PGS Publication: PGP000057

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.
Released in PGS: March 27, 2020

Associated Polygenic Score(s)

External PGS Evaluated By This Publication

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 Metrics

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

Evaluated Samples

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
[
  • 126 cases
  • , 10,884 controls
]
,
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
[
  • 239 cases
  • , 10,064 controls
]
,
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
[
  • 828 cases
  • , 8,701 controls
]
,
0.0 % Male samples
European CG Samples are individuals whose healthcare provider had ordered a Color Genomics multi-gene panel test