PGS Publication: PGP000154

Publication Information (EuropePMC)
Title Improved prediction of fracture risk leveraging a genome-wide polygenic risk score.
PubMed ID 33536041(Europe PMC)
doi 10.1186/s13073-021-00838-6
Publication Date Feb. 3, 2021
Journal Genome Med
Author(s) Lu T, Forgetta V, Keller-Baruch J, Nethander M, Bennett D, Forest M, Bhatnagar S, Walters RG, Lin K, Chen Z, Li L, Karlsson M, Mellström D, Orwoll E, McCloskey EV, Kanis JA, Leslie WD, Clarke RJ, Ohlsson C, Greenwood CMT, Richards JB.
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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South Asian
Additional Asian Ancestries
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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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000657
(gSOS)
 PGP000120 |
Forgetta V et al. PLoS Med (2020)
 Heel quantitative ultrasound speed of sound (SOS) heel bone mineral density 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
PPM001862 PGS000657
(gSOS)
 PSS000950|
European Ancestry|
90,172 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture — AUROC: 0.798 [0.791, 0.805] Odds ratio (OR, bottom 25% vs. remaining 75%): 1.2 [1.02, 1.41] Age, sex —
PPM001863 PGS000657
(gSOS)
 PSS000944|
European Ancestry|
8,278 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture — C-index: 0.623 [0.603, 0.642] — Sex —
PPM001864 PGS000657
(gSOS)
 PSS000943|
European Ancestry|
8,278 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture — C-index: 0.672 [0.65, 0.695] — Sex —
PPM001861 PGS000657
(gSOS)
 PSS000951|
European Ancestry|
90,172 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture — AUROC: 0.734 [0.727, 0.74] Odds ratio (OR, bottom 25% vs. remaining 75%): 1.68 [1.47, 1.89] Age, sex —
PPM001867 PGS000657
(gSOS)
 PSS000942|
European Ancestry|
4,663 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.72 [0.66, 0.79] — — Age, sex —
PPM001865 PGS000657
(gSOS)
 PSS000948|
European Ancestry|
80,014 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.68 [0.65, 0.72] AUROC: 0.68 [0.673, 0.688] — Age, sex —
PPM001868 PGS000657
(gSOS)
 PSS000942|
European Ancestry|
4,663 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.76 [0.69, 0.85] — — Age, sex, body mass index, prior fracture, smoking, corticosteroids use, rheumatoid arthritis, parental fracture, at-risk drinking, falls at baseline, secondary osteoperosis —
PPM001869 PGS000657
(gSOS)
 PSS000940|
European Ancestry|
1,880 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.69 [0.61, 0.78] — — Age, sex —
PPM001870 PGS000657
(gSOS)
 PSS000940|
European Ancestry|
1,880 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.72 [0.61, 0.85] — — Age, sex, body mass index, prior fracture, smoking, corticosteroids use, rheumatoid arthritis, parental fracture, at-risk drinking, falls at baseline, secondary osteoperosis —
PPM001871 PGS000657
(gSOS)
 PSS000946|
European Ancestry|
3,615 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.74 [0.68, 0.81] — — Age, sex —
PPM001872 PGS000657
(gSOS)
 PSS000946|
European Ancestry|
3,615 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.75 [0.68, 0.83] — — Age, sex, body mass index, prior fracture, smoking, corticosteroids use, rheumatoid arthritis, parental fracture, at-risk drinking, falls at baseline, secondary osteoperosis —
PPM001873 PGS000657
(gSOS)
 PSS000938|
East Asian Ancestry|
25,034 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.79 [0.71, 0.88] — — Age, sex Only 13,848 of the original 21717 SNPs (63.8%) were used due to difference in reference panel.
PPM001874 PGS000657
(gSOS)
 PSS000938|
East Asian Ancestry|
25,034 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.82 [0.74, 0.92] — — Age, sex, body mass index, prior fracture, smoking, corticosteroids use, rheumatoid arthritis, parental fracture, at-risk drinking, falls at baseline, secondary osteoperosis Only 13,848 of the original 21717 SNPs (63.8%) were used due to difference in reference panel.
PPM001875 PGS000657
(gSOS)
 PSS000947|
European Ancestry|
80,014 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.73 [0.63, 0.84] AUROC: 0.739 [0.724, 0.754] — Age, sex —
PPM001876 PGS000657
(gSOS)
 PSS000947|
European Ancestry|
80,014 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.75 [0.65, 0.86] — — Age, sex, body mass index, prior fracture, smoking, corticosteroids use, rheumatoid arthritis, parental fracture, at-risk drinking, falls at baseline, secondary osteoperosis —
PPM001877 PGS000657
(gSOS)
 PSS000941|
European Ancestry|
4,663 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.73 [0.64, 0.83] — — Age, sex —
PPM001878 PGS000657
(gSOS)
 PSS000941|
European Ancestry|
4,663 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.75 [0.65, 0.87] — — Age, sex, body mass index, prior fracture, smoking, corticosteroids use, rheumatoid arthritis, parental fracture, at-risk drinking, falls at baseline, secondary osteoperosis —
PPM001879 PGS000657
(gSOS)
 PSS000939|
European Ancestry|
1,880 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.76 [0.63, 0.93] — — Age, sex —
PPM001880 PGS000657
(gSOS)
 PSS000939|
European Ancestry|
1,880 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.74 [0.58, 0.95] — — Age, sex, body mass index, prior fracture, smoking, corticosteroids use, rheumatoid arthritis, parental fracture, at-risk drinking, falls at baseline, secondary osteoperosis —
PPM001881 PGS000657
(gSOS)
 PSS000945|
European Ancestry|
3,615 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.76 [0.7, 0.84] — — Age, sex —
PPM001882 PGS000657
(gSOS)
 PSS000945|
European Ancestry|
3,615 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.76 [0.68, 0.84] — — Age, sex, body mass index, prior fracture, smoking, corticosteroids use, rheumatoid arthritis, parental fracture, at-risk drinking, falls at baseline, secondary osteoperosis —
PPM001883 PGS000657
(gSOS)
 PSS000949|
European Ancestry|
4,717 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.71 [0.59, 0.85] — — Clinical risk factor-based score (FRAX-CRF) —
PPM001884 PGS000657
(gSOS)
 PSS000942|
European Ancestry|
4,663 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.74 [0.67, 0.81] — — Clinical risk factor-based score (FRAX-CRF) —
PPM001885 PGS000657
(gSOS)
 PSS000940|
European Ancestry|
1,880 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.72 [0.63, 0.81] — — Clinical risk factor-based score (FRAX-CRF) —
PPM001886 PGS000657
(gSOS)
 PSS000946|
European Ancestry|
3,615 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.77 [0.7, 0.84] — — Clinical risk factor-based score (FRAX-CRF) —
PPM001887 PGS000657
(gSOS)
 PSS000941|
European Ancestry|
4,663 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.74 [0.65, 0.83] — — Clinical risk factor-based score (FRAX-CRF) —
PPM001888 PGS000657
(gSOS)
 PSS000939|
European Ancestry|
1,880 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.8 [0.67, 0.96] — — Clinical risk factor-based score (FRAX-CRF) —
PPM001889 PGS000657
(gSOS)
 PSS000945|
European Ancestry|
3,615 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.76 [0.69, 0.84] — — Clinical risk factor-based score (FRAX-CRF) —
PPM001890 PGS000657
(gSOS)
 PSS000949|
European Ancestry|
4,717 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.75 [0.63, 0.9] — — Age, sex, measured femoral neck bone mineral density —
PPM001891 PGS000657
(gSOS)
 PSS000942|
European Ancestry|
4,663 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.82 [0.75, 0.9] — — Age, sex, measured femoral neck bone mineral density —
PPM001892 PGS000657
(gSOS)
 PSS000940|
European Ancestry|
1,880 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.78 [0.68, 0.88] — — Age, sex, measured femoral neck bone mineral density —
PPM001893 PGS000657
(gSOS)
 PSS000946|
European Ancestry|
3,615 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.82 [0.75, 0.9] — — Age, sex, measured femoral neck bone mineral density —
PPM001894 PGS000657
(gSOS)
 PSS000941|
European Ancestry|
4,663 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.85 [0.75, 0.97] — — Age, sex, measured femoral neck bone mineral density —
PPM001895 PGS000657
(gSOS)
 PSS000945|
European Ancestry|
3,615 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.83 [0.76, 0.93] — — Age, sex, measured femoral neck bone mineral density —
PPM001896 PGS000657
(gSOS)
 PSS000949|
European Ancestry|
4,717 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.75 [0.63, 0.89] — — Clinical risk factor-based score including bone mineral density (FRAX-BMD) —
PPM001897 PGS000657
(gSOS)
 PSS000942|
European Ancestry|
4,663 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.78 [0.71, 0.85] — — Clinical risk factor-based score including bone mineral density (FRAX-BMD) —
PPM001898 PGS000657
(gSOS)
 PSS000940|
European Ancestry|
1,880 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.75 [0.66, 0.85] — — Clinical risk factor-based score including bone mineral density (FRAX-BMD) —
PPM001899 PGS000657
(gSOS)
 PSS000946|
European Ancestry|
3,615 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.82 [0.75, 0.89] — — Clinical risk factor-based score including bone mineral density (FRAX-BMD) —
