PGS Publication: PGP000589

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.Show more
Released in PGS Catalog: Feb. 20, 2024

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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Multi-ancestry (including European)
Multi-ancestry (excluding European)
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East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

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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 cancercolorectal cancer95
G
-
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000765/ScoringFiles/PGS000765.txt.gz
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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.

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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
PPM020782PGS000765
(PRS_CRC95)
PSS011409|
European Ancestry|
2,059 individuals
PGP000589 |
Mur P et al. Cancers (Basel) (2021)
|Ext.
Reported Trait: Familial / early-onset colorectal cancerOR: 1.12 [1.09, 1.14]Age, sexOnly 92 SNPs were included. 3 SNPs had an R^2 lower than 0.3 and were excluded
PPM020783PGS000765
(PRS_CRC95)
PSS011410|
European Ancestry|
2,719 individuals
PGP000589 |
Mur P et al. Cancers (Basel) (2021)
|Ext.
Reported Trait: Sporadic colorectal cancerOR: 1.08 [1.06, 1.09]Age, sexOnly 92 SNPs were included. 3 SNPs had an R^2 lower than 0.3 and were excluded
PPM020784PGS000765
(PRS_CRC95)
PSS011409|
European Ancestry|
2,059 individuals
PGP000589 |
Mur P et al. Cancers (Basel) (2021)
|Ext.
Reported Trait: Familial / early-onset colorectal cancerAUROC: 0.833: 0.373Age at cancer diagnosis, sexOnly 92 SNPs were included. 3 SNPs had an R^2 lower than 0.3 and were excluded
PPM020785PGS000765
(PRS_CRC95)
PSS011409|
European Ancestry|
2,059 individuals
PGP000589 |
Mur P et al. Cancers (Basel) (2021)
|Ext.
Reported Trait: Familial / early-onset colorectal cancerAUROC: 0.905: 0.598Age at cancer diagnosis, sex, family history of colorectal cancerOnly 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 analysisShow more
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Evaluated Samples

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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
PSS011409Cases were individuals with familial/early-onset mismatch repair (MMR)-proficient unrelated colorect... al 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.Show more
[
  • 417 cases
  • , 1,642 controls
]
,
51.97 % Male samples
EuropeanCRCGENCases were obtained from the Hereditary Cancer Program of the Catalan Institute of Oncology
PSS011410Cases were individuals with sporadic colorectal cancer (CRC).
[
  • 1,077 cases
  • , 1,642 controls
]
,
56.53 % Male samples
EuropeanCRCGEN
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