Predicted Trait | |
Reported Trait | Schizophrenia |
Mapped Trait(s) | schizophrenia (EFO_0000692) |
Score Construction | |
PGS Name | SCZ_BVU |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 604,645 |
Development Method | |
Name | PRS-CS |
Parameters | Bayesian polygenic prediction method, with continuous shrinkage. Parameters: b = 0.5, phi = 1, LD-reference panel = 1000 Genomes Project European samples, # of available SNPs in BVU = 604,645 |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000065 |
Citation (link to publication) | Zheutlin AB et al. Am J Psychiatry (2019) |
Study Identifiers | Sample Numbers | Sample Ancestry |
---|---|---|
GWAS Catalog: GCST002539 EuropePMC: 25056061 |
5,219 individuals | East Asian |
GWAS Catalog: GCST002539 EuropePMC: 25056061 |
82,315 individuals | European (Portugal, U.K., Republic of Ireland, Denmark) |
PGS Performance Metric ID (PPM ID) |
PGS Sample Set ID (PSS ID) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
PGS Classification Metrics | Other Metrics | Covariates Included in the Model | PGS Performance: Other Relevant Information |
---|---|---|---|---|---|---|---|---|
PPM000417 | PSS000238 | PGP000065 Zheutlin AB et al. Am J Psychiatry (2019) |
Reported Trait: Psychosis | OR: 1.3755 | — | — | age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch | *SNP weights were adjusted for use in this cohort |
PPM000413 | PSS000237 | PGP000065 Zheutlin AB et al. Am J Psychiatry (2019) |
Reported Trait: Schizophrenia | OR: 1.691 | AUROC: 0.6 [0.55, 0.66] | — | age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch | *SNP weights were adjusted for use in this cohort |
PGS Sample Set ID (PSS ID) |
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 |
---|---|---|---|---|---|---|---|---|
PSS000237 | Schizophrenia case subjects had two or more ICD codes included in phecode 295.1 | — | [ ,
46.0 % Male samples |
Mean = 57.9 years Sd = 20.0 years |
European | — | BioVu | Vanderbilt University Medical Center (VUMC) biobank (BioVU) |
PSS000238 | Psychosis case subjects were identified with phecode 295 | — | [ ,
46.0 % Male samples |
Mean = 57.9 years Sd = 20.0 years |
European | — | BioVu | Vanderbilt University Medical Center (VUMC) biobank (BioVU) |