PGS Catalog - PGS000802 / Colorectal cancer (Polygenic Score)

Polygenic Score (PGS) ID: PGS000802

Predicted Trait
Reported Trait	Colorectal cancer
Mapped Trait(s)	colorectal cancer (MONDO_0005575)

Released in PGS Catalog: June 11, 2021

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Score Details

Score Construction
PGS Name	CRC_19
Development Method
Name	LASSO penalized regression
Parameters	10-fold cross-validation, lambda (λ) = 0.012, r^2 < 0.20
Variants
Original Genome Build	NR
Number of Variants	19
Effect Weight Type	NR

PGS Source
PGS Catalog Publication (PGP) ID	PGP000191
Citation (link to publication)	He CY et al. Genomics (2021)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 63.6% East Asian: 36.4% 111,769 individuals (100%)
Score Development/Training	East Asian: 100% 5,606 individuals (100%)
PGS Evaluation	East Asian: 100% 3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
GWAS Catalog: GCST001161 Europe PMC: 21761138	6,322 individuals	European	CCFR, DALS, PLCO, WHI
Europe PMC: 21655089	17,274 individuals [ 8,021 cases , 9,253 controls ]	European	8 cohorts B58C ,CoRGI ,EPICOLON ,FCCPS ,NSCCG ,QUASAR2 ,SEARCH ,VICTOR
GWAS Catalog: GCST000948 Europe PMC: 21242260	3,481 individuals	East Asian	BBJ, O-MRC
GWAS Catalog: GCST001792 Europe PMC: 23263487	7,847 individuals	East Asian	Aichi_Con, Guangzhou, KCPS, Shanghai
GWAS Catalog: GCST002454 Europe PMC: 24836286	8,270 individuals	East Asian	Aichi_Con, Guangzhou, KCPS, Shanghai
GWAS Catalog: GCST003799 Europe PMC: 26965516	21,096 individuals	East Asian	BBJ, Guangzhou, KCPS, Shanghai
GWAS Catalog: GCST001787 Europe PMC: 23266556	27,809 individuals	European	NR
GWAS Catalog: GCST001544 Europe PMC: 22634755	17,780 individuals	European	COGS, CoRGI, NSCCG, SOCCS, VICTOR
GWAS Catalog: GCST000113 Europe PMC: 17934461	1,890 individuals	European	CoRGI

Score Development/Training

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)	Phenotype Definitions & Methods	Age of Study Participants	Participant Follow-up Time	Additional Ancestry Description	Additional Sample/Cohort Information
—	5,606 individuals [ 2,557 cases , 3,049 controls ] , 54.07 % Male samples	East Asian (Han-Chinese)	NR	Exclusion criteria for healthy controls included subjects with polyposis, adenomas, and diseases related to or causing a predisposition for cancer. Cases included subjects with colorectal cancer, confirmed by endoscopic and histological examinations.	—	—	—	Subjects obtained from Sun Yat-Sen University Cancer Center (SYSUCC)

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)	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
PPM002098	PSS001032\| East Asian Ancestry\| 2,566 individuals	PGP000191 \| He CY et al. Genomics (2021)	Reported Trait: Colorectal cancer	—	—	Odds Ratio (OR, top 75% vs bottom 25%): 2.53 [1.99, 3.22]	Gender, age	—
PPM002099	PSS001031\| East Asian Ancestry\| 2,269 individuals	PGP000191 \| He CY et al. Genomics (2021)	Reported Trait: Colorectal cancer	—	—	Odds Ratio (OR, top 75% vs bottom 25%): 2.12 [1.63, 2.77]	Gender, age	—
PPM002094	PSS001033\| East Asian Ancestry\| 5,465 individuals	PGP000191 \| He CY et al. Genomics (2021)	Reported Trait: Colorectal cancer	—	AUROC: 0.59 [0.57, 0.6]	—	—	Possible overlap with score development samples
PPM002095	PSS001032\| East Asian Ancestry\| 2,566 individuals	PGP000191 \| He CY et al. Genomics (2021)	Reported Trait: Colorectal cancer	—	AUROC: 0.61 [0.59, 0.63]	—	—	—
PPM002096	PSS001031\| East Asian Ancestry\| 2,269 individuals	PGP000191 \| He CY et al. Genomics (2021)	Reported Trait: Colorectal cancer	—	AUROC: 0.59 [0.57, 0.61]	—	—	—
PPM002097	PSS001033\| East Asian Ancestry\| 5,465 individuals	PGP000191 \| He CY et al. Genomics (2021)	Reported Trait: Colorectal cancer	—	—	Odds Ratio (OR, top 75% vs bottom 25%): 2.27 [1.95, 2.64]	Gender, age	possible overlap with score development samples

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
PSS001031	Exclusion criteria for healthy controls included subjects with polyposis, adenomas, and diseases related to or causing a predisposition for cancer. Cases included subjects with colorectal cancer, confirmed by endoscopic and histological examinations.	—	2,269 individuals [ 1,027 cases , 1,242 controls ] , 51.39 % Male samples	—	East Asian (Han-Chinese)	—	NR	Subects obtained from First Hospital of China Medical University (CMU)
PSS001032	Exclusion criteria for healthy controls included subjects with polyposis, adenomas, and diseases related to or causing a predisposition for cancer. Cases included subjects with colorectal cancer, confirmed by endoscopic and histological examinations.	—	2,566 individuals [ 1,152 cases , 1,414 controls ] , 53.86 % Male samples	—	East Asian (Han-Chinese)	—	NR	Subjects obtained from Fudan University Shanghai Cancer Center (FUSCC)
PSS001033	Exclusion criteria for healthy controls included subjects with polyposis, adenomas, and diseases related to or causing a predisposition for cancer. Cases included subjects with colorectal cancer, confirmed by endoscopic and histological examinations.	—	5,465 individuals [ 2,448 cases , 3,017 controls ] , 53.72 % Male samples	—	East Asian (Han-Chinese)	—	NR	Subjects obtained from Sun Yat-Sen University Cancer Center (SYSUCC)