Polygenic Score (PGS) ID: PGS000801

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (MONDO_0005575)
Released in PGS Catalog: June 11, 2021
Download Score FTP directory
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 GRS40_CRC
Development Method
Name LD clumping
Parameters R^2 > 0.01. Effect_weight obtained from the Genetics and Epidemiology of Colorectal Cancer Consor... tium (GECCO) dataset.Show more
Variants
Original Genome Build NR
Number of Variants 40
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000190
Citation (link to publication) Hang D et al. Int J Epidemiol (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 77.2%
East Asian: 19.8%
African: 3%
220,743 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
Europe PMC: 21655089
[
  • 10,385 cases
  • , 11,090 controls
]
European10 cohorts
  • B58C
  • ,BTNS
  • ,CCFR
  • ,COGS
  • ,CoRGI
  • ,GIMS
  • ,NSCCG
  • ,QUASAR2
  • ,SOCCS
  • ,VICTOR
GWAS Catalog: GCST000053
Europe PMC: 17618284
1,890 individualsEuropeanCoRGI
GWAS Catalog: GCST000168
Europe PMC: 18372901
1,983 individualsEuropean
(U.K.)		NR
GWAS Catalog: GCST000169
Europe PMC: 18372905
1,849 individualsEuropeanCoRGI
GWAS Catalog: GCST000270
Europe PMC: 19011631
3,831 individualsEuropeanCOGS, CoRGI
GWAS Catalog: GCST000843
Europe PMC: 20972440
30,420 individualsEuropean11 cohorts
  • B58C
  • ,COGS
  • ,COIN
  • ,COIN-B
  • ,CoRGI
  • ,FCCPS
  • ,NSCCG
  • ,SEARCH
  • ,SOCCS
  • ,UKBS
  • ,VICTOR
GWAS Catalog: GCST000843
Europe PMC: 20972440
7,962 individualsEuropean11 cohorts
  • B58C
  • ,COGS
  • ,COIN
  • ,COIN-B
  • ,CoRGI
  • ,FCCPS
  • ,NSCCG
  • ,SEARCH
  • ,SOCCS
  • ,UKBS
  • ,VICTOR
GWAS Catalog: GCST001544
Europe PMC: 22634755
17,780 individualsEuropeanCOGS, CoRGI, NSCCG, SOCCS, VICTOR
GWAS Catalog: GCST001787
Europe PMC: 23266556
27,809 individualsEuropean20 cohorts
  • ASTERISK
  • ,Aichi_Con
  • ,CCFR
  • ,DACHS
  • ,DALS
  • ,Guangzhou
  • ,HPFS
  • ,Hawaiian_Colo2&3
  • ,KCPS
  • ,MEC
  • ,NHS
  • ,NHS_Ad
  • ,OFCCR
  • ,PHS
  • ,PLCO
  • ,PMH
  • ,Shanghai
  • ,TCPS
  • ,VITAL
  • ,WHI
GWAS Catalog: GCST001792
Europe PMC: 23263487
7,847 individualsEast AsianAichi_Con, Guangzhou, KCPS, Shanghai
GWAS Catalog: GCST002454
Europe PMC: 24836286
8,270 individualsEast AsianAichi_Con, Guangzhou, KCPS, Shanghai
GWAS Catalog: GCST002561
Europe PMC: 25105248
6,424 individualsEast Asian11 cohorts
  • CCFR
  • ,FCCS
  • ,Hawaiian_Colo2&3
  • ,JPHC
  • ,MDACCS
  • ,MEC
  • ,NCCS
  • ,PLCO
  • ,SCCS
  • ,UNC-Rectal
  • ,UNCCanCORS
GWAS Catalog: GCST002561
Europe PMC: 25105248
6,596 individualsAfrican American or Afro-Caribbean11 cohorts
  • CCFR
  • ,FCCS
  • ,Hawaiian_Colo2&3
  • ,JPHC
  • ,MDACCS
  • ,MEC
  • ,NCCS
  • ,PLCO
  • ,SCCS
  • ,UNC-Rectal
  • ,UNCCanCORS
GWAS Catalog: GCST002919
Europe PMC: 25990418
17,556 individualsEuropeanBBJ
GWAS Catalog: GCST003017
Europe PMC: 26151821
37,955 individualsEuropean20 cohorts
  • ACS
  • ,ASTERISK
  • ,CCFR
  • ,CCFR-II
  • ,DACHS
  • ,DALS
  • ,HPFS
  • ,Hawaiian_Colo2&3
  • ,KCCS
  • ,MEC
  • ,MECC
  • ,NFCCR
  • ,NHS
  • ,NHS_Ad
  • ,OFCCR
  • ,PHS
  • ,PLCO
  • ,PMH
  • ,VITAL
  • ,WHI
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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)
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
PPM002085PSS001030|
European Ancestry|
27,426 individuals
PGP000190 |
Hang D et al. Int J Epidemiol (2020)
Reported Trait: Conventional adeonmaOR: 1.17 [1.12, 1.21]—Odds Ratio (OR, top 20% vs bottom 20%): 1.63 [1.44, 1.83]Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous e... ndoscopies, time in years since the most recent endoscopy, age, PCs(1-3)Show moreEffect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorect... al Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.Show more
PPM002086PSS001030|
European Ancestry|
27,426 individuals
PGP000190 |
Hang D et al. Int J Epidemiol (2020)
Reported Trait: Non-advanced conventional adenomaOR: 1.12 [1.07, 1.18]—Odds Ratio (OR, top 20% vs bottom 20%): 1.44 [1.23, 1.68]Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous e... ndoscopies, time in years since the most recent endoscopy, age, PCs(1-3)Show moreEffect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorect... al Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.Show more
PPM002087PSS001030|
European Ancestry|
27,426 individuals
PGP000190 |
Hang D et al. Int J Epidemiol (2020)
