Predicted Trait | |
Reported Trait | Red blood cell (erythrocyte) count |
Mapped Trait(s) | erythrocyte count (EFO_0004305) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30010 |
Score Construction | |
PGS Name | INI30010 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 27,293 |
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 |
---|---|---|---|---|---|---|---|---|
— | 316,085 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 |
---|---|---|---|---|---|---|---|---|
PPM018944 | PSS011136| European Ancestry| 65,932 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Red blood cell (erythrocyte) count | — | — | R²: 0.38181 [0.37606, 0.38756] PGS R2 (no covariates): 0.1179 [0.11333, 0.12246] Incremental R2 (full-covars): 0.1164 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018945 | PSS011109| European Ancestry| 2,813 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Red blood cell (erythrocyte) count | — | — | R²: 0.38936 [0.36163, 0.41709] PGS R2 (no covariates): 0.09281 [0.0727, 0.11293] Incremental R2 (full-covars): 0.09305 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018946 | PSS011113| South Asian Ancestry| 1,433 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Red blood cell (erythrocyte) count | — | — | R²: 0.35286 [0.31388, 0.39185] PGS R2 (no covariates): 0.07492 [0.04924, 0.1006] Incremental R2 (full-covars): 0.0761 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018947 | PSS011155| African Ancestry| 1,157 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Red blood cell (erythrocyte) count | — | — | R²: 0.29476 [0.25179, 0.33773] PGS R2 (no covariates): 0.04144 [0.01954, 0.06333] Incremental R2 (full-covars): 0.03544 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018948 | PSS011166| Multi-ancestry (excluding European)| 7,746 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Red blood cell (erythrocyte) count | — | — | R²: 0.38816 [0.37147, 0.40486] PGS R2 (no covariates): 0.10146 [0.08893, 0.114] Incremental R2 (full-covars): 0.07754 |
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 |
---|---|---|---|---|---|---|---|---|
PSS011109 | — | — | 2,813 individuals | — | European (non-white British ancestry) |
— | UKB | — |
PSS011113 | — | — | 1,433 individuals | — | South Asian | — | UKB | — |
PSS011155 | — | — | 1,157 individuals | — | African unspecified | — | UKB | — |
PSS011166 | — | — | 7,746 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |
PSS011136 | — | — | 65,932 individuals | — | European (white British ancestry) |
— | UKB | — |