PGS Publication: PGP000397

Publication Information (EuropePMC)
Title Prostate cancer risk stratification improvement across multiple ancestries with new polygenic hazard score.
PubMed ID 35152271(Europe PMC)
doi 10.1038/s41391-022-00497-7
Publication Date Feb. 12, 2022
Journal Prostate Cancer Prostatic Dis
Author(s) Huynh-Le MP, Karunamuni R, Fan CC, Asona L, Thompson WK, Martinez ME, Eeles RA, Kote-Jarai Z, Muir KR, Lophatananon A, Schleutker J, Pashayan N, Batra J, Grönberg H, Neal DE, Nordestgaard BG, Tangen CM, MacInnis RJ, Wolk A, Albanes D, Haiman CA, Travis RC, Blot WJ, Stanford JL, Mucci LA, West CML, Nielsen SF, Kibel AS, Cussenot O, Berndt SI, Koutros S, Sørensen KD, Cybulski C, Grindedal EM, Menegaux F, Park JY, Ingles SA, Maier C, Hamilton RJ, Rosenstein BS, Lu YJ, Watya S, Vega A, Kogevinas M, Wiklund F, Penney KL, Huff CD, Teixeira MR, Multigner L, Leach RJ, Brenner H, John EM, Kaneva R, Logothetis CJ, Neuhausen SL, De Ruyck K, Ost P, Razack A, Newcomb LF, Fowke JH, Gamulin M, Abraham A, Claessens F, Castelao JE, Townsend PA, Crawford DC, Petrovics G, van Schaik RHN, Parent MÉ, Hu JJ, Zheng W, UKGPCS collaborators, APCB (Australian Prostate Cancer BioResource), NC-LA PCaP Investigators, IMPACT Study Steering Committee and Collaborators, Canary PASS Investigators, Profile Study Steering Committee, PRACTICAL Consortium, Mills IG, Andreassen OA, Dale AM, Seibert TM.
Released in PGS Catalog: Nov. 23, 2022

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)
PGS003331
(PHS290)
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Prostate cancer prostate carcinoma 290
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003331/ScoringFiles/PGS003331.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
PPM016134 PGS003331
(PHS290)
 PSS010046|
Ancestry Not Reported|
6,411 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Any prostate cancer β: 2.11 — Hazard ratio (HR, top vs bottom 20%): 11.16 [10.48, 11.88] — —
PPM016135 PGS003331
(PHS290)
 PSS010046|
Ancestry Not Reported|
6,411 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Clinically significant prostate cancer β: 2.32 — Hazard ratio (HR, top vs bottom 20%): 13.73 [12.43, 15.16] — —
PPM016136 PGS003331
(PHS290)
 PSS010043|
African Ancestry|
6,253 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Any prostate cancer β: 1.64 — Hazard ratio (HR, top vs bottom 20%): 5.95 [5.59, 6.34] — —
PPM016137 PGS003331
(PHS290)
 PSS010043|
African Ancestry|
6,253 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Clinically significant prostate cancer β: 1.67 — Hazard ratio (HR, top vs bottom 20%): 7.07 [6.58, 7.6] — —
PPM016138 PGS003331
(PHS290)
 PSS010044|
Additional Asian Ancestries|
2,378 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Any prostate cancer β: 1.99 — Hazard ratio (HR, top vs bottom 20%): 8.75 [8.21, 9.32] — —
PPM016139 PGS003331
(PHS290)
 PSS010044|
Additional Asian Ancestries|
2,378 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Clinically significant prostate cancer β: 1.89 — Hazard ratio (HR, top vs bottom 20%): 10.31 [9.58, 11.11] — —
PPM016140 PGS003331
(PHS290)
 PSS010045|
European Ancestry|
3,279 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Any prostate cancer β: 2.13 — Hazard ratio (HR, top vs bottom 20%): 10.87 [10.21, 11.57] — —
PPM016141 PGS003331
(PHS290)
 PSS010045|
European Ancestry|
3,279 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Clinically significant prostate cancer β: 2.13 — Hazard ratio (HR, top vs bottom 20%): 11.18 [10.34, 12.09] — —
PPM016142 PGS003331
(PHS290)
 PSS010045|
European Ancestry|
3,279 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Fatal prostate cancer β: 1.68 — Hazard ratio (HR, top vs bottom 20%): 7.73 [6.45, 9.27] — —

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
PSS010043 — —
[
  • 3,240 cases
  • , 3,013 controls
]
,
100.0 % Male samples
 — African unspecified — NR —
PSS010044 — —
[
  • 1,194 cases
  • , 1,184 controls
]
,
100.0 % Male samples
 — Asian unspecified — NR —
PSS010045 — —
[
  • 2,163 cases
  • , 1,116 controls
]
,
100.0 % Male samples
 — European
(Swedish)		 — COSM —
PSS010046 — —
[
  • 1,583 cases
  • , 4,828 controls
]
,
100.0 % Male samples
 — Not reported — ProtecT —