PGS Publication: PGP000715

Publication Information (EuropePMC)
Title Polygenic Risk Score Modifies Prostate Cancer Risk of Pathogenic Variants in Men of African Ancestry.
PubMed ID 38014910(Europe PMC)
doi 10.1158/2767-9764.crc-23-0022
Publication Date Dec. 1, 2023
Journal Cancer Res Commun
Author(s) Hughley RW, Matejcic M, Song Z, Sheng X, Wan P, Xia L, Hart SN, Hu C, Yadav S, Lubmawa A, Kiddu V, Asiimwe F, Amanya C, Mutema G, Job K, Ssebakumba MK, Ingles SA, Hamilton AS, Couch FJ, Watya S, Conti DV, Darst BF, Haiman CA.
Released in PGS Catalog: March 17, 2025

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)
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

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
PPM022455 PGS000662
(GRS.PCa.269)
 PSS011949|
African Ancestry|
2,760 individuals
 PGP000715 |
Hughley RW et al. Cancer Res Commun (2023)
|Ext.		 Reported Trait: Overall prostate cancer — — Hazard ratio (HR, intermediate vs low tertile): 3.0 [2.52, 3.57] — —
PPM022456 PGS000662
(GRS.PCa.269)
 PSS011949|
African Ancestry|
2,760 individuals
 PGP000715 |
Hughley RW et al. Cancer Res Commun (2023)
|Ext.		 Reported Trait: Metastatic prostate cancer — — Hazard ratio (HR, intermediate vs low tertile): 3.11 [2.14, 4.52] — —
PPM022457 PGS000662
(GRS.PCa.269)
 PSS011949|
African Ancestry|
2,760 individuals
 PGP000715 |
Hughley RW et al. Cancer Res Commun (2023)
|Ext.		 Reported Trait: Aggressive prostate cancer — — Hazard ratio (HR, intermediate vs low tertile): 3.14 [2.54, 3.86] — —
PPM022458 PGS000662
(GRS.PCa.269)
 PSS011949|
African Ancestry|
2,760 individuals
 PGP000715 |
Hughley RW et al. Cancer Res Commun (2023)
|Ext.		 Reported Trait: Non-aggressive prostate cancer — — Hazard ratio (HR, intermediate vs low tertile): 3.1 [2.43, 3.95] — —
PPM022459 PGS000662
(GRS.PCa.269)
 PSS011949|
African Ancestry|
2,760 individuals
 PGP000715 |
Hughley RW et al. Cancer Res Commun (2023)
|Ext.		 Reported Trait: Overall prostate cancer x P/LP/D variants in BRCA2, ATM, NBN, and PALB2 carrier status interaction — — Hazard ratio (HR, non-carrier of P/LP/D variants in BRCA2, ATM, NBN, and PALB2 and high PRS vs. carrier of P/LP/D variants in BRCA2, ATM, NBN, and PALB2 and intermediate PRS): 18.06 [4.24, 76.84] — —
PPM022460 PGS000662
(GRS.PCa.269)
 PSS011949|
African Ancestry|
2,760 individuals
 PGP000715 |
Hughley RW et al. Cancer Res Commun (2023)
|Ext.		 Reported Trait: Metastatic prostate cancer x P/LP/D variants in BRCA2, ATM, NBN, and PALB2 carrier status interaction — — Hazard ratio (HR, non-carrier of P/LP/D variants in BRCA2, ATM, NBN, and PALB2 and high PRS vs. carrier of P/LP/D variants in BRCA2, ATM, NBN, and PALB2 and intermediate PRS): 28.99 [4.39, 191.43] — —
PPM022461 PGS000662
(GRS.PCa.269)
 PSS011949|
African Ancestry|
2,760 individuals
 PGP000715 |
Hughley RW et al. Cancer Res Commun (2023)
|Ext.		 Reported Trait: Aggressive prostate cancer x P/LP/D variants in BRCA2, ATM, NBN, and PALB2 carrier status interaction — — Hazard ratio (HR, non-carrier of P/LP/D variants in BRCA2, ATM, NBN, and PALB2 and high PRS vs. carrier of P/LP/D variants in BRCA2, ATM, NBN, and PALB2 and intermediate PRS): 23.58 [5.39, 103.2] — —

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
PSS011949 — —
[
  • 1,286 cases
  • , 965 controls
]
,
100.0 % Male samples
 — African American or Afro-Caribbean — LAAPC, MEC —
PSS011949 — —
[
  • 50 cases
  • , 459 controls
]
,
100.0 % Male samples
 — Sub-Saharan African — CA UG Study —