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. |
Polygenic Score (PGS) ID | PGS Name | PGS Publication (PGP) ID | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | PGS 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 | 21,717 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000657/ScoringFiles/PGS000657.txt.gz |
PGS Performance Metric ID (PPM ID) |
Evaluated Score |
PGS Sample Set ID (PSS ID) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
PGS Classification Metrics | Other Metrics | Covariates Included in the Model | PGS Performance: Other Relevant Information |
---|---|---|---|---|---|---|---|---|---|
PPM001893 | PGS000657 (gSOS) |
PSS000946 | 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 | — |
PPM001867 | PGS000657 (gSOS) |
PSS000942 | PGP000154 Lu T et al. Genome Med (2021) Ext. |
Reported Trait: Incident major osteoporotic fracture | OR: 0.72 [0.66, 0.79] | — | — | Age, sex | — |
PPM001861 | PGS000657 (gSOS) |
PSS000951 | 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 | — |
PPM001862 | PGS000657 (gSOS) |
PSS000950 | 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 | 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 | PGP000154 Lu T et al. Genome Med (2021) Ext. |
Reported Trait: Incident hip fracture | — | C-index: 0.672 [0.65, 0.695] | — | Sex | — |
PPM001865 | PGS000657 (gSOS) |
PSS000948 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | — |
PPM001894 | PGS000657 (gSOS) |
PSS000941 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | — |
PGS Sample Set ID (PSS ID) |
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. | — | [ ,
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 | [ ,
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 | [ ,
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 | [ ,
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 | [ ,
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 | [ ,
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 | [ ,
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. | — | [ ,
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. | — | [ ,
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. | — | [
|
— | European | — | UKB | — |
PSS000950 | Cases included individuals with a hip fracture that occurred after the baseline visit. | Range = [4.5, 14.5] years | [ ,
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 | [ ,
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. | — | [ ,
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. | — | [ ,
100.0 % Male samples |
Mean = 75.4 years Sd = 3.2 years |
European | — | MrOS-SWE | — |