| Publication Information (EuropePMC) | |
| Title | Validation of a prostate cancer polygenic risk score. |
| PubMed ID | 33258481(Europe PMC) |
| doi | 10.1002/pros.24058 |
| Publication Date | Aug. 17, 2020 |
| Journal | Prostate |
| Author(s) | Black MH, Li S, LaDuca H, Lo MT, Chen J, Hoiness R, Gutierrez S, Tippin-Davis B, Lu HM, Gielzak M, Wiley K, Shi Z, Wei J, Zheng SL, Helfand BT, Isaacs W, Xu J. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000348 (PRS_PrCa) |
PGP000113 | Black MH et al. Prostate (2020) |
Prostate cancer | prostate carcinoma | 72 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000348/ScoringFiles/PGS000348.txt.gz |
|
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000987 | PGS000348 (PRS_PrCa) |
PSS000502| European Ancestry| 1,039 individuals |
PGP000113 | Black MH et al. Prostate (2020) |
Reported Trait: Prostate cancer in men with a family history of prostate cancer | OR: 1.9 [1.53, 2.4] | — | — | Age | — |
| PPM000986 | PGS000348 (PRS_PrCa) |
PSS000501| European Ancestry| 3,891 individuals |
PGP000113 | Black MH et al. Prostate (2020) |
Reported Trait: Prostate cancer | — | AUROC: 0.64 | — | Age | — |
| PPM000985 | PGS000348 (PRS_PrCa) |
PSS000501| European Ancestry| 3,891 individuals |
PGP000113 | Black MH et al. Prostate (2020) |
Reported Trait: Prostate cancer | OR: 1.72 [1.59, 1.88] | AUROC: 0.64 [0.62, 0.66] | — | — | — |
| PPM000988 | PGS000348 (PRS_PrCa) |
PSS000503| European Ancestry| 2,305 individuals |
PGP000113 | Black MH et al. Prostate (2020) |
Reported Trait: Prostate cancer in men with no family history of prostate cancer | OR: 1.65 [1.49, 1.84] | — | — | Age | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000501 | Cases: Male, self-reported European ancestry, greater or equal to 18 years of age at prostate cancer diagnosis. JHH cases were patients undergoing radical prostatectomy for the treatment of clinically localized PrCa in 2002 to 2015 and were included if disease was organ‐confined and Gleason score ≤6 or ≥8, as determined upon pathological evaluation of the prostatectomy specimen. Only the high‐ and low‐grade PrCa JHH cases were included because they were previously curated to assess the association of RPVs in cancer susceptibility genes with PrCa. JHH controls were included if they self repored with European American ancestry, had a normal digital rectal examination, PSA level less than 4.0 ng/mL and were older than 55 years. AG cases and controls were men referred for multigene panel testing in 2017 to 2019. Among AG cases, 104 patients had Gleason ≥8, and 59 patients had Gleason ≤6, and 230 patients had no pathology information. AG controls were unaffected with prostate cancer at the time of testing. NSGI controls had a minimum of 1 year clincal history available in the EHR and were exlucded if any ICD9/10 diagnosis of cancer was present at any time in the EHR. Men who tested positive for RPVs in any prostate cancer susceptibility gene were exlcuded from further analysis. | — | [ ,
100.0 % Male samples |
— | European | — | AG, JHH, NSGHI | — |
| PSS000502 | Cases: Male, self-reported European ancestry, greater or equal to 18 years of age at prostate cancer diagnosis. JHH cases were patients undergoing radical prostatectomy for the treatment of clinically localized PrCa in 2002 to 2015 and were included if disease was organ‐confined and Gleason score ≤6 or ≥8, as determined upon pathological evaluation of the prostatectomy specimen. Only the high‐ and low‐grade PrCa JHH cases were included because they were previously curated to assess the association of RPVs in cancer susceptibility genes with PrCa. JHH controls were included if they self repored with European American ancestry, had a normal digital rectal examination, PSA level less than 4.0 ng/mL and were older than 55 years. AG cases and controls were men referred for multigene panel testing in 2017 to 2019. Among AG cases, 104 patients had Gleason ≥8, and 59 patients had Gleason ≤6, and 230 patients had no pathology information. AG controls were unaffected with prostate cancer at the time of testing. | — | [ ,
100.0 % Male samples |
— | European | — | AG, JHH | — |
| PSS000503 | Cases: Male, self-reported European ancestry, greater or equal to 18 years of age at prostate cancer diagnosis. JHH cases were patients undergoing radical prostatectomy for the treatment of clinically localized PrCa in 2002 to 2015 and were included if disease was organ‐confined and Gleason score ≤6 or ≥8, as determined upon pathological evaluation of the prostatectomy specimen. Only the high‐ and low‐grade PrCa JHH cases were included because they were previously curated to assess the association of RPVs in cancer susceptibility genes with PrCa. JHH controls were included if they self repored with European American ancestry, had a normal digital rectal examination, PSA level less than 4.0 ng/mL and were older than 55 years. AG cases and controls were men referred for multigene panel testing in 2017 to 2019. Among AG cases, 104 patients had Gleason ≥8, and 59 patients had Gleason ≤6, and 230 patients had no pathology information. AG controls were unaffected with prostate cancer at the time of testing. | — | [ ,
100.0 % Male samples |
— | European | — | AG, JHH | — |