Predicted Trait | |
Reported Trait | Platelet count |
Mapped Trait(s) | platelet count (EFO_0004309) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30080 |
Score Construction | |
PGS Name | INI30080 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 32,944 |
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 |
---|---|---|---|---|---|---|---|---|
— | 316,085 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 |
---|---|---|---|---|---|---|---|---|
PPM018979 | PSS011145| European Ancestry| 65,931 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Platelet count | — | — | R²: 0.26848 [0.26277, 0.27419] PGS R2 (no covariates): 0.20939 [0.20394, 0.21484] Incremental R2 (full-covars): 0.20822 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018980 | PSS011109| European Ancestry| 2,813 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Platelet count | — | — | R²: 0.26562 [0.23807, 0.29316] PGS R2 (no covariates): 0.22463 [0.19789, 0.25138] Incremental R2 (full-covars): 0.22027 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018981 | PSS011113| South Asian Ancestry| 1,433 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Platelet count | — | — | R²: 0.23486 [0.19726, 0.27247] PGS R2 (no covariates): 0.15582 [0.12203, 0.18962] Incremental R2 (full-covars): 0.15006 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018982 | PSS011155| African Ancestry| 1,157 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Platelet count | — | — | R²: 0.13941 [0.10335, 0.17547] PGS R2 (no covariates): 0.06653 [0.03951, 0.09355] Incremental R2 (full-covars): 0.0492 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM018983 | PSS011166| Multi-ancestry (excluding European)| 7,746 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Platelet count | — | — | R²: 0.24864 [0.23223, 0.26504] PGS R2 (no covariates): 0.19334 [0.17781, 0.20888] Incremental R2 (full-covars): 0.18573 |
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 | — |
PSS011145 | — | — | 65,931 individuals | — | European (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 | — |