (PRS81_CoC) |
PGP000470 | Xin J et al. EBioMedicine (2023) |
Colorectal cancer | colorectal carcinoma | 81 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003739/ScoringFiles/PGS003739.txt.gz |
|
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000203 | PGS000083 (CC_Pancreas) |
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 | PGS000083 (CC_Pancreas) |
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 | PGS000083 (CC_Pancreas) |
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 | — |
| PPM000490 | PGS000159 (cGRS_Pancreatic) |
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 | PGS000159 (cGRS_Pancreatic) |
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 |
— | — |
| PPM001061 | PGS000376 (PRSWEB_PHECODE153.2_C18_PRS-CS_MGI_20200608) |
PSS000538| European Ancestry| 5,031 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Colon cancer | OR: 1.177 [1.069, 1.297] β: 0.163 (0.0491) |
AUROC: 0.547 [0.518, 0.576] | Nagelkerke's Pseudo-R²: 0.0046 Brier score: 0.0832 Odds Ratio (OR, top 1% vs. Rest): 1.65 [0.753, 3.61] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_C18_PRS-CS_MGI_20200608 |
| PPM001062 | PGS000377 (PRSWEB_PHECODE153.2_C18_LASSOSUM_MGI_20200608) |
PSS000538| European Ancestry| 5,031 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Colon cancer | OR: 1.174 [1.066, 1.292] β: 0.16 (0.049) |
AUROC: 0.545 [0.518, 0.574] | Nagelkerke's Pseudo-R²: 0.00441 Brier score: 0.0831 Odds Ratio (OR, top 1% vs. Rest): 1.4 [0.607, 3.22] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_C18_LASSOSUM_MGI_20200608 |
| PPM001063 | PGS000378 (PRSWEB_PHECODE153.2_C3-COLON_PRS-CS_MGI_20200608) |
PSS000538| European Ancestry| 5,031 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Colon cancer | OR: 1.141 [1.038, 1.254] β: 0.132 (0.0484) |
AUROC: 0.536 [0.509, 0.565] | Nagelkerke's Pseudo-R²: 0.00301 Brier score: 0.0832 Odds Ratio (OR, top 1% vs. Rest): 1.82 [0.867, 3.84] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_C3-COLON_PRS-CS_MGI_20200608 |
| PPM001064 | PGS000379 (PRSWEB_PHECODE153.2_C3-COLON_LASSOSUM_MGI_20200608) |
PSS000538| European Ancestry| 5,031 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Colon cancer | OR: 1.143 [1.038, 1.258] β: 0.134 (0.049) |
AUROC: 0.536 [0.51, 0.567] | Nagelkerke's Pseudo-R²: 0.00302 Brier score: 0.0832 Odds Ratio (OR, top 1% vs. Rest): 0.757 [0.252, 2.28] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_C3-COLON_LASSOSUM_MGI_20200608 |
| PPM001065 | PGS000380 (PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PRS-CS_MGI_20200608) |
PSS000538| European Ancestry| 5,031 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Colon cancer | OR: 1.324 [1.203, 1.457] β: 0.281 (0.0489) |
AUROC: 0.569 [0.539, 0.599] | Nagelkerke's Pseudo-R²: 0.0138 Brier score: 0.0827 Odds Ratio (OR, top 1% vs. Rest): 3.85 [2.19, 6.77] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PRS-CS_MGI_20200608 |
| PPM001066 | PGS000381 (PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PT_MGI_20200608) |
PSS000538| European Ancestry| 5,031 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Colon cancer | OR: 1.212 [1.105, 1.33] β: 0.193 (0.0472) |
AUROC: 0.55 [0.522, 0.577] | Nagelkerke's Pseudo-R²: 0.00703 Brier score: 0.0831 Odds Ratio (OR, top 1% vs. Rest): 1.6 [0.733, 3.51] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PT_MGI_20200608 |
| PPM001067 | PGS000382 (PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_LASSOSUM_MGI_20200608) |
PSS000538| European Ancestry| 5,031 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Colon cancer | OR: 1.247 [1.134, 1.371] β: 0.221 (0.0483) |
AUROC: 0.567 [0.54, 0.594] | Nagelkerke's Pseudo-R²: 0.00899 Brier score: 0.083 Odds Ratio (OR, top 1% vs. Rest): 1.17 [0.477, 2.87] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_LASSOSUM_MGI_20200608 |
| PPM001070 | PGS000385 (PRSWEB_PHECODE157_GWAS-Catalog-r2019-05-03-X157_P_5e-08_UKB_20200608) |
PSS000565| European Ancestry| 3,591 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Pancreatic cancer | OR: 1.384 [1.235, 1.552] β: 0.325 (0.0583) |
AUROC: 0.589 [0.559, 0.622] | Nagelkerke's Pseudo-R²: 0.019 Brier score: 0.082 Odds Ratio (OR, top 1% vs. Rest): 2.58 [1.19, 5.57] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE157_GWAS-Catalog-r2019-05-03-X157_P_5e-08_UKB_20200608 |
