Predicted Trait | |
Reported Trait | Reticulocyte percentage |
Mapped Trait(s) | reticulocyte measurement (EFO_0010700) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30240 |
Score Construction | |
PGS Name | INI30240 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 7,884 |
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 |
---|---|---|---|---|---|---|---|---|
— | 310,916 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 |
---|---|---|---|---|---|---|---|---|
PPM019049 | PSS011141| European Ancestry| 64,860 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Reticulocyte percentage | — | — | R²: 0.0298 [0.02728, 0.03233] PGS R2 (no covariates): 0.02838 [0.02592, 0.03085] Incremental R2 (full-covars): 0.02829 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019050 | PSS011099| European Ancestry| 2,770 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Reticulocyte percentage | — | — | R²: 0.07465 [0.05625, 0.09305] PGS R2 (no covariates): 0.06854 [0.05079, 0.08629] Incremental R2 (full-covars): 0.06923 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019051 | PSS011111| South Asian Ancestry| 1,393 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Reticulocyte percentage | — | — | R²: 0.08898 [0.06142, 0.11654] PGS R2 (no covariates): 0.08201 [0.05535, 0.10867] Incremental R2 (full-covars): 0.07867 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019052 | PSS011153| African Ancestry| 1,125 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Reticulocyte percentage | — | — | R²: 0.01247 [0.00009, 0.02484] PGS R2 (no covariates): 0.01579 [0.00191, 0.02967] Incremental R2 (full-covars): 0.012 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019053 | PSS011169| Multi-ancestry (excluding European)| 7,578 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Reticulocyte percentage | — | — | R²: 0.04153 [0.03298, 0.05009] PGS R2 (no covariates): 0.03618 [0.02815, 0.04421] Incremental R2 (full-covars): 0.03446 |
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 |
---|---|---|---|---|---|---|---|---|
PSS011141 | — | — | 64,860 individuals | — | European (white British ancestry) |
— | UKB | — |
PSS011111 | — | — | 1,393 individuals | — | South Asian | — | UKB | — |
PSS011153 | — | — | 1,125 individuals | — | African unspecified | — | UKB | — |
PSS011099 | — | — | 2,770 individuals | — | European (non-white British ancestry) |
— | UKB | — |
PSS011169 | — | — | 7,578 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |