PGS Publication: PGP000150

Publication Information (EuropePMC)
Title Additional SNPs improve risk stratification of a polygenic hazard score for prostate cancer.
PubMed ID 33420416(Europe PMC)
doi 10.1038/s41391-020-00311-2
Publication Date Jan. 8, 2021
Journal Prostate Cancer Prostatic Dis
Author(s) Karunamuni RA, Huynh-Le MP, Fan CC, Thompson W, Eeles RA, Kote-Jarai Z, Muir K, Lophatananon A, UKGPCS collaborators, Schleutker J, Pashayan N, Batra J, APCB BioResource (Australian Prostate Cancer BioResource), Grönberg H, Walsh EI, Turner EL, Lane A, Martin RM, Neal DE, Donovan JL, Hamdy FC, Nordestgaard BG, Tangen CM, MacInnis RJ, Wolk A, Albanes D, Haiman CA, Travis RC, Stanford JL, Mucci LA, West CML, Nielsen SF, Kibel AS, Wiklund F, Cussenot O, Berndt SI, Koutros S, Sørensen KD, Cybulski C, Grindedal EM, Park JY, Ingles SA, Maier C, Hamilton RJ, Rosenstein BS, Vega A, IMPACT Study Steering Committee and Collaborators, Kogevinas M, Penney KL, Teixeira MR, Brenner H, John EM, Kaneva R, Logothetis CJ, Neuhausen SL, Razack A, Newcomb LF, Canary PASS Investigators, Gamulin M, Usmani N, Claessens F, Gago-Dominguez M, Townsend PA, Roobol MJ, Zheng W, Profile Study Steering Committee, Mills IG, Andreassen OA, Dale AM, Seibert TM, PRACTICAL Consortium.
Released in PGS Catalog: March 22, 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:
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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)
PGS000742
(PHS166)
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
 Prostate cancer prostate carcinoma 166
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000742/ScoringFiles/PGS000742.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
PPM001808 PGS000742
(PHS166)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
 Reported Trait: Prostate cancer (age of onset) — — Hazard Ratio (HR, top 5% vs. middle 40%): 4.45 [3.68, 5.06] — —
PPM001809 PGS000742
(PHS166)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
 Reported Trait: Prostate cancer (age of onset) — — Hazard Ratio (HR, top 20% vs. bottom 20%): 7.85 [6.04, 9.33] — —
PPM001810 PGS000742
(PHS166)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
 Reported Trait: Prostate cancer (age of onset) — — Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.37 [0.33, 0.4] — —
PPM001812 PGS000067
(PCa_PHS)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Prostate cancer (age of onset) — — Hazard Ratio (HR, top 20% vs. bottom 20%): 5.15 [3.29, 6.18] — Only 46 out of the 54 variants were used from Seibert et al's polygenic risk score (PGS000067)
PPM001813 PGS000067
(PCa_PHS)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Prostate cancer (age of onset) — — Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.44 [0.4, 0.49] — Only 46 out of the 54 variants were used from Seibert et al's polygenic risk score (PGS000067)
PPM001814 PGS000742
(PHS166)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
 Reported Trait: Clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 5% vs. middle 40%): 5.09 [3.84, 6.05] — —
PPM001815 PGS000742
(PHS166)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
 Reported Trait: Clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 20% vs. bottom 20%): 9.45 [6.17, 11.79] — —
PPM001816 PGS000742
(PHS166)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
 Reported Trait: Clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.34 [0.29, 0.39] — —
PPM001817 PGS000067
(PCa_PHS)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 5% vs. middle 40%): 3.72 [2.89, 4.43] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001818 PGS000067
(PCa_PHS)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 20% vs. bottom 20%): 6.12 [4.18, 7.67] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001819 PGS000067
(PCa_PHS)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.41 [0.35, 0.47] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001820 PGS000742
(PHS166)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
 Reported Trait: Non-clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 5% vs. middle 40%): 4.28 [3.49, 4.96] — —
PPM001821 PGS000742
(PHS166)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
 Reported Trait: Non-clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 20% vs. bottom 20%): 7.47 [5.49, 9.07] — —
PPM001822 PGS000742
(PHS166)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
 Reported Trait: Non-clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.37 [0.33, 0.42] — —
PPM001823 PGS000067
(PCa_PHS)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Non-clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 5% vs. middle 40%): 3.2 [2.59, 3.78] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001824 PGS000067
(PCa_PHS)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Non-clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 20% vs. bottom 20%): 4.96 [3.61, 6.14] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001825 PGS000067
(PCa_PHS)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Non-clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.45 [0.39, 0.5] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001811 PGS000067
(PCa_PHS)
 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Prostate cancer (age of onset) — — Hazard Ratio (HR, top 5% vs. middle 40%): 3.29 [2.73, 3.77] — Only 46 out of the 54 variants were used from Seibert et al's polygenic risk score (PGS000067)

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
PSS000926 Cases included individuals with any type of prostate cancer (PCa). For any clinically significant PCa, cases were defined as individuals with any of the following: Gleason score ≥ 7, stage T3-T4, PSA concentration ≥ 10 ng/mL, pelvic lymph nodal metastasis, or distant metastasis. —
[
  • 1,583 cases
  • , 4,828 controls
]
,
100.0 % Male samples
 — European — ProtecT, UKGPCS —