| PPM001071 | PGS000386 (PRSWEB_PHECODE157_GWAS-Catalog-r2019-05-03-X157_PT_UKB_20200608) |
PSS000565| European Ancestry| 3,591 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Pancreatic cancer | OR: 1.342 [1.199, 1.503] β: 0.294 (0.0577) |
AUROC: 0.579 [0.548, 0.611] | Nagelkerke's Pseudo-R²: 0.0157 Brier score: 0.0822 Odds Ratio (OR, top 1% vs. Rest): 1.64 [0.655, 4.12] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE157_GWAS-Catalog-r2019-05-03-X157_PT_UKB_20200608 |
| PPM001367 | PGS000663 (wGRS22) |
PSS000598| European Ancestry| 1,591 individuals |
PGP000123 | Kim J et al. Cancer Epidemiol Biomarkers Prev (2020) |
Reported Trait: Pancreatic cancer | OR: 1.37 [1.23, 1.53] | — | — | — | Cross validation approach-testing sample = 20% |
| PPM001368 | PGS000663 (wGRS22) |
PSS000597| European Ancestry| 956 individuals |
PGP000123 | Kim J et al. Cancer Epidemiol Biomarkers Prev (2020) |
Reported Trait: Pancreatic cancer (0-10 years of follow-up) | OR: 1.46 [1.27, 1.68] | — | — | — | Cross validation approach-testing sample = 20% |
| PPM001369 | PGS000663 (wGRS22) |
PSS000598| European Ancestry| 1,591 individuals |
PGP000123 | Kim J et al. Cancer Epidemiol Biomarkers Prev (2020) |
Reported Trait: Pancreatic cancer | OR: 1.37 [1.22, 1.53] | AUROC: 0.65 | — | matching factors, age, cohort (also gender), race/ethnicity, smoking status, fasting status, month/year of blood collection, body mass index, waist-to-hip ratio, diabetic status | Cross validation approach-testing sample = 20% |
| PPM001370 | PGS000663 (wGRS22) |
PSS000597| European Ancestry| 956 individuals |
PGP000123 | Kim J et al. Cancer Epidemiol Biomarkers Prev (2020) |
Reported Trait: Pancreatic cancer (0-10 years of follow-up) | OR: 1.44 [1.25, 1.67] | AUROC: 0.67 | — | matching factors, age, cohort (also gender), race/ethnicity, smoking status, fasting status, month/year of blood collection, body mass index, waist-to-hip ratio, diabetic status | Cross validation approach-testing sample = 20% |
| PPM001655 | PGS000725 (PRS_Pancreas) |
PSS000859| European Ancestry| 400,812 individuals |
PGP000135 | Jia G et al. JNCI Cancer Spectr (2020) |
Reported Trait: Incident Pancreatic cancer | — | AUROC: 0.639 [0.613, 0.664] | — | Genotyping array | — |
| PPM002065 | PGS000794 (CC_Pancreas_IV) |
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. |
| 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) | — |
| PPM013027 | PGS002298 (PRS14_esophageal) |
PSS009661| European Ancestry| 406 individuals |
PGP000328 | Choi J et al. Int J Cancer (2020) |
Reported Trait: Esophageal cancer | — | AUROC: 0.53 [0.51, 0.56] | — | — | — |
| PPM014844 | PGS002740 (PRS22_PC) |
PSS009913| European Ancestry| 13,952 individuals |
PGP000347 | Yuan C et al. Ann Oncol (2022) |
Reported Trait: Pancreatic cancer in those aged <= 60 years | — | — | Odds ratio (OR, top vs bottom 10%): 6.91 [4.6, 10.4] | — | — |
| PPM014843 | PGS002740 (PRS22_PC) |
PSS009913| European Ancestry| 13,952 individuals |
PGP000347 | Yuan C et al. Ann Oncol (2022) |
Reported Trait: Pancreatic cancer in those aged >70 years | — | — | Odds ratio (OR, top vs bottom 10%): 4.12 [3.08, 5.52] | — | — |
| PPM014926 | PGS002747 (PRS_GI) |
PSS009932| European Ancestry| 430,036 individuals |
PGP000359 | Liu Y et al. Cancer Med (2022) |
Reported Trait: Incident gastrointestinal cancer | — | — | Hazard Ratio (HR, high vs low): 2.28 [2.09, 2.49] | Age group, gender, qualification, Townsend Deprivation Index, family history of cancer, smoking status, alcohol consumption and the top 10 genetic principal components | — |
| PPM014927 | PGS002747 (PRS_GI) |
PSS009932| European Ancestry| 430,036 individuals |
PGP000359 | Liu Y et al. Cancer Med (2022) |
Reported Trait: Incident gastrointestinal cancer (with metabolic syndrome) | — | — | Hazard Ratio (HR, high vs low): 2.75 [2.43, 3.12] | — | — |
| PPM016261 | PGS003386 (best_COADREAD) |
PSS010076| European Ancestry| 274,069 individuals |
PGP000413 | Namba S et al. Cancer Res (2022) |
Reported Trait: colorectal cancer | — | AUROC: 0.724 | R²: 0.0115 | age, sex, top 20 genetic principal components | — |
| PPM016262 | PGS003387 (best_ESCA_BEEA) |
PSS010077| European Ancestry| 270,026 individuals |
PGP000413 | Namba S et al. Cancer Res (2022) |
