PGS Publication: PGP000564

Publication Information (EuropePMC)
Title Integration of pathologic characteristics, genetic risk and lifestyle exposure for colorectal cancer survival assessment.
PubMed ID 38589358(Europe PMC)
doi 10.1038/s41467-024-47204-9
Publication Date April 8, 2024
Journal Nat Commun
Author(s) Xin J, Gu D, Li S, Qian S, Cheng Y, Shao W, Ben S, Chen S, Zhu L, Jin M, Chen K, Hu Z, Zhang Z, Du M, Shen H, Wang M.
Released in PGS Catalog: June 27, 2024

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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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)
PGS004586
(PPS_CRC)
 PGP000564 |
Xin J et al. Nat Commun (2024)
 Colorectal cancer colorectal carcinoma 287
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004586/ScoringFiles/PGS004586.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
PPM020702 PGS004586
(PPS_CRC)
 PSS011374|
East Asian Ancestry|
543 individuals
 PGP000564 |
Xin J et al. Nat Commun (2024)
 Reported Trait: Overall survival of colorectal cancer HR: 1.9 [1.61, 2.24] AUROC: 0.649 — sex, age, smoking status, drinking status and top 10 principal components —
PPM020701 PGS004586
(PPS_CRC)
 PSS011373|
European Ancestry|
470 individuals
 PGP000564 |
Xin J et al. Nat Commun (2024)
 Reported Trait: Overall survival of colorectal cancer HR: 1.99 [1.57, 2.52] AUROC: 0.652 — sex, age, stage and top 10 principal components —
PPM020703 PGS004586
(PPS_CRC)
 PSS011372|
European Ancestry|
713 individuals
 PGP000564 |
Xin J et al. Nat Commun (2024)
 Reported Trait: Overall survival of colorectal cancer HR: 1.8 [1.49, 2.17] AUROC: 0.658 — sex, age, smoking status, drinking status, research center, arm, stage, grade and top 10 principal components —

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
PSS011373 — — 470 individuals — European — TCGA —
PSS011374 — — 543 individuals — East Asian
(Chinese)		 — NCRCC ZJCRC
PSS011372 — — 713 individuals — European — PLCO —