| Publication Information (EuropePMC) | |
| Title | Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores. |
| PubMed ID | 31771638(Europe PMC) |
| doi | 10.1186/s13073-019-0682-2 |
| Publication Date | Nov. 26, 2019 |
| Journal | Genome Med |
| Author(s) | Homburger JR, Neben CL, Mishne G, Zhou AY, Kathiresan S, Khera AV. |
| Polygenic Score (PGS) ID | PGS Name | PGS Publication (PGP) ID | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | PGS Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS000016 | GPS_AF | PGP000006 Khera AV et al. Nat Genet (2018) |
Atrial fibrillation | atrial fibrillation | 6,730,541 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000016/ScoringFiles/PGS000016.txt.gz |
| PGS000013 | GPS_CAD | PGP000006 Khera AV et al. Nat Genet (2018) |
Coronary artery disease | coronary artery disease | 6,630,150 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz |
| PGS000007 | PRS3820_BC | PGP000002 Mavaddat N et al. Am J Hum Genet (2018) |
Breast Cancer | breast carcinoma | 3,820 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000007/ScoringFiles/PGS000007.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000384 | PGS000007 (PRS3820_BC) | PSS000218 | PGP000057 Homburger JR et al. (2019) Ext. |
Reported Trait: Breast Cancer (personal history) | OR: 1.56[1.45, 1.68] | — | — | age at menarche | — |
| PPM000386 | PGS000007 (PRS3820_BC) | PSS000218 | PGP000057 Homburger JR et al. (2019) Ext. |
Reported Trait: Breast Cancer (personal history) | — | AUROC: 0.78 | — | age, sex | — |
| PPM000388 | PGS000007 (PRS3820_BC) | PSS000218 | PGP000057 Homburger JR et al. (2019) Ext. |
Reported Trait: Breast Cancer (personal history) | — | AUROC: 0.63 | — | — | — |
| PPM000383 | PGS000013 (GPS_CAD) | PSS000219 | PGP000057 Homburger JR et al. (2019) Ext. |
Reported Trait: Coronary artery disease (personal history) | OR: 1.589[1.32, 1.92] | AUROC: 0.86 | — | age, sex | — |
| PPM000387 | PGS000013 (GPS_CAD) | PSS000219 | PGP000057 Homburger JR et al. (2019) Ext. |
Reported Trait: Coronary artery disease (personal history) | — | AUROC: 0.6 | — | — | — |
| PPM000385 | PGS000016 (GPS_AF) | PSS000217 | PGP000057 Homburger JR et al. (2019) Ext. |
Reported Trait: Atrial Fibrillation (personal history) | OR: 1.277[1.12, 1.46] | AUROC: 0.78 | — | age, sex | — |
| PPM000389 | PGS000016 (GPS_AF) | PSS000217 | PGP000057 Homburger JR et al. (2019) Ext. |
Reported Trait: Atrial Fibrillation (personal history) | — | AUROC: 0.57 | — | — | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000219 | Phenotypic information was self-reported by the individual through an online, interactive health history tool | — | [ ,
17.1 % Male samples |
— | European | — | CG | Samples are individuals whose healthcare provider had ordered a Color Genomics multi-gene panel test |
| PSS000217 | Phenotypic information was self-reported by the individual through an online, interactive health history tool | — | [ ,
17.1 % Male samples |
— | European | — | CG | Samples are individuals whose healthcare provider had ordered a Color Genomics multi-gene panel test |
| PSS000218 | Phenotypic information was self-reported by the individual through an online, interactive health history tool | — | [ ,
0.0 % Male samples |
— | European | — | CG | Samples are individuals whose healthcare provider had ordered a Color Genomics multi-gene panel test |