Reported Trait: esophageal adenocarcinoma | — | AUROC: 0.819 | R²: 0.0123 | age, sex, top 20 genetic principal components | — |
| PPM016263 | PGS003388 (best_ESCA_EA) |
PSS010077| European Ancestry| 270,026 individuals |
PGP000413 | Namba S et al. Cancer Res (2022) |
Reported Trait: esophageal adenocarcinoma | — | AUROC: 0.814 | R²: 0.00875 | age, sex, top 20 genetic principal components | — |
| PPM018495 | PGS003739 (PRS81_CoC) |
PSS010988| European Ancestry| 470 individuals |
PGP000470 | Xin J et al. EBioMedicine (2023) |
Reported Trait: Colorectal cancer | OR: 1.37 [1.24, 1.51] | — | — | — | — |
|
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 | — | [ ,
46.0 % Male samples |
Mean = 58.0 years | European | — | GERA, UKB | — |
| PSS009913 | — | — | [
|
— | European | — | PANSCAN | — |
| PSS000565 | PheCode:157; ICD9:157, 157.0, 157.1, 157.2, 157.3, 157.4, 157.8, 157.9; ICD10:C25.0, C25.1, C25.2, C25.3, C25.4, C25.7, C25.8, C25.9 | — | [
|
— | European | — | UKB | — |
| PSS010988 | — | — | 470 individuals | Mean = 67.3 years | European | — | TCGA | — |
| PSS009932 | MetS is defined as having any three or more of five MetS components, including central obesity, hypertension, dyslipidemia, hypertriglyceridemia, and hyperglyce- mia, according to the National Cholesterol Education Programme Adult Treatment Panel III criteria (NCEP- ATP III) | — | [
|
— | European | — | UKB | — |
| 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 | [ ,
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. | — | [
|
— | 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. | — | [
|
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. | — | [
|
— | 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. | — | [
|
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. | — | [
|
— | 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. | — | [
|
— | Not reported | European, African American or Afro-Caribbean, South Asian, East Asian, African unspecified | UKB | — |
| PSS010076 | C18, C19, C20 | — | [
|
— | European (British) |
— | UKB | Controls were samples without any cancer diagnosis or self-reported cancer |
| PSS010077 | C15, histology was one of the followings: Adenocarcinoma, NOS; Adenocarcinoma, intestinal type; Adenocarcinoma in tubulovillous adenoma | — | [
|
— | European (British) |
— | UKB | Controls were samples without any cancer diagnosis or self-reported cancer |
| PSS000597 | In this study, cases were incident patients with primary pancreatic adenocarcinoma ascertained between 1984 and 2010 through self- report, report of next-of-kin, or death certificates and confirmed by medical record review and tumor registry data. Cases Diagnosed within 10 years of blood collection. | Mean = 10.0 years | [ ,
28.1 % Male samples |
— | European | — | HPFS, NHS, PHS, WHI | Overlap with GWAS samples (percentage unknown). Cross validation approach used (20% as testing sample) |
| PSS000598 | In this study, cases were incident patients with primary pancreatic adenocarcinoma ascertained between 1984 and 2010 through self- report, report of next-of-kin, or death certificates and confirmed by medical record review and tumor registry data. | — | [ ,
33.4 % Male samples |
— | European | — | HPFS, NHS, PHS, WHI | Overlap with GWAS samples (percentage unknown). Cross validation approach used (20% as testing sample) |
| PSS000859 | Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Pancreatic Cancer=(ICD-9 = 157 or ICD-10 = C25) | Median = 5.8 years | [ ,
46.5 % Male samples |
— | European | — | UKB | — |
| PSS010154 | — | — | [
|
— | European | — | UKB | — |
| PSS000279 | Primary tumor samples from TCGA | — | [
|
Mean = 66.0 years Sd = 11.0 years |
European | — | TCGA | — |
| PSS000279 | — | — | [
|
— | European | — | eMERGE | — |
| PSS009661 | esophageal cancer (ICD-9 = 150 or ICD-10 = C15) | — | 406 individuals | — | European | — | UKB | — |
| PSS000538 | PheCode:153.2; ICD9CM:153.0, 153.1, 153.2, 153.3, 153.4, 153.5, 153.6, 153.7, 153.8, 153.9, 159.0, 209.10, 209.11, 209.12, 209.13, 209.14, 209.15, 209.16, 230.3, V10.05; ICD10CM:C18, C18.0, C18.1, C18.2, C18.3, C18.4, C18.5, C18.6, C18.7, C18.8, C18.9, C26.0, C7A.020, C7A.021, C7A.022, C7A.023, C7A.024, C7A.025, C7A.029, D01.0 | — | [
|
— | European | — | MGI | — |
| PSS001022 | Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. | — | [
|
— | European | — | UKB | — |