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 Catalog: March 27, 2020

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

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)
PGS000016
(GPS_AF)
 PGP000006 |
Khera AV et al. Nat Genet (2018)
 Atrial fibrillation atrial fibrillation 6,730,541
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000016/ScoringFiles/PGS000016.txt.gz - Check Terms/Licenses
PGS000013
(GPS_CAD)
 PGP000006 |
Khera AV et al. Nat Genet (2018)
 Coronary artery disease coronary artery disease 6,630,150
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz - Check Terms/Licenses
PGS000007
(PRS3820_BC)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 Breast cancer breast carcinoma 3,820
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000007/ScoringFiles/PGS000007.txt.gz

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) 		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
PPM000383 PGS000013
(GPS_CAD)
 PSS000219|
European Ancestry|
11,010 individuals
 PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.		 Reported Trait: Coronary artery disease (personal history) OR: 1.589 [1.32, 1.92] AUROC: 0.86 — age, sex —
PPM000385 PGS000016
(GPS_AF)
 PSS000217|
European Ancestry|
10,303 individuals
 PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.		 Reported Trait: Atrial Fibrillation (personal history) OR: 1.277 [1.12, 1.46] AUROC: 0.78 — age, sex —
PPM000386 PGS000007
(PRS3820_BC)
 PSS000218|
European Ancestry|
9,529 individuals
 PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.		 Reported Trait: Breast Cancer (personal history) — AUROC: 0.78 — age, sex —
PPM000384 PGS000007
(PRS3820_BC)
 PSS000218|
European Ancestry|
9,529 individuals
 PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.		 Reported Trait: Breast Cancer (personal history) OR: 1.56 [1.45, 1.68] — — age at menarche —
PPM000389 PGS000016
(GPS_AF)
 PSS000217|
European Ancestry|
10,303 individuals
 PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.		 Reported Trait: Atrial Fibrillation (personal history) — AUROC: 0.57 — — —
PPM000388 PGS000007
(PRS3820_BC)
 PSS000218|
European Ancestry|
9,529 individuals
 PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.		 Reported Trait: Breast Cancer (personal history) — AUROC: 0.63 — — —
PPM000387 PGS000013
(GPS_CAD)
 PSS000219|
European Ancestry|
11,010 individuals
 PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.		 Reported Trait: Coronary artery disease (personal history) — AUROC: 0.6 — — —

Evaluated Samples

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
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