| 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 (PGS) ID | PGS Name | PGS Publication (PGP) ID | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | PGS Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS000136 | SCZ_PBK | PGP000065 Zheutlin AB et al. Am J Psychiatry (2019) |
Schizophrenia | schizophrenia | 833,502 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000136/ScoringFiles/PGS000136.txt.gz |
| PGS000135 | SCZ_MTS | PGP000065 Zheutlin AB et al. Am J Psychiatry (2019) |
Schizophrenia | schizophrenia | 972,439 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000135/ScoringFiles/PGS000135.txt.gz |
| PGS000134 | SCZ_GHS | PGP000065 Zheutlin AB et al. Am J Psychiatry (2019) |
Schizophrenia | schizophrenia | 830,589 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000134/ScoringFiles/PGS000134.txt.gz |
| PGS000133 | SCZ_BVU | PGP000065 Zheutlin AB et al. Am J Psychiatry (2019) |
Schizophrenia | schizophrenia | 604,645 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000133/ScoringFiles/PGS000133.txt.gz |
Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.
|
PGS Performance Metric ID (PPM ID) |
Evaluated Score |
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000416 | PGS000136 (SCZ_PBK) | PSS000243 | PGP000065 Zheutlin AB et al. (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 |
| PPM000420 | PGS000136 (SCZ_PBK) | PSS000244 | PGP000065 Zheutlin AB et al. (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 |
| PPM000415 | PGS000135 (SCZ_MTS) | PSS000241 | PGP000065 Zheutlin AB et al. (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 |
| PPM000419 | PGS000135 (SCZ_MTS) | PSS000242 | PGP000065 Zheutlin AB et al. (2019) |
Reported Trait: Psychosis | — | — | — | age, sex, 10 PCs of ancestry, genotyping platform, genotyping batch | *SNP weights were adjusted for use in this cohort |
| PPM000414 | PGS000134 (SCZ_GHS) | PSS000239 | PGP000065 Zheutlin AB et al. (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 |
| PPM000418 | PGS000134 (SCZ_GHS) | PSS000240 | PGP000065 Zheutlin AB et al. (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 |
| PPM000413 | PGS000133 (SCZ_BVU) | PSS000237 | PGP000065 Zheutlin AB et al. (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 |
| PPM000417 | PGS000133 (SCZ_BVU) | PSS000238 | PGP000065 Zheutlin AB et al. (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 |
|
PGS Sample Set ID (PSS ID) |
Detailed Phenotype Description | 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 | — | GeHS | 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 | — | GeHS | 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 | — | BMBB, IMP, Mount Sinai | BioMe Biobank at the Mount Sinai School of Medicine (MSSM) |
| PSS000242 | Psychosis case subjects were identified with phecode 295 | — | [ ,
48.0 % Male samples |
Mean = 57.2 years Sd = 19.8 years |
European | — | BMBB, IMP, Mount Sinai | 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 | — | Partners | 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 | — | Partners | Partners HealthCare System (PHS) biobank |