PGS Publication: PGP000373

Publication Information (EuropePMC)
Title Testing the generalizability of ancestry-specific polygenic risk scores to predict prostate cancer in sub-Saharan Africa.
PubMed ID 36100952(Europe PMC)
doi 10.1186/s13059-022-02766-z
Publication Date Sept. 13, 2022
Journal Genome Biol
Author(s) Kim MS, Naidoo D, Hazra U, Quiver MH, Chen WC, Simonti CN, Kachambwa P, Harlemon M, Agalliu I, Baichoo S, Fernandez P, Hsing AW, Jalloh M, Gueye SM, Niang L, Diop H, Ndoye M, Snyper NY, Adusei B, Mensah JE, Abrahams AOD, Biritwum R, Adjei AA, Adebiyi AO, Shittu O, Ogunbiyi O, Adebayo S, Aisuodionoe-Shadrach OI, Nwegbu MM, Ajibola HO, Oluwole OP, Jamda MA, Singh E, Pentz A, Joffe M, Darst BF, Conti DV, Haiman CA, Spies PV, van der Merwe A, Rohan TE, Jacobson J, Neugut AI, McBride J, Andrews C, Petersen LN, Rebbeck TR, Lachance J.
Released in PGS Catalog: Sept. 29, 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

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 Scoring File (FTP Link)
PGS000662
(GRS.PCa.269)
 PGP000122 |
Conti DV et al. Nat Genet (2021)
 Prostate cancer prostate carcinoma 269
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000662/ScoringFiles/PGS000662.txt.gz
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
PGS000030
(PrCa)
 PGP000019 |
Schumacher FR et al. Nat Genet (2018)
 Prostate cancer prostate carcinoma 147
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000030/ScoringFiles/PGS000030.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
PPM015483 PGS000733
(PHS46+African)
 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Prostate cancer OR: 1.58 [1.2, 2.11] AUROC: 0.547 [0.525, 0.569] — — —
PPM015484 PGS000030
(PrCa)
 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Aggressive prostate cancer (tumor stage T4) OR: 1.14 [0.93, 1.4] AUROC: 0.51 [0.438, 0.578] — — —
PPM015482 PGS000662
(GRS.PCa.269)
 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Prostate cancer OR: 1.86 [1.41, 2.47] AUROC: 0.579 [0.558, 0.601] — — —
PPM015485 PGS000662
(GRS.PCa.269)
 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Aggressive prostate cancer (tumor stage T4) OR: 1.17 [0.95, 1.43] AUROC: 0.505 [0.435, 0.574] — — —
PPM015487 PGS000662
(GRS.PCa.269)
 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Aggressive prostate cancer (Gleason score >=8) OR: 1.26 [1.15, 1.4] AUROC: 0.523 [0.488, 0.559] — — —
PPM015488 PGS000733
(PHS46+African)
 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Aggressive prostate cancer (tumor stage T4) OR: 0.96 [0.78, 1.17] AUROC: 0.568 [0.494, 0.631] — — —
PPM015489 PGS000733
(PHS46+African)
 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Aggressive prostate cancer (Gleason score >=8) OR: 1.18 [1.07, 1.13] AUROC: 0.515 [0.479, 0.55] — — —
PPM015481 PGS000030
(PrCa)
 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Prostate cancer OR: 1.23 [0.91, 1.67] AUROC: 0.538 [0.516, 0.56] — — —
PPM015486 PGS000030
(PrCa)
 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Aggressive prostate cancer (Gleason score >=8) OR: 1.13 [1.02, 1.25] AUROC: 0.511 [0.475, 0.547] — — —

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
PSS009959 — —
[
  • 1,298 cases
  • , 1,333 controls
]
 — African unspecified — MADCaP —