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, Dampi... er 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.Show more
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:
Display options:
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

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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)
PGS002265
(PRS140_CRC)
PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
Colorectal cancercolorectal cancer140
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002265/ScoringFiles/PGS002265.txt.gz
PGS003851
(CRC_PRS_EUR)
PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
Colorectal cancercolorectal cancer1,180,765
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003851/ScoringFiles/PGS003851.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
PPM018664PGS002265
(PRS140_CRC)
PSS011059|
European Ancestry|
72,791 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, sex—
PPM018665PGS002265
(PRS140_CRC)
PSS011058|
East Asian Ancestry|
6,966 individuals
PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
Reported Trait: Colorectal cancer—AUROC: 0.591 [0.536, 0.625]—age, sex—
PPM018666PGS002265
(PRS140_CRC)
PSS011060|
Hispanic or Latin American Ancestry|
6,660 individuals
PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
Reported Trait: Colorectal cancer—AUROC: 0.592 [0.531, 0.652]—age, sex—
PPM018667PGS002265
(PRS140_CRC)
PSS011057|
African Ancestry|
5,249 individuals
PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
Reported Trait: Colorectal cancer—AUROC: 0.581 [0.5, 0.645]—age, sex—
PPM018668PGS002265
(PRS140_CRC)
PSS011061|
European Ancestry|
38,214 individuals
PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
Reported Trait: Colorectal cancer—AUROC: 0.591—age, sex—
PPM018669PGS003851
(CRC_PRS_EUR)
PSS011059|
European Ancestry|
72,791 individuals
PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
Reported Trait: Colorectal cancer—AUROC: 0.654 [0.639, 0.669]—age, sex—
PPM018670PGS003851
(CRC_PRS_EUR)
PSS011058|
East Asian Ancestry|
6,966 individuals
PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
Reported Trait: Colorectal cancer—AUROC: 0.601 [0.538, 0.664]—age, sex—
PPM018671PGS003851
(CRC_PRS_EUR)
PSS011057|
African Ancestry|
5,249 individuals
PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
Reported Trait: Colorectal cancer—AUROC: 0.543 [0.5, 0.6241]—age, sex—
PPM018672PGS003851
(CRC_PRS_EUR)
PSS011060|
Hispanic or Latin American Ancestry|
6,660 individuals
PGP000294 |
Thomas M et al. Am J Hum Genet (2020)
Reported Trait: Colorectal cancer—AUROC: 0.602 [0.542, 0.662]—age, sex—
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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
PSS011057——
[
  • 56 cases
  • , 5,193 controls
]
,
65.5 % Male samples
Mean = 61.6 years
Range = [20.0, 90.0] years		African American or Afro-Caribbean
(African American)		—GERA—
PSS011058——
[
  • 96 cases
  • , 6,870 controls
]
,
42.1 % Male samples
Mean = 55.8 years
Range = [20.0, 90.0] years		East Asian—GERA—
PSS011059——
[
  • 1,311 cases
  • , 71,480 controls
]
,
41.6 % Male samples
Mean = 62.3 years
Range = [20.0, 90.0] years		European—GERA—
PSS011060——
[
  • 70 cases
  • , 6,590 controls
]
,
38.7 % Male samples
Mean = 55.0 years
Range = [20.0, 90.0] years		Hispanic or Latin American—GERA—
PSS011061The 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.Show more—
[
  • 573 cases
  • , 37,641 controls
]
—European—eMERGE—
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