PGS Publication: PGP000006

Publication Information (EuropePMC)
Title Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations.
PubMed ID 30104762(Europe PMC)
doi 10.1038/s41588-018-0183-z
Publication Date Aug. 13, 2018
Journal Nat Genet
Author(s) Khera AV, Chaffin M, Aragam KG, Haas ME, Roselli C, Choi SH, Natarajan P, Lander ES, Lubitz SA, Ellinor PT, Kathiresan S.
Released in PGS Catalog: Oct. 14, 2019

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:
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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

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
PGS000015
(GPS_BC)
PGP000006 |
Khera AV et al. Nat Genet (2018)
Breast cancer breast carcinoma 5,218
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000015/ScoringFiles/PGS000015.txt.gz - Check Terms/Licenses
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 - Check Terms/Licenses
PGS000017
(GPS_IBD)
PGP000006 |
Khera AV et al. Nat Genet (2018)
Inflammatory bowel disease inflammatory bowel disease 6,907,112
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000017/ScoringFiles/PGS000017.txt.gz - Check Terms/Licenses
PGS000014
(GPS_T2D)
PGP000006 |
Khera AV et al. Nat Genet (2018)
Type 2 diabetes type II diabetes mellitus 6,917,436
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000014/ScoringFiles/PGS000014.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
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz - Check Terms/Licenses

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
PPM000022 PGS000013
(GPS_CAD)
PSS000015|
European Ancestry|
288,978 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Coronary artery disease AUROC: 0.81 [0.81, 0.81] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.04 age; sex; Ancestry PC 1-4; genotyping chip
PPM000023 PGS000014
(GPS_T2D)
PSS000017|
European Ancestry|
288,978 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Type 2 diabetes AUROC: 0.73 [0.72, 0.73] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.029 age; sex; Ancestry PC 1-4; genotyping chip
PPM000024 PGS000015
(GPS_BC)
PSS000014|
European Ancestry|
157,895 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Breast cancer AUROC: 0.69 [0.68, 0.69] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.027 age; sex; Ancestry PC 1-4; genotyping chip
PPM000025 PGS000016
(GPS_AF)
PSS000013|
European Ancestry|
288,978 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Atrial fibrillation AUROC: 0.77 [0.76, 0.77] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.029 age; sex; Ancestry PC 1-4; genotyping chip
PPM000026 PGS000017
(GPS_IBD)
PSS000016|
European Ancestry|
288,978 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Inflammatory bowel disease AUROC: 0.63 [0.62, 0.64] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.021 age; sex; Ancestry PC 1-4; genotyping chip

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
PSS000013 Atrial fibrillation ascertainment was based on self-report of atrial fibrillation, atrial flutter, or cardioversion in an interview with a trained nurse, an ICD-9 code of 427.3 or ICD-10 code of I48.X in hospitalization records, or a history of a percutaneous ablation or cardioversion based on the OPCS-4 coded procedure (K57.1, K62.1, K62.2, K62.3, or K 62.4), as performed previously
[
  • 4,576 cases
  • , 284,402 controls
]
European UKB UKB Phase 2
PSS000014 Breast cancer ascertainment was based on self-report in an interview with a trained nurse, ICD-9 codes (174 or 174.9) or ICD-10 codes (C50.X) in hospitalization records, or a breast cancer diagnosis reported to the national registry before the date of enrollment.
[
  • 6,586 cases
  • , 151,309 controls
]
,
0.0 % Male samples
European UKB UKB Phase 2
PSS000015 CAD ascertainment was based on a composite of myocardial infarction or coronary revascularization. Myocardial infarction was based on self-report or hospital admission diagnosis, as performed centrally. This included individuals with ICD-9 codes of 410.X, 411.0, 412.X, or 429.79, or ICD-10 codes of I21.X, I22.X, I23.X, I24.1, or I25.2 in hospitalization records. Coronary revascularization was assessed based on an OPCS-4 coded procedure for coronary artery bypass grafting (K40.1–40.4, K41.1–41.4, or K45.1–45.5), or coronary angioplasty with or without stenting (K49.1–49.2, K49.8–49.9, K50.2, K75.1–75.4, or K75.8–75.9).
[
  • 8,676 cases
  • , 280,302 controls
]
European UKB UKB Phase 2
PSS000016 Inflammatory bowel disease ascertainment was based on report in an interview with a trained nurse, or an ICD-9 code of 555.X or ICD-10 code of K51.X in hospitalization records.
[
  • 5,853 cases
  • , 283,125 controls
]
European UKB UKB Phase 2
PSS000017 Type 2 diabetes ascertainment was based on self-report in an interview with a trained nurse or an ICD-10 code of E11.X in hospitalization records.
[
  • 5,853 cases
  • , 283,125 controls
]
European UKB UKB Phase 2