Predicted Trait | |
Reported Trait | Log triglycerides |
Mapped Trait(s) | triglyceride measurement (EFO_0004530) |
Additional Trait Information | Phenotype defined in GLGC. Please refer the paper for more details. |
Score Construction | |
PGS Name | logTG_AFR_lassosum2 |
Development Method | |
Name | lassosum2 |
Parameters | Default parameter setting in bigsnpr version 1.12 -- length of tuning parameter path for the the lasso penalty = 30; and regularization parameter for LD matrix is chosen from c(0.001, 0.01, 0.1, 1). |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 446 |
Effect Weight Type | beta |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000595 |
Citation (link to publication) | Zhang J et al. Nat Commun (2024) |
Ancestry Distribution | |
Source of Variant Associations (GWAS) | African: 100% 89,468 individuals (100%) |
Score Development/Training | African: 100% 4,298 individuals (100%) |
PGS Evaluation | African: 100% 1 Sample Sets |
Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
---|---|---|---|
Europe PMC: 34887591 |
89,468 individuals | African American or Afro-Caribbean | GLGC |
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 |
---|---|---|---|---|---|---|---|---|
— | 4,298 individuals, 42.0 % Male samples |
African American or Afro-Caribbean (African American) |
UKB | — | Mean = 51.82 years Sd = 8.06 years |
— | — | — |
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 |
---|---|---|---|---|---|---|---|---|
PPM020837 | PSS011423| African Ancestry| 4,300 individuals |
PGP000595 | Zhang J et al. Nat Commun (2024) |
Reported Trait: Log triglycerides | — | — | adjusted R2: 0.0367 | — | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS011423 | — | — | 4,300 individuals, 42.0 % Male samples |
Mean = 51.82 years Sd = 8.06 years |
African American or Afro-Caribbean | — | UKB | — |