Reported Trait: Advanced conventional adenomaOR: 1.22 [1.16, 1.28]—Odds Ratio (OR, top 20% vs bottom 20%): 1.91 [1.59, 2.29]Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous e... ndoscopies, time in years since the most recent endoscopy, age, PCs(1-3)Show moreEffect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorect... al Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.Show more
PPM002088PSS001030|
European Ancestry|
27,426 individuals
PGP000190 |
Hang D et al. Int J Epidemiol (2020)
Reported Trait: Serrated polypOR: 1.09 [1.03, 1.14]—Odds Ratio (OR, top 20% vs bottom 20%): 1.24 [1.06, 1.45]Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous e... ndoscopies, time in years since the most recent endoscopy, age, PCs(1-3)Show moreEffect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorect... al Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.Show more
PPM002089PSS001030|
European Ancestry|
27,426 individuals
PGP000190 |
Hang D et al. Int J Epidemiol (2020)
Reported Trait: Serrated polyp with high risk of malignancyOR: 1.1 [1.01, 1.19]——Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous e... ndoscopies, time in years since the most recent endoscopy, age, PCs(1-3)Show moreEffect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorect... al Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.Show more
PPM002090PSS001030|
European Ancestry|
27,426 individuals
PGP000190 |
Hang D et al. Int J Epidemiol (2020)
Reported Trait: Serrated polyp with low risk of malignancyOR: 1.08 [1.02, 1.15]—Odds Ratio (OR, top 20% vs bottom 20%): 1.25 [1.03, 1.53]Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous e... ndoscopies, time in years since the most recent endoscopy, age, PCs(1-3)Show moreEffect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorect... al Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.Show more
PPM002091PSS001030|
European Ancestry|
27,426 individuals
PGP000190 |
Hang D et al. Int J Epidemiol (2020)
Reported Trait: Synchronous conventional adenoma and serrated polypOR: 1.24 [1.16, 1.32]—Odds Ratio (OR, top 20% vs bottom 20%): 1.96 [1.54, 2.49]Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous e... ndoscopies, time in years since the most recent endoscopy, age, PCs(1-3)Show moreEffect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorect... al Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.Show more
PPM002092PSS001030|
European Ancestry|
27,426 individuals
PGP000190 |
Hang D et al. Int J Epidemiol (2020)
Reported Trait: Multiple conventional adenomasOR: 1.25 [1.17, 1.34]——Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous e... ndoscopies, time in years since the most recent endoscopy, age, PCs(1-3)Show moreEffect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorect... al Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.Show more
PPM002093PSS001030|
European Ancestry|
27,426 individuals
PGP000190 |
Hang D et al. Int J Epidemiol (2020)
Reported Trait: Multiple serrated polypsOR: 1.09 [1.01, 1.18]——Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous e... ndoscopies, time in years since the most recent endoscopy, age, PCs(1-3)Show moreEffect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorect... al Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.Show 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
PSS001030Cases included individuals with polyps. Of the 5331 cases, 2952 had conventional adenomas (CAs), 158... 5 had serrated polyps (SAs) and 794 had sychronous CAs and SPs. CAs were defined as tubular, tubulovillous and villous adenomas and adenomas with high-grade dysplasia. Advanced CAs were defined by at least one CA ≥10 mm in diameter or with advanced histology (tubulovillous/villous histological features or high-grade/severe dysplasia) or ≥3 CAs regardless of histology or size. SPs were defined as hyperplastic polyps and mixed/serrated adenomas. Individuals at high risk of malignancy were defined as having SPs located in the proximal colon or with a size of ≥10 mm. Mixed/serrated ademonas were defined as both mixed polyps (those with both adenomatous and hyperplastic changes in histology) and polyps with any serrated diagnosis (e.g. serrated adenomas, serrated polyps and SSA/Ps). If a participant had both CAs and SPs in an endoscopy, each type of the polyps were recorded separately, and considered the patient as a synchronous SP and CA case.Show more—
[
  • 5,331 cases
  • , 22,095 controls
]
,
30.0 % Male samples
Mean = 63.2 years
Sd = 10.0 years		European—HPFS, NHS, NHS2—
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