PGS Publication: PGP000488

Publication Information (EuropePMC)
Title Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants
PubMed ID 37945903(Europe PMC)
doi 10.1038/s41588-023-01534-4
Publication Date Aug. 21, 2023
Journal Nature Genetics
Author(s) Wang A, Shen J, Rodriguez AA, Saunders EJ, Chen F, Janivara R, Darst BF, Sheng X, Xu Y, Chou AJ, Benlloch S, Dadaev T, Brook MN, Plym A, Sahimi A, Hoffman TJ, Takahashi A, Matsuda K, Momozawa Y, Fujita M, Laisk T, Figuerêdo J, Muir K, Ito S, Liu X, Biobank Japan Project, Uchio Y, Kubo M, Kamatani Y, Lophatananon A, Wan P, Andrews C, Lori A, Choudhury PP, Schleutker J, Tammela TLJ, Sipeky C, Auvinen A, Giles GG, Southey MC, MacInnis RJ, Cybulski C, Wokolorczyk D, Lubinski J, Rentsch CT, Cho K, Mcmahon BH, Neal DE, Donovan JL, Hamdy FC, Martin RM, Nordestgaard BG, Nielsen SF, Weischer M, Bojesen SE, Røder A, Stroomberg HV, Batra J, Chambers S, Horvath L, Clements JA, Tilly W, Risbridger GP, Gronberg H, Aly M, Szulkin R, Eklund M, Nordstrom T, Pashayan N, Dunning AM, Ghoussaini M, Travis RC, Key TJ, Riboli E, Park JY, Sellers TA, Lin HY, Albanes D, Weinstein S, Cook MB, Mucci LA, Giovannucci E, Lindstrom S, Kraft P, Hunter DJ, Penney KL, Turman C, Tangen CM, Goodman PJ, Thompson IM, Hamilton RJ, Fleshner NE, Finelli A, Parent MÉ, Stanford JL, Ostrander EA, Koutros S, Beane Freeman LE, Stampfer M, Wolk A, Håkansson N, Andriole GL, Hoover RN, Machiela MJ, Sørensen KD, Borre M, Blot WJ, Zheng W, Yeboah ED, Mensah JE, Lu YJ, Zhang HW, Feng N, Mao X, Wu Y, Zhao SC, Sun Z, Thibodeau SN, McDonnell SK, Schaid DJ, West CML, Barnett G, Maier C, Schnoeller T, Luedeke M, Kibel AS, Drake BF, Cussenot O, Cancel-Tassin G, Menegaux F, Truong T, Koudou YA, John EM, Grindedal EM, Maehle L, Khaw KT, Ingles SA, Stern MC, Vega A, Gómez-Caamaño A, Fachal L, Rosenstein BS, Kerns SL, Ostrer H, Teixeira MR, Paulo P, Brandão A, Watya S, Lubwama A, Bensen JT, Butler EN, Mohler JL, Taylor JA, Kogevinas M, Dierssen-Sotos T, Castaño-Vinyals G, Cannon-Albright L, Teerlink CC, Huff CD, Pilie P, Yu Y, Bohlender RJ, Gu J, Strom SS, Multigner L, Blanchet P, Brureau L, Kaneva R, Slavov C, Mitev V, Leach RJ, Brenner H, Chen X, Holleczek B, Schöttker B, Klein EA, Hsing AW, Kittles RA, Murphy AB, Logothetis CJ, Kim J, Neuhausen SL, Steele L, Ding YC, Isaacs WB, Nemesure B, Hennis AJM, Carpten J, Pandha H, Michael A, De Ruyck K, De Meerleer G, Ost P, Xu J, Razack A, Lim J, Teo SH, Newcomb LF, Lin DW, Fowke JH, Neslund-Dudas CM, Rybicki BA, Gamulin M, Lessel D, Kulis T, Usmani N, Abraham A, Singhal S, Parliament M, Claessens F, Joniau S, Van den Broeck T, Gago-Dominguez M, Castelao JE, Martinez ME, Larkin S, Townsend PA, Aukim-Hastie C, Bush WS, Aldrich MC, Crawford DC, Srivastava S, Cullen J, Petrovics G, Casey G, Wang Y, Tettey Y, Lachance J, Tang W, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Yamoah K, Govindasami K, Chokkalingam AP, Keaton JM, Hellwege JN, Clark PE, Jalloh M, Gueye SM, Niang L, Ogunbiyi O, Shittu O, Amodu O, Adebiyi AO, Aisuodionoe-Shadrach OI, Ajibola HO, Jamda MA, Oluwole OP, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Diop H, Gundell SM, Roobol MJ, Jenster G, van Schaik RHN, Hu JJ, Sanderson M, Kachuri L, Varma R, McKean-Cowdin R, Torres M, Preuss MH, Loos RJF, Zawistowski M, Zöllner S, Lu Z, Van Den Eeden SK, Easton DF, Ambs S, Edwards TL, Mägi R, Rebbeck TR, Fritsche L, Chanock SJ, Berndt SI, Wiklund F, Nakagawa H, Witte JS, Gaziano JM, Justice AC, Mancuso N, Terao C, Eeles RA, Kote-Jarai Z, Madduri RK, Conti DV, Haiman CA.
Released in PGS Catalog: Dec. 19, 2023

