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 |
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 |
---|---|---|---|---|---|---|---|---|---|
PPM000386 | PGS000007 (PRS3820_BC) |
PSS000218 | PGP000057 Homburger JR et al. (2019) Ext. | Reported Trait: Breast Cancer (personal history) | — | AUROC: 0.78 | — | age, sex | — |
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 | — |
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 | — |
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 | — |
PPM000389 | PGS000016 (GPS_AF) |
PSS000217 | PGP000057 Homburger JR et al. (2019) Ext. | Reported Trait: Atrial Fibrillation (personal history) | — | AUROC: 0.57 | — | — | — |
PPM000388 | PGS000007 (PRS3820_BC) |
PSS000218 | PGP000057 Homburger JR et al. (2019) Ext. | Reported Trait: Breast Cancer (personal history) | — | AUROC: 0.63 | — | — | — |
PPM000387 | PGS000013 (GPS_CAD) |
PSS000219 | PGP000057 Homburger JR et al. (2019) Ext. | Reported Trait: Coronary artery disease (personal history) | — | AUROC: 0.6 | — | — | — |
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 |
---|---|---|---|---|---|---|---|---|
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 |