PGS Publication: PGP000294

Publication Information (EuropePMC)
Title Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk.
PubMed ID 32758450(Europe PMC)
doi 10.1016/j.ajhg.2020.07.006
Publication Date Aug. 5, 2020
Journal Am J Hum Genet
Author(s) Thomas M, Sakoda LC, Hoffmeister M, Rosenthal EA, Lee JK, van Duijnhoven FJB, Platz EA, Wu AH, Dampier CH, de la Chapelle A, Wolk A, Joshi AD, Burnett-Hartman A, Gsur A, Lindblom A, Castells A, Win AK, Namjou B, Van Guelpen B, Tangen CM, He Q, Li CI, Schafmayer C, Joshu CE, Ulrich CM, Bishop DT, Buchanan DD, Schaid D, Drew DA, Muller DC, Duggan D, Crosslin DR, Albanes D, Giovannucci EL, Larson E, Qu F, Mentch F, Giles GG, Hakonarson H, Hampel H, Stanaway IB, Figueiredo JC, Huyghe JR, Minnier J, Chang-Claude J, Hampe J, Harley JB, Visvanathan K, Curtis KR, Offit K, Li L, Le Marchand L, Vodickova L, Gunter MJ, Jenkins MA, Slattery ML, Lemire M, Woods MO, Song M, Murphy N, Lindor NM, Dikilitas O, Pharoah PDP, Campbell PT, Newcomb PA, Milne RL, MacInnis RJ, Castellví-Bel S, Ogino S, Berndt SI, Bézieau S, Thibodeau SN, Gallinger SJ, Zaidi SH, Harrison TA, Keku TO, Hudson TJ, Vymetalkova V, Moreno V, Martín V, Arndt V, Wei WQ, Chung W, Su YR, Hayes RB, White E, Vodicka P, Casey G, Gruber SB, Schoen RE, Chan AT, Potter JD, Brenner H, Jarvik GP, Corley DA, Peters U, Hsu L.
Released in PGS Catalog: March 16, 2022

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

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS002265
(PRS140_CRC)
 PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
 Colorectal cancer colorectal cancer 140
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002265/ScoringFiles/PGS002265.txt.gz

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) 		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
PPM012902 PGS002265
(PRS140_CRC)
 PSS009604|
European Ancestry|
55,033 individuals
 PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
 Reported Trait: Colorectal cancer — AUROC: 0.629 [0.613, 0.645] Hazard Ratio (HR, top 30% of PGS vs. remainder): 1.92 [1.75, 2.23] age and sex —
PPM012903 PGS002265
(PRS140_CRC)
 PSS009603|
East Asian Ancestry|
5,854 individuals
 PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
 Reported Trait: Colorectal cancer — AUROC: 0.591 [0.536, 0.625] — age and sex —
PPM012904 PGS002265
(PRS140_CRC)
 PSS009605|
Hispanic or Latin American Ancestry|
5,291 individuals
 PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
 Reported Trait: Colorectal cancer — AUROC: 0.592 [0.531, 0.652] — age and sex —
PPM012905 PGS002265
(PRS140_CRC)
 PSS009602|
African Ancestry|
2,465 individuals
 PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
 Reported Trait: Colorectal cancer — AUROC: 0.581 [0.5, 0.645] — age and sex —
PPM012906 PGS002265
(PRS140_CRC)
 PSS009606|
European Ancestry|
38,214 individuals
 PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
 Reported Trait: Colorectal cancer — AUROC: 0.591 — age and sex —

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
PSS009602 — —
[
  • 56 cases
  • , 2,409 controls
]
,
65.5 % Male samples
 Mean = 61.6 years
Range = [20.0, 90.0] years		 African American or Afro-Caribbean
(African American)		 — GERA —
PSS009603 — —
[
  • 96 cases
  • , 5,758 controls
]
,
42.1 % Male samples
 Mean = 55.8 years
Range = [20.0, 90.0] years		 East Asian — GERA —
PSS009604 — —
[
  • 1,311 cases
  • , 53,722 controls
]
,
41.6 % Male samples
 Mean = 62.3 years
Range = [20.0, 90.0] years		 European — GERA —
PSS009605 — —
[
  • 70 cases
  • , 5,221 controls
]
,
38.7 % Male samples
 Mean = 55.0 years
Range = [20.0, 90.0] years		 Hispanic or Latin American — GERA —
PSS009606 The colorectal cancer case subjects were defined as those who had at least two ICD9/10 codes for CRC. Control sub- jects had zero ICD9/10 codes for CRC. Participants with a single ICD9/10 code for CRC were excluded from analysis. —
[
  • 573 cases
  • , 37,641 controls
]
 — European — eMERGE —