Predicted Trait | |
Reported Trait | Mean reticulocyte volume |
Mapped Trait(s) | mean reticulocyte volume (EFO_0010701) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30260 |
Score Construction | |
PGS Name | INI30260 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 18,832 |
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 |
---|---|---|---|---|---|---|---|---|
— | 310,915 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 |
---|---|---|---|---|---|---|---|---|
PPM019059 | PSS011140| European Ancestry| 64,861 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Mean reticulocyte volume | — | — | R²: 0.16087 [0.1558, 0.16594] PGS R2 (no covariates): 0.14603 [0.14111, 0.15095] Incremental R2 (full-covars): 0.14515 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019060 | PSS011099| European Ancestry| 2,770 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Mean reticulocyte volume | — | — | R²: 0.17217 [0.14717, 0.19717] PGS R2 (no covariates): 0.14414 [0.1205, 0.16779] Incremental R2 (full-covars): 0.14281 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019061 | PSS011111| South Asian Ancestry| 1,393 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Mean reticulocyte volume | — | — | R²: 0.13781 [0.10535, 0.17027] PGS R2 (no covariates): 0.11019 [0.08024, 0.14015] Incremental R2 (full-covars): 0.10391 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019062 | PSS011152| African Ancestry| 1,124 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Mean reticulocyte volume | — | — | R²: 0.03874 [0.01751, 0.05997] PGS R2 (no covariates): 0.03349 [0.01364, 0.05333] Incremental R2 (full-covars): 0.033 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019063 | PSS011169| Multi-ancestry (excluding European)| 7,578 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Mean reticulocyte volume | — | — | R²: 0.15509 [0.14052, 0.16966] PGS R2 (no covariates): 0.13046 [0.11671, 0.14422] Incremental R2 (full-covars): 0.11887 |
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 |
---|---|---|---|---|---|---|---|---|
PSS011140 | — | — | 64,861 individuals | — | European (white British ancestry) |
— | UKB | — |
PSS011111 | — | — | 1,393 individuals | — | South Asian | — | UKB | — |
PSS011152 | — | — | 1,124 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 | — |