Predicted Trait | |
Reported Trait | Hemoglobin concentration |
Mapped Trait(s) | hemoglobin measurement (EFO_0004509) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30020 |
Score Construction | |
PGS Name | INI30020 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 21,078 |
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 |
---|---|---|---|---|---|---|---|---|
— | 316,084 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 |
---|---|---|---|---|---|---|---|---|
PPM018949 | PSS011136| European Ancestry| 65,932 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Hemoglobin concentration | — | — | R²: 0.4378 [0.43219, 0.4434] PGS R2 (no covariates): 0.06821 [0.06455, 0.07188] Incremental R2 (full-covars): 0.06859 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018950 | PSS011109| European Ancestry| 2,813 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Hemoglobin concentration | — | — | R²: 0.46462 [0.43806, 0.49117] PGS R2 (no covariates): 0.06272 [0.04564, 0.0798] Incremental R2 (full-covars): 0.06567 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018951 | PSS011113| South Asian Ancestry| 1,433 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Hemoglobin concentration | — | — | R²: 0.43017 [0.39227, 0.46807] PGS R2 (no covariates): 0.02868 [0.012, 0.04536] Incremental R2 (full-covars): 0.03286 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018952 | PSS011155| African Ancestry| 1,157 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Hemoglobin concentration | — | — | R²: 0.40118 [0.35861, 0.44374] PGS R2 (no covariates): 0.01753 [0.00293, 0.03213] Incremental R2 (full-covars): 0.00674 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018953 | PSS011166| Multi-ancestry (excluding European)| 7,746 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Hemoglobin concentration | — | — | R²: 0.43523 [0.41892, 0.45155] PGS R2 (no covariates): 0.04824 [0.03908, 0.05739] Incremental R2 (full-covars): 0.0422 |
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 | — |