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)
PGS003765
(GRS.PCa.451)
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Prostate cancer prostate carcinoma 451
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003765/ScoringFiles/PGS003765.txt.gz
PGS003766
(GRS.PCa.451.TOPMed)
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Prostate cancer prostate carcinoma 451
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003766/ScoringFiles/PGS003766.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
PPM018569 PGS003766
(GRS.PCa.451.TOPMed)
 PSS011035|
European Ancestry|
13,781 individuals
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Reported Trait: Prostate Cancer OR: 2.09 — Odds ratio (OR, top 10% vs 40-60%): 3.95 Age, 10 PCs —
PPM018573 PGS003766
(GRS.PCa.451.TOPMed)
 PSS011031|
African Ancestry|
4,665 individuals
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Reported Trait: Prostate Cancer OR: 1.78 — Odds ratio (OR, top 10% vs 40-60%): 3.54 Age, sub-studies, 10 PCs —
PPM018570 PGS003766
(GRS.PCa.451.TOPMed)
 PSS011030|
European Ancestry|
30,898 individuals
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Reported Trait: Prostate Cancer OR: 2.32 — Odds ratio (OR, top 10% vs 40-60%): 3.51 Age, 10 PCs —
PPM018571 PGS003765
(GRS.PCa.451)
 PSS011032|
African Ancestry|
556 individuals
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Reported Trait: Prostate Cancer OR: 2.08 — Odds ratio (OR, top 10% vs 40-60%): 4.93 Age, 10 PCs —
PPM018572 PGS003766
(GRS.PCa.451.TOPMed)
 PSS011034|
African Ancestry|
639 individuals
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Reported Trait: Prostate Cancer OR: 1.76 — Odds ratio (OR, top 10% vs 40-60%): 3.54 Age, 10 PCs —
PPM018568 PGS003765
(GRS.PCa.451)
 PSS011033|
European Ancestry|
12,848 individuals
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Reported Trait: Prostate Cancer OR: 2.21 — Odds ratio (OR, top 10% vs 40-60%): 4.33 Age, 10 PCs —

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
PSS011030 — —
[
  • 2,352 cases
  • , 28,546 controls
]
,
100.0 % Male samples
 — European — EB —
PSS011031 — —
[
  • 2,505 cases
  • , 2,160 controls
]
,
100.0 % Male samples
 — African unspecified — MADCaP —
PSS011032 — —
[
  • 85 cases
  • , 471 controls
]
,
100.0 % Male samples
 — African American or Afro-Caribbean — MGBB —
PSS011033 — —
[
  • 1,868 cases
  • , 10,980 controls
]
,
100.0 % Male samples
 — European — MGBB —
PSS011034 — —
[
  • 189 cases
  • , 450 controls
]
,
100.0 % Male samples
 — African American or Afro-Caribbean — MGI —
PSS011035 — —
[
  • 3,244 cases
  • , 10,537 controls
]
,
100.0 % Male samples
 — European — MGI —