Polygenic Score (PGS) ID: PGS000765

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (MONDO_0005575)
Released in PGS Catalog: April 28, 2021
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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 PRS_CRC95
Development Method
Name SNPs associated with colorectal cancer
Parameters Exclusion of variants only reaching suggestive levels of statistical significance.
Variants
Original Genome Build GRCh37
Number of Variants 95
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000170
Citation (link to publication) Huyghe JR et al. Nat Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 95.8%
East Asian: 4.2%
125,478 individuals (100%)
PGS Evaluation
European: 50%
Multi-ancestry (including European): 50%
  • European
  • African
  • Additional Asian Ancestries
  • Not Reported
  • Additional Diverse Ancestries
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST007856
Europe PMC: 30510241
 120,184 individuals European 41 cohorts
  • ASTERISK
  • ,ATBC
  • ,CCFR
  • ,CLUEII
  • ,COLON
  • ,CORSA
  • ,COSM
  • ,CPSII
  • ,ColoCare
  • ,DACHS
  • ,DALS
  • ,EPIC
  • ,EPICOLON
  • ,HCES-CRC
  • ,HPFS
  • ,Hawaiian_Colo2&3
  • ,KIEL
  • ,MCCS
  • ,MEC
  • ,MECC
  • ,MSKCC
  • ,NCCS
  • ,NFCCR
  • ,NHS
  • ,NHS2
  • ,NHS_Ad
  • ,NSHDS
  • ,OFCCR
  • ,Ohio_SU
  • ,PHS
  • ,PLCO
  • ,PMH-CCFR
  • ,SEARCH
  • ,SLRCCSG
  • ,SMC
  • ,SWOG-SELECT
  • ,UKB
  • ,USC-HRT-CRC
  • ,VERDI
  • ,VITAL
  • ,WHI
GWAS Catalog: GCST007856
Europe PMC: 30510241
 5,294 individuals East Asian 41 cohorts
  • ASTERISK
  • ,ATBC
  • ,CCFR
  • ,CLUEII
  • ,COLON
  • ,CORSA
  • ,COSM
  • ,CPSII
  • ,ColoCare
  • ,DACHS
  • ,DALS
  • ,EPIC
  • ,EPICOLON
  • ,HCES-CRC
  • ,HPFS
  • ,Hawaiian_Colo2&3
  • ,KIEL
  • ,MCCS
  • ,MEC
  • ,MECC
  • ,MSKCC
  • ,NCCS
  • ,NFCCR
  • ,NHS
  • ,NHS2
  • ,NHS_Ad
  • ,NSHDS
  • ,OFCCR
  • ,Ohio_SU
  • ,PHS
  • ,PLCO
  • ,PMH-CCFR
  • ,SEARCH
  • ,SLRCCSG
  • ,SMC
  • ,SWOG-SELECT
  • ,UKB
  • ,USC-HRT-CRC
  • ,VERDI
  • ,VITAL
  • ,WHI

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
PPM001961 PSS000981|
Multi-ancestry (including European)|
48,807 individuals
 PGP000171 |
Fahed AC et al. Nat Commun (2020)
|Ext.		 Reported Trait: Prevalent colorectal cancer OR: 1.65 [1.48, 1.85] — — Age, sex, PCs (1-4) —
PPM015518 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Colorectal cancer OR: 2.37 [1.74, 3.24] — — 4 genetic PCs —
PPM018551 PSS011020|
Multi-ancestry (including European)|
163,516 individuals
 PGP000482 |
Hassanin E et al. BMC Med Genomics (2023)
|Ext.		 Reported Trait: Colorectal cancer with pathogenic variant carriers — AUROC: 0.693 [0.66, 0.71]
C-index: 0.646		 Odds ratio (OR, high vs low tertile): 17.5 [9.0, 32.4] — —
PPM018552 PSS011020|
Multi-ancestry (including European)|
163,516 individuals
 PGP000482 |
Hassanin E et al. BMC Med Genomics (2023)
|Ext.		 Reported Trait: Incident colorectal cancer with pathogenic variant carriers — — Odds ratio (OR, high vs low tertile): 7.0 [2.04, 23.7] — —
PPM018553 PSS011020|
Multi-ancestry (including European)|
163,516 individuals
 PGP000482 |
Hassanin E et al. BMC Med Genomics (2023)
|Ext.		 Reported Trait: Colorectal cancer with family history of cancer — AUROC: 0.698 [0.67, 0.72]
C-index: 0.652		 Odds ratio (OR, high vs low tertile): 3.1 [2.6, 3.8] — —
PPM018554 PSS011020|
Multi-ancestry (including European)|
163,516 individuals
 PGP000482 |
Hassanin E et al. BMC Med Genomics (2023)
|Ext.		 Reported Trait: Colorectal cancer with family history of cancer and pathogenic variant carriers — AUROC: 0.704 [0.68, 0.73]
C-index: 0.657		 Odds ratio (OR, high vs low tertile): 39.9 [12.69, 125.41] — —
PPM018555 PSS011020|
Multi-ancestry (including European)|
163,516 individuals
 PGP000482 |
Hassanin E et al. BMC Med Genomics (2023)
|Ext.		 Reported Trait: Colorectal cancer — AUROC: 0.688 [0.66, 0.71]
C-index: 0.64		 — — —
PPM020769 PSS011399|
European Ancestry|
1,428 individuals
 PGP000583 |
Dueñas N et al. J Med Genet (2023)
|Ext.		 Reported Trait: Colorectal cancer or advanced adenoma in individuals with Lynch syndrome HR: 1.019 [1.005, 1.032] — — Sex, birth cohort, other Lynch syndrome-related cancers —
PPM020782 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 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 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 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

