PGS Publication: PGP000381

Publication Information (EuropePMC)
Title Development of a clinical polygenic risk score assay and reporting workflow.
PubMed ID 35437332(Europe PMC)
doi 10.1038/s41591-022-01767-6
Publication Date April 18, 2022
Journal Nat Med
Author(s) Hao L, Kraft P, Berriz GF, Hynes ED, Koch C, Korategere V Kumar P, Parpattedar SS, Steeves M, Yu W, Antwi AA, Brunette CA, Danowski M, Gala MK, Green RC, Jones NE, Lewis ACF, Lubitz SA, Natarajan P, Vassy JL, Lebo MS.
Released in PGS Catalog: Oct. 19, 2022

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)
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
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
PGS000014
(GPS_T2D)
 PGP000006 |
Khera AV et al. Nat Genet (2018)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 6,917,436
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000014/ScoringFiles/PGS000014.txt.gz - Check Terms/Licenses
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
PGS000765
(PRS_CRC95)
 PGP000170 |
Huyghe JR et al. Nat Genet (2018)
 Colorectal cancer colorectal cancer 95
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000765/ScoringFiles/PGS000765.txt.gz
PGS000030
(PrCa)
 PGP000019 |
Schumacher FR et al. Nat Genet (2018)
 Prostate cancer prostate carcinoma 147
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000030/ScoringFiles/PGS000030.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
PPM015517 PGS000007
(PRS3820_BC)
 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Breast cancer OR: 2.38 [2.07, 2.73] — — 4 genetic PCs —
PPM015518 PGS000765
(PRS_CRC95)
 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Colorectal cancer OR: 2.37 [1.74, 3.24] — — 4 genetic PCs —
PPM015519 PGS000030
(PrCa)
 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Prostate cancer OR: 2.22 [1.98, 2.48] — — 4 genetic PCs —
PPM015520 PGS000016
(GPS_AF)
 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Atrial fibrillation OR: 2.37 [2.12, 2.64] — — 4 genetic PCs —
PPM015521 PGS000013
(GPS_CAD)
 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Coronary artery disease OR: 1.86 [1.69, 2.05] — — 4 genetic PCs —
PPM015522 PGS000014
(GPS_T2D)
 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Type 2 diabetes mellitus OR: 1.75 [1.57, 1.95] — — 4 genetic PCs —

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
PSS009971 — — 1,807 individuals — African unspecified
(Black)		 — MGBB —
PSS009971 — — 786 individuals — Asian unspecified — MGBB —
PSS009971 — — 3,113 individuals — Other — MGBB —
PSS009971 — — 30,716 individuals — European — MGBB —