Predicted Trait | |
Reported Trait | High light scatter reticulocyte percentage |
Mapped Trait(s) | reticulocyte measurement (EFO_0010700) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30290 |
Score Construction | |
PGS Name | INI30290 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 11,641 |
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 |
---|---|---|---|---|---|---|---|---|
— | 310,755 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 |
---|---|---|---|---|---|---|---|---|
PPM019075 | PSS011100| European Ancestry| 2,768 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: High light scatter reticulocyte percentage | — | — | R²: 0.10452 [0.08345, 0.12558] PGS R2 (no covariates): 0.09885 [0.07823, 0.11947] Incremental R2 (full-covars): 0.09847 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019076 | PSS011111| South Asian Ancestry| 1,393 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: High light scatter reticulocyte percentage | — | — | R²: 0.09744 [0.06887, 0.12601] PGS R2 (no covariates): 0.08757 [0.06019, 0.11496] Incremental R2 (full-covars): 0.08129 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019077 | PSS011153| African Ancestry| 1,125 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: High light scatter reticulocyte percentage | — | — | R²: 0.02997 [0.01112, 0.04881] PGS R2 (no covariates): 0.03101 [0.01186, 0.05016] Incremental R2 (full-covars): 0.0295 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019078 | PSS011170| Multi-ancestry (excluding European)| 7,574 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: High light scatter reticulocyte percentage | — | — | R²: 0.09491 [0.0827, 0.10712] PGS R2 (no covariates): 0.08288 [0.07132, 0.09444] Incremental R2 (full-covars): 0.07762 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019074 | PSS011143| European Ancestry| 64,816 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: High light scatter reticulocyte percentage | — | — | R²: 0.01834 [0.01634, 0.02034] PGS R2 (no covariates): 0.01717 [0.01523, 0.01911] Incremental R2 (full-covars): 0.01712 |
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 |
---|---|---|---|---|---|---|---|---|
PSS011143 | — | — | 64,816 individuals | — | European (white British ancestry) |
— | UKB | — |
PSS011111 | — | — | 1,393 individuals | — | South Asian | — | UKB | — |
PSS011153 | — | — | 1,125 individuals | — | African unspecified | — | UKB | — |
PSS011100 | — | — | 2,768 individuals | — | European (non-white British ancestry) |
— | UKB | — |
PSS011170 | — | — | 7,574 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |