Predicted Trait | |
Reported Trait | Neutrophil count |
Mapped Trait(s) | neutrophil count (EFO_0004833) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30140 |
Score Construction | |
PGS Name | INI30140 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 18,612 |
Effect Weight Type | beta |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000502 |
Citation (link to publication) | Tanigawa Y et al. AJHG (2023) |
Ancestry Distribution | |
Score Development/Training | |
PGS Evaluation |
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 |
---|---|---|---|---|---|---|---|---|
— | 315,523 individuals | European, South Asian, African unspecified, Other admixed ancestry | UKB | — | — | — | European, South Asian, African unspecified, Other admixed ancestry | — |
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 |
---|---|---|---|---|---|---|---|---|
PPM019009 | PSS011139| European Ancestry| 65,814 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Neutrophil count | — | — | R²: 0.10887 [0.10444, 0.1133] PGS R2 (no covariates): 0.09021 [0.0861, 0.09433] Incremental R2 (full-covars): 0.08972 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019010 | PSS011110| European Ancestry| 2,810 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Neutrophil count | — | — | R²: 0.11328 [0.09156, 0.13501] PGS R2 (no covariates): 0.09258 [0.07249, 0.11268] Incremental R2 (full-covars): 0.09167 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019011 | PSS011112| South Asian Ancestry| 1,428 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Neutrophil count | — | — | R²: 0.0886 [0.06109, 0.11611] PGS R2 (no covariates): 0.08009 [0.05369, 0.10649] Incremental R2 (full-covars): 0.07779 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019012 | PSS011154| African Ancestry| 1,154 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Neutrophil count | — | — | R²: 0.07013 [0.0425, 0.09777] PGS R2 (no covariates): 0.05672 [0.03151, 0.08193] Incremental R2 (full-covars): 0.05374 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019013 | PSS011168| Multi-ancestry (excluding European)| 7,732 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Neutrophil count | — | — | R²: 0.10909 [0.0962, 0.12197] PGS R2 (no covariates): 0.09632 [0.08404, 0.1086] Incremental R2 (full-covars): 0.07245 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS011110 | — | — | 2,810 individuals | — | European (non-white British ancestry) |
— | UKB | — |
PSS011112 | — | — | 1,428 individuals | — | South Asian | — | UKB | — |
PSS011154 | — | — | 1,154 individuals | — | African unspecified | — | UKB | — |
PSS011168 | — | — | 7,732 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |
PSS011139 | — | — | 65,814 individuals | — | European (white British ancestry) |
— | UKB | — |