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
PSS011410 Cases were individuals with sporadic colorectal cancer (CRC). —
[
  • 1,077 cases
  • , 1,642 controls
]
,
56.53 % Male samples
 — European — CRCGEN —
PSS011399 — —
[
  • 733 cases
  • , 695 controls
]
 — European — ICO, UKBonn —
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. —
[
  • 417 cases
  • , 1,642 controls
]
,
51.97 % Male samples
 — European — CRCGEN Cases were obtained from the Hereditary Cancer Program of the Catalan Institute of Oncology
PSS009971 — — 30,716 individuals — European — MGBB —
PSS009971 — — 1,807 individuals — African unspecified
(Black)		 — MGBB —
PSS009971 — — 786 individuals — Asian unspecified — MGBB —
PSS009971 — — 3,113 individuals — Other — MGBB —
PSS011020 ICD-10: C18.X or C20.X, D01.[0,1,2], D37.[4, 5] —
[
  • 1,902 cases
  • , 161,614 controls
]
 — European, Not reported — UKB —
PSS000981 Cases were individuals with colorectal cancer based on self-reporting at the baseline (Coding IDs: 10,221,023), primary cause of death (ICD-10) from the death registry (Coding IDsC180,C182,C183,C184,C185,C186,C187,C188,C189), secondary cause of death (ICD-10) from the death registry (Coding IDs: C180,C182,C183,C184,C185,C186,C187,C188,C189), type of cancer (ICD-10) from the cancer registry (Coding IDs: C18,C180,C181,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375, 153,154,1530,1531,1532,1533,1534,1535,1536,1537,1538,1539,1540,1541,1 548,2303,2304), primary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), primary diagnoses (ICD-9) from hopsitalization records (Coding IDs: 153,154,1530,1532,1533,1534,1536,1537,1539,1540,1541), secondary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), secondary diagnoses (ICD-9) from hospitialization records (Coding IDs: 153,153,154,1532,1533,1541). Of the total number of cases and controls, 76 were carriers of a pathogenic or likely pathogenic variant in any of the following genes: MLH1, MSH2, MSH6 and PMS2. —
[
  • 303 cases
  • , 45,233 controls
]
 — European — UKB —
PSS000981 Cases were individuals with colorectal cancer based on self-reporting at the baseline (Coding IDs: 10,221,023), primary cause of death (ICD-10) from the death registry (Coding IDsC180,C182,C183,C184,C185,C186,C187,C188,C189), secondary cause of death (ICD-10) from the death registry (Coding IDs: C180,C182,C183,C184,C185,C186,C187,C188,C189), type of cancer (ICD-10) from the cancer registry (Coding IDs: C18,C180,C181,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375, 153,154,1530,1531,1532,1533,1534,1535,1536,1537,1538,1539,1540,1541,1 548,2303,2304), primary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), primary diagnoses (ICD-9) from hopsitalization records (Coding IDs: 153,154,1530,1532,1533,1534,1536,1537,1539,1540,1541), secondary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), secondary diagnoses (ICD-9) from hospitialization records (Coding IDs: 153,153,154,1532,1533,1541). Of the total number of cases and controls, 76 were carriers of a pathogenic or likely pathogenic variant in any of the following genes: MLH1, MSH2, MSH6 and PMS2. —
[
  • 6 cases
  • , 993 controls
]
 — African unspecified — UKB —
PSS000981 Cases were individuals with colorectal cancer based on self-reporting at the baseline (Coding IDs: 10,221,023), primary cause of death (ICD-10) from the death registry (Coding IDsC180,C182,C183,C184,C185,C186,C187,C188,C189), secondary cause of death (ICD-10) from the death registry (Coding IDs: C180,C182,C183,C184,C185,C186,C187,C188,C189), type of cancer (ICD-10) from the cancer registry (Coding IDs: C18,C180,C181,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375, 153,154,1530,1531,1532,1533,1534,1535,1536,1537,1538,1539,1540,1541,1 548,2303,2304), primary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), primary diagnoses (ICD-9) from hopsitalization records (Coding IDs: 153,154,1530,1532,1533,1534,1536,1537,1539,1540,1541), secondary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), secondary diagnoses (ICD-9) from hospitialization records (Coding IDs: 153,153,154,1532,1533,1541). Of the total number of cases and controls, 76 were carriers of a pathogenic or likely pathogenic variant in any of the following genes: MLH1, MSH2, MSH6 and PMS2. —
[
  • 3 cases
  • , 1,216 controls
]
 — Asian unspecified — UKB —
PSS000981 Cases were individuals with colorectal cancer based on self-reporting at the baseline (Coding IDs: 10,221,023), primary cause of death (ICD-10) from the death registry (Coding IDsC180,C182,C183,C184,C185,C186,C187,C188,C189), secondary cause of death (ICD-10) from the death registry (Coding IDs: C180,C182,C183,C184,C185,C186,C187,C188,C189), type of cancer (ICD-10) from the cancer registry (Coding IDs: C18,C180,C181,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375, 153,154,1530,1531,1532,1533,1534,1535,1536,1537,1538,1539,1540,1541,1 548,2303,2304), primary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), primary diagnoses (ICD-9) from hopsitalization records (Coding IDs: 153,154,1530,1532,1533,1534,1536,1537,1539,1540,1541), secondary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), secondary diagnoses (ICD-9) from hospitialization records (Coding IDs: 153,153,154,1532,1533,1541). Of the total number of cases and controls, 76 were carriers of a pathogenic or likely pathogenic variant in any of the following genes: MLH1, MSH2, MSH6 and PMS2. —
[
  • 3 cases
  • , 1,050 controls
]
 — Not reported — UKB —