PGS Publication: PGP000494

Publication Information (EuropePMC)
Title Polygenic risk scores for the prediction of common cancers in East Asians: A population-based prospective cohort study.
PubMed ID 36971353(Europe PMC)
doi 10.7554/elife.82608
Publication Date March 27, 2023
Journal Elife
Author(s) Ho PJ, Tan IB, Chong DQ, Khor CC, Yuan JM, Koh WP, Dorajoo R, Li J.
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

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)
PGS000070
(PRS_LC_C)
 PGP000049 |
Dai J et al. Lancet Respir Med (2019)
 Lung cancer lung adenocarcinoma 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000070/ScoringFiles/PGS000070.txt.gz
PGS000873
(SNP143)
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Breast cancer breast carcinoma 143
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000873/ScoringFiles/PGS000873.txt.gz
PGS000721
(PRS_Lung)
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Lung cancer lung carcinoma 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000721/ScoringFiles/PGS000721.txt.gz
PGS000662
(GRS.PCa.269)
 PGP000122 |
Conti DV et al. Nat Genet (2021)
 Prostate cancer prostate carcinoma 269
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000662/ScoringFiles/PGS000662.txt.gz
PGS000055
(PRS_CRC)
 PGP000040 |
Schmit SL et al. J Natl Cancer Inst (2019)
 Colorectal cancer colorectal cancer 76
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000055/ScoringFiles/PGS000055.txt.gz
PGS000734
(PRS95_CRC)
 PGP000142 |
Archambault AN et al. Gastroenterology (2019)
 Colorectal cancer colorectal cancer 95
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000734/ScoringFiles/PGS000734.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
PPM018697 PGS000873
(SNP143)
 PSS011069|
East Asian Ancestry|
495 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.6 [0.58, 0.63] Hazard ratio (HR, high vs low tertile): 2.68 [1.97, 3.66] age at recruitment —
PPM018698 PGS000055
(PRS_CRC)
 PSS011070|
East Asian Ancestry|
332 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Colorectal cancer — AUROC: 0.65 [0.62, 0.69] Hazard ratio (HR, high vs low tertile): 2.27 [1.6, 3.21] age at recruitment —
PPM018699 PGS000734
(PRS95_CRC)
 PSS011071|
East Asian Ancestry|
409 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Colorectal cancer — AUROC: 0.66 [0.63, 0.69] Hazard ratio (HR, high vs low tertile): 3.25 [2.24, 4.73] age at recruitment —
PPM018700 PGS000070
(PRS_LC_C)
 PSS011073|
East Asian Ancestry|
381 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Lung cancer — AUROC: 0.68 [0.65, 0.71] Hazard ratio (HR, high vs low tertile): 2.01 [1.44, 2.81] age at recruitment —
PPM018701 PGS000721
(PRS_Lung)
 PSS011072|
East Asian Ancestry|
181 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Lung cancer — AUROC: 0.69 [0.65, 0.73] Hazard ratio (HR, high vs low tertile): 1.69 [1.03, 2.79] age at recruitment —
PPM018702 PGS000662
(GRS.PCa.269)
 PSS011074|
East Asian Ancestry|
308 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Prostate cancer — AUROC: 0.72 [0.7, 0.75] Hazard ratio (HR, high vs low tertile): 8.99 [5.27, 15.35] age at recruitment —

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
PSS011069 — — 495 individuals,
0.0 % Male samples
 Median = 53.0 years
IQR = [48.0, 59.0] years		 East Asian
(Chinese)		 — SCHS —
PSS011070 — — 332 individuals,
0.0 % Male samples
 Median = 58.0 years
IQR = [52.0, 64.0] years		 East Asian
(Chinese)		 — SCHS —
PSS011071 — — 409 individuals,
100.0 % Male samples
 Median = 59.0 years
IQR = [52.0, 65.0] years		 East Asian
(Chinese)		 — SCHS —
PSS011072 — — 181 individuals,
0.0 % Male samples
 Median = 59.0 years
IQR = [55.0, 64.0] years		 East Asian
(Chinese)		 — SCHS —
PSS011073 — — 381 individuals,
100.0 % Male samples
 Median = 60.0 years
IQR = [55.0, 64.0] years		 East Asian
(Chinese)		 — SCHS —
PSS011074 — — 308 individuals,
100.0 % Male samples
 Median = 59.0 years
IQR = [54.0, 64.0] years		 East Asian
(Chinese)		 — SCHS —