Predicted Trait | |
Reported Trait | Mean corpuscular hemoglobin |
Mapped Trait(s) | mean corpuscular hemoglobin (EFO_0004527) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30050 |
Score Construction | |
PGS Name | INI30050 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 17,127 |
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 |
---|---|---|---|---|---|---|---|---|
— | 316,081 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 |
---|---|---|---|---|---|---|---|---|
PPM018964 | PSS011136| European Ancestry| 65,932 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Mean corpuscular hemoglobin | — | — | R²: 0.1843 [0.17903, 0.18957] PGS R2 (no covariates): 0.16693 [0.1618, 0.17205] Incremental R2 (full-covars): 0.16424 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018965 | PSS011109| European Ancestry| 2,813 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Mean corpuscular hemoglobin | — | — | R²: 0.20494 [0.17875, 0.23114] PGS R2 (no covariates): 0.18314 [0.1577, 0.20858] Incremental R2 (full-covars): 0.17698 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018966 | PSS011113| South Asian Ancestry| 1,433 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Mean corpuscular hemoglobin | — | — | R²: 0.11596 [0.08543, 0.14649] PGS R2 (no covariates): 0.08633 [0.05911, 0.11356] Incremental R2 (full-covars): 0.08195 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018967 | PSS011155| African Ancestry| 1,157 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Mean corpuscular hemoglobin | — | — | R²: 0.07189 [0.04397, 0.09982] PGS R2 (no covariates): 0.05454 [0.02976, 0.07932] Incremental R2 (full-covars): 0.05029 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018968 | PSS011166| Multi-ancestry (excluding European)| 7,746 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Mean corpuscular hemoglobin | — | — | R²: 0.17414 [0.15905, 0.18923] PGS R2 (no covariates): 0.1276 [0.11395, 0.14124] Incremental R2 (full-covars): 0.0916 |
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 | — |