PGS Preprint: PGP000492

Publication Information (EuropePMC)
Title Combining Asian-European Genome-Wide Association Studies of Colorectal Cancer Improves Risk Prediction Across Race and Ethnicity.
doi 10.1101/2023.01.19.23284737
Publication Date Jan. 19, 2023
Journal medRxiv Preprint
Author(s) Thomas M, Su YR, Rosenthal EA, Sakoda LC, Schmit SL, Timofeeva MN, Chen Z, Fernandez-Rozadilla C, Law PJ, Murphy N, Carreras-Torres R, Diez-Obrero V, van Duijnhoven FJB, Jiang S, Shin A, Wolk A, Phipps AI, Burnett-Hartman A, Gsur A, Chan AT, Zauber AG, Wu AH, Lindblom A, Um CY, Tangen CM, Gignoux C, Newton C, Haiman CA, Qu C, Bishop DT, Buchanan DD, Crosslin DR, Conti DV, Kim DH, Hauser E, White E, Siegel E, Schumacher FR, Rennert G, Giles GG, Hampel H, Brenner H, Oze I, Oh JH, Lee JK, Schneider JL, Chang-Claude J, Kim J, Huyghe JR, Zheng J, Hampe J, Greenson J, Hopper JL, Palmer JR, Visvanathan K, Matsuo K, Matsuda K, Jung KJ, Li L, Le Marchand L, Vodickova L, Bujanda L, Gunter MJ, Matejcic M, Jenkins MA, Slattery ML, D’Amato M, Wang M, Hoffmeister M, Woods MO, Kim M, Song M, Iwasaki M, Du M, Udaltsova N, Sawada N, Vodicka P, Campbell PT, Newcomb PA, Cai Q, Pearlman R, Pai RK, Schoen RE, Steinfelder RS, Haile RW, Vandenputtelaar R, Prentice RL, Küry S, Castellví-Bel S, Tsugane S, Berndt SI, Lee SC, Brezina S, Weinstein SJ, Chanock SJ, Jee SH, Kweon SS, Vadaparampil S, Harrison TA, Yamaji T, Keku TO, Vymetalkova V, Arndt V, Jia WH, Shu XO, Lin Y, Ahn YO, Stadler ZK, Van Guelpen B, Ulrich CM, Platz EA, Potter JD, Li CI, Meester R, Moreno V, Figueiredo JC, Casey G, Landorp-Vogelaar I, Dunlop MG, ruber SB, Hayes RB, Pharoah PDP, Houlston RS, Jarvik GP, Tomlinson IP, Zheng W, Corley DA, Peters U, Hsu L.
Released in PGS Catalog: Sept. 1, 2023

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

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)
PGS003852
(CRC_PRS_EUR_EAS)
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Pre		 Colorectal cancer colorectal cancer 1,016,596
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003852/ScoringFiles/PGS003852.txt.gz

External PGS Evaluated By This Publication

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)
PGS003850
(CRC_PRS_200loci)
 PGP000491 |
Fernandez-Rozadilla C et al. Nat Genet (2022)
 Colorectal cancer colorectal cancer 205
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003850/ScoringFiles/PGS003850.txt.gz
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

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
PPM018673 PGS003852
(CRC_PRS_EUR_EAS)
 PSS011062|
Additional Asian Ancestries|
12,025 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Pre		 Reported Trait: Colorectal cancer OR: 1.64 [1.55, 1.74] AUROC: 0.63 [0.62, 0.64] — Age, sex, PCs 1-4 —
PPM018674 PGS003852
(CRC_PRS_EUR_EAS)
 PSS011063|
African Ancestry|
13,823 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Pre		 Reported Trait: Colorectal cancer OR: 1.39 [1.31, 1.47] AUROC: 0.59 [0.57, 0.61] — Age, sex, PCs 1-4 —
PPM018675 PGS003852
(CRC_PRS_EUR_EAS)
 PSS011064|
Hispanic or Latin American Ancestry|
10,377 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Pre		 Reported Trait: Colorectal cancer OR: 1.62 [1.51, 1.73] AUROC: 0.62 [0.6, 0.63] — Age, sex, PCs 1-4 —
PPM018676 PGS003852
(CRC_PRS_EUR_EAS)
 PSS011065|
European Ancestry|
118,756 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Pre		 Reported Trait: Colorectal cancer OR: 1.67 [1.6, 1.75] AUROC: 0.65 [0.64, 0.66] — Age, sex, PCs 1-4 —
PPM018677 PGS003850
(CRC_PRS_200loci)
 PSS011062|
Additional Asian Ancestries|
12,025 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Colorectal cancer OR: 1.3 AUROC: 0.6 [0.59, 0.62] — Age, sex, PCs 1-4 —
PPM018678 PGS003850
(CRC_PRS_200loci)
 PSS011063|
African Ancestry|
13,823 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Colorectal cancer OR: 1.25 AUROC: 0.58 [0.56, 0.59] — Age, sex, PCs 1-4 —
PPM018679 PGS003850
(CRC_PRS_200loci)
 PSS011064|
Hispanic or Latin American Ancestry|
10,377 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Colorectal cancer OR: 1.37 AUROC: 0.59 [0.57, 0.6] — Age, sex, PCs 1-4 —
PPM018680 PGS003850
(CRC_PRS_200loci)
 PSS011065|
European Ancestry|
118,756 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Colorectal cancer OR: 1.62 AUROC: 0.61 [0.6, 0.62] — Age, sex, PCs 1-4 —
PPM018681 PGS003851
(CRC_PRS_EUR)
 PSS011062|
Additional Asian Ancestries|
12,025 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Colorectal cancer — AUROC: 0.619 [0.547, 0.689] — Age, sex, PCs 1-10 —
PPM018682 PGS003851
(CRC_PRS_EUR)
 PSS011063|
African Ancestry|
13,823 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Colorectal cancer — AUROC: 0.526 [0.419, 0.62] — Age, sex, PCs 1-10 —
PPM018683 PGS003851
(CRC_PRS_EUR)
 PSS011064|
Hispanic or Latin American Ancestry|
10,377 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Colorectal cancer — AUROC: 0.584 [0.511, 0.656] — Age, sex, PCs 1-10 —
PPM018684 PGS003851
(CRC_PRS_EUR)
 PSS011065|
European Ancestry|
118,756 individuals
 PGP000492 |
Thomas M T et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Colorectal cancer — AUROC: 0.638 [0.624, 0.652] — Age, sex, PCs 1-10 —

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
PSS011062 — —
[
  • 2,420 cases
  • , 9,605 controls
]
,
50.5 % Male samples
 Mean = 64.5 years Asian unspecified — GERA, MG-JPN —
PSS011063 — —
[
  • 1,954 cases
  • , 11,869 controls
]
,
44.0 % Male samples
 Mean = 61.33 years African American or Afro-Caribbean — GERA, MG-AA, eMERGE —
PSS011064 — —
[
  • 1,681 cases
  • , 8,696 controls
]
,
47.5 % Male samples
 Mean = 64.0 years Hispanic or Latin American — GERA, HCCS —
PSS011065 — —
[
  • 3,651 cases
  • , 115,105 controls
]
,
52.75 % Male samples
 Mean = 65.75 years European — BCC, CPSII, GERA, eMERGE —