PGS Publication: PGP000139

Publication Information (EuropePMC)
Title African-specific improvement of a polygenic hazard score for age at diagnosis of prostate cancer.
PubMed ID 32930425(Europe PMC)
doi 10.1002/ijc.33282
Publication Date Sept. 24, 2020
Journal Int J Cancer
Author(s) Karunamuni RA, Huynh-Le MP, Fan CC, Thompson W, Eeles RA, Kote-Jarai Z, Muir K, UKGPCS Collaborators, Lophatananon A, Tangen CM, Goodman PJ, Thompson IM, Blot WJ, Zheng W, Kibel AS, Drake BF, Cussenot O, Cancel-Tassin G, Menegaux F, Truong T, Park JY, Lin HY, Bensen JT, Fontham ETH, Mohler JL, Taylor JA, Multigner L, Blanchet P, Brureau L, Romana M, Leach RJ, John EM, Fowke J, Bush WS, Aldrich M, Crawford DC, Srivastava S, Cullen JC, Petrovics G, Parent MÉ, Hu JJ, Sanderson M, Mills IG, Andreassen OA, Dale AM, Seibert TM, PRACTICAL Consortium.
Released in PGS Catalog: Feb. 23, 2021

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

PGS Developed 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)
PGS000733
(PHS46+African)
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
 Prostate cancer prostate carcinoma 49
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000733/ScoringFiles/PGS000733.txt.gz

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)
PGS000067
(PCa_PHS)
 PGP000047 |
Seibert TM et al. BMJ (2018)
 Prostate cancer prostate carcinoma 54
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000067/ScoringFiles/PGS000067.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
PPM001674 PGS000733
(PHS46+African)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
 Reported Trait: Age at diagnosis of any prostate cancer — — Hazard Ratio (HR top 20% vs. bottom 20%): 4.42 [4.16, 4.67] — Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001675 PGS000067
(PCa_PHS)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of any prostate cancer — — Hazard Ratio (HR top 2% vs. middle 40%): 2.1 [1.99, 2.21] — 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM001676 PGS000733
(PHS46+African)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
 Reported Trait: Age at diagnosis of any prostate cancer — — Hazard Ratio (HR top 2% vs. middle 40%): 3.67 [3.48, 3.87] — Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001677 PGS000067
(PCa_PHS)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of any prostate cancer — — Hazard Ratio (HR bottom 20% vs. middle 40%): 0.65 [0.63, 0.67] — 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM001678 PGS000733
(PHS46+African)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
 Reported Trait: Age at diagnosis of any prostate cancer — — Hazard Ratio (HR bottom 20% vs. middle 40%): 0.51 [0.49, 0.52] — Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001679 PGS000067
(PCa_PHS)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of clinically significant prostate cancer — — Hazard Ratio (HR top 20% vs. bottom 20%): 2.21 [2.04, 2.38] — 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM001680 PGS000733
(PHS46+African)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
 Reported Trait: Age at diagnosis of clinically significant prostate cancer — — Hazard Ratio (top 20% vs. bottom 20%): 4.71 [4.38, 5.05] — Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001682 PGS000733
(PHS46+African)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
 Reported Trait: Age at diagnosis of clinically significant prostate cancer — — Hazard Ratio (top 2% vs. middle 40%): 3.89 [3.64, 4.13] — Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001683 PGS000067
(PCa_PHS)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of clinically significant prostate cancer — — Hazard Ratio (bottom 20% vs. middle 40%): 0.7 [0.68, 0.73] — 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM001684 PGS000733
(PHS46+African)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
 Reported Trait: Age at diagnosis of clinically significant prostate cancer — — Hazard Ratio (bottom 20% vs. middle 40%): 0.5 [0.48, 0.52] — Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001681 PGS000067
(PCa_PHS)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of clinically significant prostate cancer — — Hazard Ratio (top 2% vs. middle 40%): 1.91 [1.79, 2.04] — 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM001673 PGS000067
(PCa_PHS)
 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of any prostate cancer — — Hazard Ratio (HR top 20% vs. bottom 20%): 2.47 [2.32, 2.62] — 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).

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
PSS000874 Clinically significant cancer were any of: Gleason score ≥ 7, stage T3-T4, PSA concentration ≥ 10 ng/mL, pelvic lymph nodal metastasis or distant metastasis. —
[
  • 3,031 cases
  • , 3,240 controls
]
,
100.0 % Male samples
 — African unspecified — 18 cohorts
  • BioVU
  • ,CPDR
  • ,CeRePP
  • ,EPICAP
  • ,KARUPROSTATE
  • ,MIAMI-WFPCS
  • ,MOFFITT
  • ,NMHS
  • ,PCPT
  • ,PCaP
  • ,PROtEuS
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SELECT
  • ,SFPCS
  • ,UKGPCS
  • ,WUGS
 PRACTICAL consortium