Predicted Trait | |
Reported Trait | Schizophrenia |
Mapped Trait(s) | schizophrenia (MONDO_0005090) |
Score Construction | |
PGS Name | SCZ_GHS |
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 GHS = 833,502 |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 830,589 |
Effect Weight Type | NR |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000065 |
Citation (link to publication) | Zheutlin AB et al. Am J Psychiatry (2019) |
Ancestry Distribution | |
Source of Variant Associations (GWAS) | European: 94% East Asian: 6% 87,534 individuals (100%) |
PGS Evaluation | European: 100% 2 Sample Sets |
Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
---|---|---|---|
GWAS Catalog: GCST002539 Europe PMC: 25056061 |
5,219 individuals | East Asian | NR |
GWAS Catalog: GCST002539 Europe PMC: 25056061 |
82,315 individuals | European (Portugal, U.K., Republic of Ireland, Denmark) |
NR |
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 |
---|---|---|---|---|---|---|---|---|
PPM000418 | PSS000240| European Ancestry| 44,436 individuals |
PGP000065 | Zheutlin AB et al. Am J Psychiatry (2019) |
Reported Trait: Psychosis | OR: 1.2224 | — | — | age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch | *SNP weights were adjusted for use in this cohort |
PPM000414 | PSS000239| European Ancestry| 44,436 individuals |
PGP000065 | Zheutlin AB et al. Am J Psychiatry (2019) |
Reported Trait: Schizophrenia | OR: 1.483 | AUROC: 0.6 [0.56, 0.64] | — | age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch | *SNP weights were adjusted for use in this cohort |
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 |
---|---|---|---|---|---|---|---|---|
PSS000239 | Schizophrenia case subjects had two or more ICD codes included in phecode 295.1 | — | [ ,
41.0 % Male samples |
Mean = 60.2 years Sd = 16.9 years |
European | — | MyCode | Geisinger Health System (GHS) |
PSS000240 | Psychosis case subjects were identified with phecode 295 | — | [ ,
41.0 % Male samples |
Mean = 60.2 years Sd = 16.9 years |
European | — | MyCode | Geisinger Health System (GHS) |