PPM001900 PGS000657
(gSOS)
 PSS000941|
European Ancestry|
4,663 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.76 [0.68, 0.87] — — Clinical risk factor-based score including bone mineral density (FRAX-BMD) —
PPM001901 PGS000657
(gSOS)
 PSS000945|
European Ancestry|
3,615 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture OR: 0.8 [0.73, 0.88] — — Clinical risk factor-based score including bone mineral density (FRAX-BMD) —
PPM001902 PGS000657
(gSOS)
 PSS000944|
European Ancestry|
8,278 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture — C-index: 0.66 [0.641, 0.679] — Clinical risk factor-based score (FRAX-CRF) —
PPM001903 PGS000657
(gSOS)
 PSS000943|
European Ancestry|
8,278 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident hip fracture — C-index: 0.682 [0.66, 0.704] — Clinical risk factor-based score (FRAX-CRF) —
PPM001866 PGS000657
(gSOS)
 PSS000948|
European Ancestry|
80,014 individuals
 PGP000154 |
Lu T et al. Genome Med (2021)
|Ext.		 Reported Trait: Incident major osteoporotic fracture OR: 0.7 [0.66, 0.75] — — Age, sex, body mass index, prior fracture, smoking, corticosteroids use, rheumatoid arthritis, parental fracture, at-risk drinking, falls at baseline, secondary osteoperosis —

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
PSS000940 Cases included individuals with a major osteoporotic fracture that occurred after the baseline visit. —
[
  • 337 cases
  • , 1,543 controls
]
,
100.0 % Male samples
 Mean = 75.4 years
Sd = 3.2 years		 European — MrOS-SWE —
PSS000941 Cases included individuals with a hip fracture that occurred after the baseline visit. Mean = 4.5 years
[
  • 273 cases
  • , 4,390 controls
]
,
100.0 % Male samples
 Mean = 74.0 years
Sd = 6.0 years		 European — MrOS-USA —
PSS000942 Cases included individuals with a major osteoporotic fracture that occurred after the baseline visit. Mean = 4.5 years
[
  • 560 cases
  • , 4,103 controls
]
,
100.0 % Male samples
 Mean = 74.0 years
Sd = 6.0 years		 European — MrOS-USA —
PSS000943 Cases included individuals with a hip fracture that occurred after the baseline visit. Range = [4.5, 14.5] years
[
  • 829 cases
  • , 7,449 controls
]
,
56.33 % Male samples
 — European — MrOS-USA, SOF —
PSS000944 Cases included individuals with a major osteoporotic fracture that occurred after the baseline visit. Range = [4.5, 14.5] years
[
  • 1,267 cases
  • , 7,011 controls
]
,
56.33 % Male samples
 — European — MrOS-USA, SOF —
PSS000945 Cases included individuals with a hip fracture that occurred after the baseline visit. Mean = 14.5 years
[
  • 556 cases
  • , 3,059 controls
]
,
0.0 % Male samples
 Mean = 71.5 years
Sd = 5.3 years		 European — SOF —
PSS000946 Cases included individuals with a major osteoporotic fracture that occurred after the baseline visit. Mean = 14.5 years
[
  • 707 cases
  • , 2,908 controls
]
,
0.0 % Male samples
 Mean = 71.5 years
Sd = 5.3 years		 European — SOF —
PSS000947 Cases included individuals with a hip fracture that occurred after the baseline visit. —
[
  • 209 cases
  • , 79,805 controls
]
,
45.36 % Male samples
 Mean = 56.8 years
Sd = 8.0 years		 European — UKB —
PSS000948 Cases included individuals with a major osteoporotic fracture that occurred after the baseline visit. ICD 10 codes include: M8002, M8003, M8005, M8008, M8082, M8083, M8085, M8088, S220, S320, S422, S423, S424, S520, S521, S522, S523, S525, S526, S529, S720, S721, and S722. —
[
  • 1,189 cases
  • , 78,825 controls
]
,
45.36 % Male samples
 Mean = 56.8 years
Sd = 8.0 years		 European — UKB —
PSS000949 Cases included individuals with a major osteoporotic fracture that occurred after the baseline visit. ICD 10 codes include: M8002, M8003, M8005, M8008, M8082, M8083, M8085, M8088, S220, S320, S422, S423, S424, S520, S521, S522, S523, S525, S526, S529, S720, S721, and S722. —
[
  • 125 cases
  • , 4,592 controls
]
 — European — UKB —
PSS000950 Cases included individuals with a hip fracture that occurred after the baseline visit. Range = [4.5, 14.5] years
[
  • 1,167 cases
  • , 89,005 controls
]
,
31.61 % Male samples
 — European — MrOS-SWE, MrOS-USA, SOF, UKB —
PSS000951 Cases included individuals with a major osteoporotic fracture that occurred after the baseline visit. UKB cohort: Sitespecific major osteoporotic fractures were defined basedon ICD10 codes of primary diagnoses (M8002, M8003, M8005, M8008, M8082, M8083, M8085, M8088, S220, S320, S422, S423, S424, S520, S521, S522, S523, S525, S526, S529, S720, S721, and S722) and self-reported medical history. Range = [4.5, 14.5] years
[
  • 2,793 cases
  • , 87,379 controls
]
,
31.61 % Male samples
 — European — MrOS-SWE, MrOS-USA, SOF, UKB —
PSS000938 Cases included individuals with a major osteoporotic fracture that occurred after the baseline visit. —
[
  • 323 cases
  • , 24,711 controls
]
,
42.7 % Male samples
 Mean = 53.7 years
Sd = 11.0 years		 East Asian — CKB —
PSS000939 Cases included individuals with a hip fracture that occurred after the baseline visit. —
[
  • 129 cases
  • , 1,751 controls
]
,
100.0 % Male samples
 Mean = 75.4 years
Sd = 3.2 years		 European — MrOS-SWE —