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. |
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 |
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. |
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. | — | [ ,
100.0 % Male samples |
— | Hispanic or Latin American | — | LAAPC, MDA, MEC, SABOR | — |