PGS Publication: PGP000156

Publication Information (EuropePMC)
Title A genome-wide association study of prostate cancer in Latinos.
PubMed ID 31226226(Europe PMC)
doi 10.1002/ijc.32525
Publication Date July 3, 2019
Journal Int J Cancer
Author(s) Du Z, Hopp H, Ingles SA, Huff C, Sheng X, Weaver B, Stern M, Hoffmann TJ, John EM, Van Den Eeden SK, Strom S, Leach RJ, Thompson IM, Witte JS, Conti DV, Haiman CA.
Released in PGS Catalog: March 22, 2021

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000751 PRS_PrCa_EuropeanWeighted PGP000156
Du Z et al. Int J Cancer (2019)
Prostate cancer prostate carcinoma 178 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000751/ScoringFiles/PGS000751.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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001907 PGS000751
(PRS_PrCa_EuropeanWeighted)
PSS000953 PGP000156
Du Z et al. Int J Cancer (2019)
Reported Trait: Prostate cancer Odds ratio (OR, top 10% vs. middle 50%): 3.1 [2.55, 3.76] Age, study, PCs(1-10) Only 176 variants of the original 181 variants were utilised as 5 variants did not meet a MAF  ≥  0.001 and imputation r^2  ≥ 0.3 in Latino men.
PPM001908 PGS000751
(PRS_PrCa_EuropeanWeighted)
PSS000953 PGP000156
Du Z et al. Int J Cancer (2019)
Reported Trait: Prostate cancer Odds ratio (OR, top 1% vs. middle 50%): 4.02 [2.46, 6.55] Age, study, PCs(1-10) Only 176 variants of the original 181 variants were utilised as 5 variants did not meet a MAF  ≥  0.001 and imputation r^2  ≥ 0.3 in Latino men.
PPM001909 PGS000751
(PRS_PrCa_EuropeanWeighted)
PSS000953 PGP000156
Du Z et al. Int J Cancer (2019)
Reported Trait: Prostate cancer Odds ratio (OR, bottom 10% vs. middle 50%): 0.38 [0.28, 0.51] Age, study, PCs(1-10) Only 176 variants of the original 181 variants were utilised as 5 variants did not meet a MAF  ≥  0.001 and imputation r^2  ≥ 0.3 in Latino men.
PPM001910 PGS000751
(PRS_PrCa_EuropeanWeighted)
PSS000953 PGP000156
Du Z et al. Int J Cancer (2019)
Reported Trait: Prostate cancer Odds ratio (OR, bottom 1% vs. middle 50%): 0.25 [0.09, 0.67] Age, study, PCs(1-10) Only 176 variants of the original 181 variants were utilised as 5 variants did not meet a MAF  ≥  0.001 and imputation r^2  ≥ 0.3 in Latino men.

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000953 In set 1 (1034 cases), prostate cancer cases were identified by linking with the cancer registries in Hawaii and California. In set 2 (1192 cases) cases were indiviuals with prostate cancer determined by cancer diagnosis, enrollment in prostate cancer studies at University of Texas M.D. Ancerson Cancer Centre or by biposy confirmation.
[
  • 2,226 cases
  • , 2,098 controls
]
,
100.0 % Male samples
Hispanic or Latin American LAAPC, MDA, MEC, SABOR