| Predicted Trait | |
| Reported Trait | IGF-1 [nmol/L] |
| Mapped Trait(s) | IGF-1 measurement (EFO_0004627) |
| Score Construction | |
| PGS Name | snpnet.IGF_1 |
| Development Method | |
| Name | snpnet |
| Parameters | 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs) |
| Variants | |
| Original Genome Build | hg19 |
| Number of Variants | 23,443 |
| Effect Weight Type | beta |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000128 |
| Citation (link to publication) | Sinnott-Armstrong N et al. Nat Genet (2021) |
| Ancestry Distribution | |
| Score Development/Training | European: 100% 255,256 individuals (100%) |
| PGS Evaluation | European: 40% African: 20% East Asian: 20% South Asian: 20% 10 Sample Sets |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) | Phenotype Definitions & Methods | Age of Study Participants | Participant Follow-up Time | Additional Ancestry Description | Additional Sample/Cohort Information |
|---|---|---|---|---|---|---|---|---|
Europe PMC: 10.1038/s41588-020-00757-z |
223,327 individuals | European (British) |
UKB | — | — | — | — | Training |
Europe PMC: 10.1038/s41588-020-00757-z |
31,929 individuals | European (British) |
UKB | — | — | — | — | Validation |
|
PGS Performance Metric ID (PPM) |
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 |
|---|---|---|---|---|---|---|---|---|
| PPM001415 | PSS000709| African Ancestry| 5,974 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: IGF-1 [nmol/L] | — | — | R²: 0.11454 Spearman's ρ: 0.182 |
Age, sex, PCs(1-40) | — |
| PPM001450 | PSS000710| East Asian Ancestry| 1,074 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: IGF-1 [nmol/L] | — | — | R²: 0.17702 Spearman's ρ: 0.258 |
Age, sex, PCs(1-40) | — |
| PPM001485 | PSS000711| European Ancestry| 23,453 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: IGF-1 [nmol/L] | — | — | R²: 0.22328 Spearman's ρ: 0.362 |
Age, sex, PCs(1-40) | — |
| PPM001520 | PSS000712| South Asian Ancestry| 7,283 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: IGF-1 [nmol/L] | — | — | R²: 0.20212 Spearman's ρ: 0.313 |
Age, sex, PCs(1-40) | — |
| PPM001555 | PSS000713| European Ancestry| 63,393 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: IGF-1 [nmol/L] | — | — | R²: 0.20434 Spearman's ρ: 0.369 |
Age, sex, PCs(1-40) | — |
| PPM007360 | PSS007166| African Ancestry| 6,058 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: IGF-1 | — | — | R²: 0.08755 [0.07443, 0.10068] Incremental R2 (full-covars): 0.00429 PGS R2 (no covariates): 0.03282 [0.0243, 0.04133] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007361 | PSS007167| East Asian Ancestry| 1,609 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: IGF-1 | — | — | R²: 0.14261 [0.11193, 0.1733] Incremental R2 (full-covars): 0.00641 PGS R2 (no covariates): 0.06187 [0.03976, 0.08399] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007362 | PSS007168| European Ancestry| 23,653 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: IGF-1 | — | — | R²: 0.10834 [0.10105, 0.11562] Incremental R2 (full-covars): 0.01189 PGS R2 (no covariates): 0.12448 [0.11681, 0.13216] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007363 | PSS007169| South Asian Ancestry| 7,373 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: IGF-1 | — | — | R²: 0.11511 [0.10181, 0.1284] Incremental R2 (full-covars): 0.00941 PGS R2 (no covariates): 0.08722 [0.07528, 0.09915] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007364 | PSS007170| European Ancestry| 64,106 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: IGF-1 | — | — | R²: 0.07984 [0.07592, 0.08377] Incremental R2 (full-covars): 0.01227 PGS R2 (no covariates): 0.12763 [0.12293, 0.13233] |
age, sex, UKB array type, Genotype PCs | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000711 | — | — | 23,453 individuals | — | European | Non-British White | UKB | — |
| PSS000712 | — | — | 7,283 individuals | — | South Asian | — | UKB | — |
| PSS000713 | — | — | 63,393 individuals | — | European (British) |
— | UKB | — |
| PSS007166 | — | — | 6,058 individuals | — | African unspecified | — | UKB | — |
| PSS007167 | — | — | 1,609 individuals | — | East Asian | — | UKB | — |
| PSS007168 | — | — | 23,653 individuals | — | European | non-white British ancestry | UKB | — |
| PSS007169 | — | — | 7,373 individuals | — | South Asian | — | UKB | — |
| PSS007170 | — | — | 64,106 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |
| PSS000709 | — | — | 5,974 individuals | — | African unspecified | — | UKB | — |
| PSS000710 | — | — | 1,074 individuals | — | East Asian | — | UKB | — |