Predicted Trait | |
Reported Trait | Monocyte count |
Mapped Trait(s) | monocyte count (EFO_0005091) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30130 |
Score Construction | |
PGS Name | INI30130 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 13,415 |
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 |
---|---|---|---|---|---|---|---|---|
— | 315,523 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 |
---|---|---|---|---|---|---|---|---|
PPM019004 | PSS011139| European Ancestry| 65,814 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Monocyte count | — | — | R²: 0.12426 [0.11961, 0.12891] PGS R2 (no covariates): 0.08189 [0.07793, 0.08585] Incremental R2 (full-covars): 0.08198 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019005 | PSS011110| European Ancestry| 2,810 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Monocyte count | — | — | R²: 0.14509 [0.12139, 0.16879] PGS R2 (no covariates): 0.0898 [0.06995, 0.10965] Incremental R2 (full-covars): 0.08851 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019006 | PSS011112| South Asian Ancestry| 1,428 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Monocyte count | — | — | R²: 0.11251 [0.08232, 0.1427] PGS R2 (no covariates): 0.07028 [0.04528, 0.09527] Incremental R2 (full-covars): 0.06806 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019007 | PSS011154| African Ancestry| 1,154 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Monocyte count | — | — | R²: 0.0334 [0.01357, 0.05322] PGS R2 (no covariates): 0.03342 [0.01359, 0.05325] Incremental R2 (full-covars): 0.02807 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019008 | PSS011168| Multi-ancestry (excluding European)| 7,732 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Monocyte count | — | — | R²: 0.11068 [0.09772, 0.12363] PGS R2 (no covariates): 0.07932 [0.06797, 0.09067] Incremental R2 (full-covars): 0.06798 |
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 |
---|---|---|---|---|---|---|---|---|
PSS011110 | — | — | 2,810 individuals | — | European (non-white British ancestry) |
— | UKB | — |
PSS011112 | — | — | 1,428 individuals | — | South Asian | — | UKB | — |
PSS011154 | — | — | 1,154 individuals | — | African unspecified | — | UKB | — |
PSS011168 | — | — | 7,732 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |
PSS011139 | — | — | 65,814 individuals | — | European (white British ancestry) |
— | UKB | — |