| Publication Information (EuropePMC) | |
| Title | Non-Lynch Familial and Early-Onset Colorectal Cancer Explained by Accumulation of Low-Risk Genetic Variants. |
| PubMed ID | 34359758(Europe PMC) |
| doi | 10.3390/cancers13153857 |
| Publication Date | July 31, 2021 |
| Journal | Cancers (Basel) |
| Author(s) | Mur P, Bonifaci N, Díez-Villanueva A, Munté E, Alonso MH, Obón-Santacana M, Aiza G, Navarro M, Piñol V, Brunet J, Tomlinson I, Capellá G, Moreno V, Valle L. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000765 (PRS_CRC95) |
PGP000170 | Huyghe JR et al. Nat Genet (2018) |
Colorectal cancer | colorectal cancer | 95 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000765/ScoringFiles/PGS000765.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM020782 | PGS000765 (PRS_CRC95) |
PSS011409| European Ancestry| 2,059 individuals |
PGP000589 | Mur P et al. Cancers (Basel) (2021) |Ext. |
Reported Trait: Familial / early-onset colorectal cancer | OR: 1.12 [1.09, 1.14] | — | — | Age, sex | Only 92 SNPs were included. 3 SNPs had an R^2 lower than 0.3 and were excluded |
| PPM020783 | PGS000765 (PRS_CRC95) |
PSS011410| European Ancestry| 2,719 individuals |
PGP000589 | Mur P et al. Cancers (Basel) (2021) |Ext. |
Reported Trait: Sporadic colorectal cancer | OR: 1.08 [1.06, 1.09] | — | — | Age, sex | Only 92 SNPs were included. 3 SNPs had an R^2 lower than 0.3 and were excluded |
| PPM020784 | PGS000765 (PRS_CRC95) |
PSS011409| European Ancestry| 2,059 individuals |
PGP000589 | Mur P et al. Cancers (Basel) (2021) |Ext. |
Reported Trait: Familial / early-onset colorectal cancer | — | AUROC: 0.833 | R²: 0.373 | Age at cancer diagnosis, sex | Only 92 SNPs were included. 3 SNPs had an R^2 lower than 0.3 and were excluded |
| PPM020785 | PGS000765 (PRS_CRC95) |
PSS011409| European Ancestry| 2,059 individuals |
PGP000589 | Mur P et al. Cancers (Basel) (2021) |Ext. |
Reported Trait: Familial / early-onset colorectal cancer | — | AUROC: 0.905 | R²: 0.598 | Age at cancer diagnosis, sex, family history of colorectal cancer | Only 92 SNPs were included. 3 SNPs had an R^2 lower than 0.3 and were excluded. Only 405 cases and 1,094 controls were included in this analysis |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS011410 | Cases were individuals with sporadic colorectal cancer (CRC). | — | [ ,
56.53 % Male samples |
— | European | — | CRCGEN | — |
| PSS011409 | Cases were individuals with familial/early-onset mismatch repair (MMR)-proficient unrelated colorectal cancer (CRC). Cases fulfilled either the Amsterdam I/ Amsterdam II criteria or the Bethesda guidelines for hereditary nonpolyposis CRC. For the Amsterdam I criteria, individuals had to fulfil the following: have at least three relatives affected with CRC, have at least two successive generations are affected, have at least one person diagnosed before the age of 50 years, have familial adenomatous polyposis excluded and have tumors verified by pathologic examination. For the Amsterdam II criteria, individuals had to fulfil the following: have at least three relatives with an HNPCC-associated cancer (large bowel, endometrium, small bowel, ureter, or renal pelvis, though not including stomach, ovary, brain, bladder, or skin), have one affected person who is a first-degree relative of the other two, have at least two successive generations affected, have at least one person diagnosed before the age of 50 years, have familial adenomatous polyposis excluded and tumors verified by pathologic examination. For the Bethesda guidelines for hereditary nonpolyposis CRC criteria, inidividuals had to fulfil at least one of the following: CRC < age 50 years, synchronous or metachronous colorectal or other HNPCC-associated tumors regardless of age, CRC with microsatellite instability-positive morphology < age 60 years, CRC with one or more first-degree relatives with CRC or other HNPCC-related tumor, with one of the cancers < age 50 years or CRC with two or more first- or second-degree relatives with CRC or other hereditary nonpolyposis colon cancer-related tumor (endometrial, stomach, ovarian, cervical, esophageal, leukemia, thyroid, bladder, ureter and renal pelvis, biliary tract, small bowel, breast, pancreas, liver, larynx, bronchus, lung, and brain (glioblastoma), sebaceous gland adenomas, and keratoacanthomas), regardless of age. | — | [ ,
51.97 % Male samples |
— | European | — | CRCGEN | Cases were obtained from the Hereditary Cancer Program of the Catalan Institute of Oncology |