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
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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 GRS40_CRC
Development Method
Name LD clumping
Parameters R^2 > 0.01. Effect_weight obtained from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset.
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)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003799
Europe PMC: 26965516
 21,096 individuals East Asian BBJ, Guangzhou, KCPS, Shanghai
GWAS Catalog: GCST003017
Europe PMC: 26151821
 37,955 individuals European 20 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
GWAS Catalog: GCST002561
Europe PMC: 25105248
 6,424 individuals East Asian 11 cohorts
  • CCFR
  • ,FCCS
  • ,Hawaiian_Colo2&3
  • ,JPHC
  • ,MDACCS
  • ,MEC
  • ,NCCS
  • ,PLCO
  • ,SCCS
  • ,UNC-Rectal
  • ,UNCCanCORS
GWAS Catalog: GCST002561
Europe PMC: 25105248
 6,596 individuals African American or Afro-Caribbean 11 cohorts
  • CCFR
  • ,FCCS
  • ,Hawaiian_Colo2&3
  • ,JPHC
  • ,MDACCS
  • ,MEC
  • ,NCCS
  • ,PLCO
  • ,SCCS
  • ,UNC-Rectal
  • ,UNCCanCORS
GWAS Catalog: GCST002454
Europe PMC: 24836286
 8,270 individuals East Asian Aichi_Con, Guangzhou, KCPS, Shanghai
GWAS Catalog: GCST001787
Europe PMC: 23266556
 27,809 individuals European 20 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 individuals East Asian Aichi_Con, Guangzhou, KCPS, Shanghai
Europe PMC: 21655089
[
  • 10,385 cases
  • , 11,090 controls
]
 European 10 cohorts
  • B58C
  • ,BTNS
  • ,CCFR
  • ,COGS
  • ,CoRGI
  • ,GIMS
  • ,NSCCG
  • ,QUASAR2
  • ,SOCCS
  • ,VICTOR
GWAS Catalog: GCST000168
Europe PMC: 18372901
 1,983 individuals European
(U.K.)		 NR
GWAS Catalog: GCST000843
Europe PMC: 20972440
 30,420 individuals European 11 cohorts
  • B58C
  • ,COGS
  • ,COIN
  • ,COIN-B
  • ,CoRGI
  • ,FCCPS
  • ,NSCCG
  • ,SEARCH
  • ,SOCCS
  • ,UKBS
  • ,VICTOR
GWAS Catalog: GCST000843
Europe PMC: 20972440
 7,962 individuals European 11 cohorts
  • B58C
  • ,COGS
  • ,COIN
  • ,COIN-B
  • ,CoRGI
  • ,FCCPS
  • ,NSCCG
  • ,SEARCH
  • ,SOCCS
  • ,UKBS
  • ,VICTOR
GWAS Catalog: GCST002919
Europe PMC: 25990418
 17,556 individuals European BBJ
GWAS Catalog: GCST001544
Europe PMC: 22634755
 17,780 individuals European COGS, CoRGI, NSCCG, SOCCS, VICTOR
GWAS Catalog: GCST000270
Europe PMC: 19011631
 3,831 individuals European COGS, CoRGI
GWAS Catalog: GCST000169
Europe PMC: 18372905
 1,849 individuals European CoRGI
GWAS Catalog: GCST000053
Europe PMC: 17618284
 1,890 individuals European CoRGI

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
PPM002087 PSS001030|
European Ancestry|
27,426 individuals
 PGP000190 |
Hang D et al. Int J Epidemiol (2020)
 Reported Trait: Advanced conventional adenoma OR: 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 endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.
PPM002092 PSS001030|
European Ancestry|
27,426 individuals
 PGP000190 |
Hang D et al. Int J Epidemiol (2020)
 Reported Trait: Multiple conventional adenomas OR: 1.25 [1.17, 1.34] — — Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.
PPM002093 PSS001030|
European Ancestry|
27,426 individuals
 PGP000190 |
Hang D et al. Int J Epidemiol (2020)
 Reported Trait: Multiple serrated polyps OR: 1.09 [1.01, 1.18] — — Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.
PPM002085 PSS001030|
European Ancestry|
27,426 individuals
 PGP000190 |
Hang D et al. Int J Epidemiol (2020)
 Reported Trait: Conventional adeonma OR: 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 endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.
PPM002086 PSS001030|
European Ancestry|
27,426 individuals
 PGP000190 |
Hang D et al. Int J Epidemiol (2020)
 Reported Trait: Non-advanced conventional adenoma OR: 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 endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.
PPM002088 PSS001030|
European Ancestry|
27,426 individuals
 PGP000190 |
Hang D et al. Int J Epidemiol (2020)
 Reported Trait: Serrated polyp OR: 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 endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.
PPM002089 PSS001030|
European Ancestry|
27,426 individuals
 PGP000190 |
Hang D et al. Int J Epidemiol (2020)
 Reported Trait: Serrated polyp with high risk of malignancy OR: 1.1 [1.01, 1.19] — — Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.
PPM002090 PSS001030|
European Ancestry|
27,426 individuals
 PGP000190 |
Hang D et al. Int J Epidemiol (2020)
 Reported Trait: Serrated polyp with low risk of malignancy OR: 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 endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.
PPM002091 PSS001030|
European Ancestry|
27,426 individuals
 PGP000190 |
Hang D et al. Int J Epidemiol (2020)
 Reported Trait: Synchronous conventional adenoma and serrated polyp OR: 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 endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score.

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
PSS001030 Cases included individuals with polyps. Of the 5331 cases, 2952 had conventional adenomas (CAs), 1585 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. —
[
  • 5,331 cases
  • , 22,095 controls
]
,
30.0 % Male samples
 Mean = 63.2 years
Sd = 10.0 years		 European — HPFS, NHS, NHS2 —