PGS Publication: PGP000120

Publication Information (EuropePMC)
Title Development of a polygenic risk score to improve screening for fracture risk: A genetic risk prediction study.
PubMed ID 32614825(Europe PMC)
doi 10.1371/journal.pmed.1003152
Publication Date July 2, 2020
Journal PLoS Med
Author(s) Forgetta V, Keller-Baruch J, Forest M, Durand A, Bhatnagar S, Kemp JP, Nethander M, Evans D, Morris JA, Kiel DP, Rivadeneira F, Johansson H, Harvey NC, Mellström D, Karlsson M, Cooper C, Evans DM, Clarke R, Kanis JA, Orwoll E, McCloskey EV, Ohlsson C, Pineau J, Leslie WD, Greenwood CMT, Richards JB.
Released in PGS Catalog: Dec. 15, 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)
PGS000657
(gSOS)
 PGP000120 |
Forgetta V et al. PLoS Med (2020)
 Heel quantitative ultrasound speed of sound (SOS) calcaneal bone quantitative ultrasound measurement 21,716
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000657/ScoringFiles/PGS000657.txt.gz - Check Terms/Licenses

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
PPM001343 PGS000657
(gSOS)
 PSS000586|
European Ancestry|
80,027 individuals
 PGP000120 |
Forgetta V et al. PLoS Med (2020)
 Reported Trait: Heel bone speed of sound — — R²: 0.2318 [0.2266, 0.2369] — —
PPM001344 PGS000657
(gSOS)
 PSS000585|
Multi-ancestry (including European)|
21,408 individuals
 PGP000120 |
Forgetta V et al. PLoS Med (2020)
 Reported Trait: Screening incorporating a gSOS-based screening step — — Positive Predictive Value (PPV): 0.954
Reduction in individuals requiring Clinical-Risk-Factor FRAX tests (%): 37.0
Percent reduction in individuals requiring BMD FRAX Tests (%): 41.0		 — —

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
PSS000585 — — 4,741 individuals,
47.5 % Male samples
 Mean = 55.8 years
Sd = 7.6 years		 European — UKB —
PSS000585 — — 6,704 individuals,
49.3 % Male samples
 Mean = 62.6 years
Sd = 9.9 years		 European, NR — CLSA —
PSS000585 — — 3,426 individuals,
0.0 % Male samples
 Mean = 71.5 years
Sd = 5.3 years		 European, NR — SOF —
PSS000585 — — 4,657 individuals,
100.0 % Male samples
 Mean = 74.0 years
Sd = 6.0 years		 European — MrOS-USA —
PSS000585 — — 1,880 individuals,
100.0 % Male samples
 Mean = 75.4 years
Sd = 3.2 years		 European
(Swedish)		 — MrOS-SWE —
PSS000586 — — 80,027 individuals,
47.5 % Male samples
 Mean = 55.8 years
Sd = 7.6 years		 European — UKB —