| 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. |
| 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) |
|---|---|---|---|---|---|---|
| PGS003851 (CRC_PRS_EUR) |
PGP000294 | Thomas M et al. Am J Hum Genet (2020) |
Colorectal cancer | colorectal cancer | 1,180,765 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003851/ScoringFiles/PGS003851.txt.gz |
| 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 |
|
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM018664 | PGS002265 (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 | — |
| PPM018665 | PGS002265 (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 | — |
| PPM018666 | PGS002265 (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 | — |
| PPM018667 | PGS002265 (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 | — |
| PPM018668 | PGS002265 (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 | — |
| PPM018669 | PGS003851 (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 | — |
| PPM018670 | PGS003851 (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 | — |
| PPM018671 | PGS003851 (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 | — |
| PPM018672 | PGS003851 (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 | — |
|
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 | — | — | [ ,
65.5 % Male samples |
Mean = 61.6 years Range = [20.0, 90.0] years |
African American or Afro-Caribbean (African American) |
— | GERA | — |
| PSS011058 | — | — | [ ,
42.1 % Male samples |
Mean = 55.8 years Range = [20.0, 90.0] years |
East Asian | — | GERA | — |
| PSS011059 | — | — | [ ,
41.6 % Male samples |
Mean = 62.3 years Range = [20.0, 90.0] years |
European | — | GERA | — |
| PSS011060 | — | — | [ ,
38.7 % Male samples |
Mean = 55.0 years Range = [20.0, 90.0] years |
Hispanic or Latin American | — | GERA | — |
| PSS011061 | 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. | — | [
|
— | European | — | eMERGE | — |