| Publication Information (EuropePMC) | |
| Title | Penetrance and Pleiotropy of Polygenic Risk Scores for Schizophrenia in 106,160 Patients Across Four Health Care Systems. |
| PubMed ID | 31416338(Europe PMC) |
| doi | 10.1176/appi.ajp.2019.18091085 |
| Publication Date | Aug. 16, 2019 |
| Journal | Am J Psychiatry |
| Author(s) | Zheutlin AB, Dennis J, Karlsson Linnér R, Moscati A, Restrepo N, Straub P, Ruderfer D, Castro VM, Chen CY, Ge T, Huckins LM, Charney A, Kirchner HL, Stahl EA, Chabris CF, Davis LK, Smoller JW. |
| Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS000134 (SCZ_GHS) |
PGP000065 | Zheutlin AB et al. Am J Psychiatry (2019) |
Schizophrenia | schizophrenia | 830,589 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000134/ScoringFiles/PGS000134.txt.gz |
| PGS000135 (SCZ_MTS) |
PGP000065 | Zheutlin AB et al. Am J Psychiatry (2019) |
Schizophrenia | schizophrenia | 972,439 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000135/ScoringFiles/PGS000135.txt.gz |
| PGS000136 (SCZ_PBK) |
PGP000065 | Zheutlin AB et al. Am J Psychiatry (2019) |
Schizophrenia | schizophrenia | 833,502 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000136/ScoringFiles/PGS000136.txt.gz |
| PGS000133 (SCZ_BVU) |
PGP000065 | Zheutlin AB et al. Am J Psychiatry (2019) |
Schizophrenia | schizophrenia | 604,645 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000133/ScoringFiles/PGS000133.txt.gz |
|
PGS Performance Metric ID (PPM) |
Evaluated Score |
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000420 | PGS000136 (SCZ_PBK) |
PSS000244| European Ancestry| 18,461 individuals |
PGP000065 | Zheutlin AB et al. Am J Psychiatry (2019) |
Reported Trait: Psychosis | OR: 1.4768 | — | — | age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch | *SNP weights were adjusted for use in this cohort |
| PPM000418 | PGS000134 (SCZ_GHS) |
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 |
| PPM000417 | PGS000133 (SCZ_BVU) |
PSS000238| European Ancestry| 33,694 individuals |
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 |
| PPM000416 | PGS000136 (SCZ_PBK) |
PSS000243| European Ancestry| 18,461 individuals |
PGP000065 | Zheutlin AB et al. Am J Psychiatry (2019) |
Reported Trait: Schizophrenia | OR: 1.7 | AUROC: 0.64 [0.6, 0.69] | — | age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch | *SNP weights were adjusted for use in this cohort |
| PPM000415 | PGS000135 (SCZ_MTS) |
PSS000241| European Ancestry| 9,569 individuals |
PGP000065 | Zheutlin AB et al. Am J Psychiatry (2019) |
Reported Trait: Schizophrenia | — | AUROC: 0.74 [0.67, 0.81] | — | age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch | *SNP weights were adjusted for use in this cohort |
| PPM000414 | PGS000134 (SCZ_GHS) |
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 |
| PPM000413 | PGS000133 (SCZ_BVU) |
PSS000237| European Ancestry| 33,694 individuals |
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) |
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) |
| 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) |
| PSS000241 | Schizophrenia case subjects had two or more ICD codes included in phecode 295.1 | — | [ ,
48.0 % Male samples |
Mean = 57.2 years Sd = 19.8 years |
European | — | BioMe | BioMe Biobank at the Mount Sinai School of Medicine (MSSM) |
| PSS000243 | Schizophrenia case subjects had two or more ICD codes included in phecode 295.1 | — | [ ,
46.0 % Male samples |
Mean = 58.5 years Sd = 16.4 years |
European | — | PHB | Partners HealthCare System (PHS) biobank |
| PSS000244 | Psychosis case subjects were identified with phecode 295 | — | [ ,
46.0 % Male samples |
Mean = 58.5 years Sd = 16.4 years |
European | — | PHB | Partners HealthCare System (PHS) biobank |