PGS Publication: PGP000047

Publication Information (EuropePMC)
Title Polygenic hazard score to guide screening for aggressive prostate cancer: development and validation in large scale cohorts.
PubMed ID 29321194(Europe PMC)
doi 10.1136/bmj.j5757
Publication Date Jan. 10, 2018
Journal BMJ
Author(s) Seibert TM, Fan CC, Wang Y, Zuber V, Karunamuni R, Parsons JK, Eeles RA, Easton DF, Kote-Jarai Z, Al Olama AA, Garcia SB, Muir K, Grönberg H, Wiklund F, Aly M, Schleutker J, Sipeky C, Tammela TL, Nordestgaard BG, Nielsen SF, Weischer M, Bisbjerg R, Røder MA, Iversen P, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Brenner H, Cuk K, Saum KU, Park JY, Sellers TA, Slavov C, Kaneva R, Mitev V, Batra J, Clements JA, Spurdle A, Teixeira MR, Paulo P, Maia S, Pandha H, Michael A, Kierzek A, Karow DS, Mills IG, Andreassen OA, Dale AM, PRACTICAL Consortium*.
Released in PGS Catalog: Feb. 12, 2020

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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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)
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
PPM000182 PGS000067
(PCa_PHS)
 PSS000105|
European Ancestry|
5,456 individuals
 PGP000047 |
Seibert TM et al. BMJ (2018)
 Reported Trait: aggressive prostate cancer — — HR (Hazard ratio; top 2% vs. average risk): 2.9 [2.4, 3.4] — —
PPM000184 PGS000067
(PCa_PHS)
 PSS000106|
European Ancestry|
6,411 individuals
 PGP000047 |
Seibert TM et al. BMJ (2018)
 Reported Trait: any prostate cancer — — HR (Hazard ratio; top 2% vs. average risk): 2.5 [2.2, 2.8] — —
PPM000186 PGS000067
(PCa_PHS)
 PSS000107|
European Ancestry|
5,048 individuals
 PGP000047 |
Seibert TM et al. BMJ (2018)
 Reported Trait: very aggressive prostate cancer — — HR (Hazard ratio; top 2% vs. average risk): 3.0 [2.2, 4.0] — —
PPM000187 PGS000067
(PCa_PHS)
 PSS000107|
European Ancestry|
5,048 individuals
 PGP000047 |
Seibert TM et al. BMJ (2018)
 Reported Trait: very aggressive prostate cancer (age at onset) — — z-test (p-value) <: 1.00e-16 — —
PPM000183 PGS000067
(PCa_PHS)
 PSS000105|
European Ancestry|
5,456 individuals
 PGP000047 |
Seibert TM et al. BMJ (2018)
 Reported Trait: aggressive prostate cancer (age at onset) — — z-test (p-value) <: 1.00e-16 — —
PPM000185 PGS000067
(PCa_PHS)
 PSS000106|
European Ancestry|
6,411 individuals
 PGP000047 |
Seibert TM et al. BMJ (2018)
 Reported Trait: any prostate cancer (age at onset) — — z-test (p-value) <: 1.00e-16 — —

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
PSS000105 Men screened with PSA testing, who did not receive a diagnosis of prostate cancer. — 4,828 individuals,
100.0 % Male samples
 Mean = 59.0 years
IQR = [55.0, 63.0] years		 European — ProtecT —
PSS000105 Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of aggressive prostate cancer (defined as any of Gleason score ≥7, stage T3-T4, PSA concentration ≥10 ng/mL, nodal metastasis, or distant metastasis) —
[
  • 628 cases
]
,
100.0 % Male samples
 Mean = 64.3 years
IQR = [60.2, 67.5] years		 European — ProtecT —
PSS000106 Men screened with PSA testing, who did not receive a diagnosis of prostate cancer. — 4,828 individuals,
100.0 % Male samples
 Mean = 59.0 years
IQR = [55.0, 63.0] years		 European — ProtecT —
PSS000106 Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of prostate cancer. —
[
  • 1,583 cases
]
,
100.0 % Male samples
 Mean = 63.4 years
IQR = [59.0, 67.5] years		 European — ProtecT —
PSS000107 Men screened with PSA testing, who did not receive a diagnosis of prostate cancer. — 4,828 individuals,
100.0 % Male samples
 Mean = 59.0 years
IQR = [55.0, 63.0] years		 European — ProtecT —
PSS000107 Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of very aggressive prostate cancer (defined as any of Gleason score ≥8, stage T3-4, positive nodes, or distant metastases) —
[
  • 220 cases
]
,
100.0 % Male samples
 — European — ProtecT —