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, Elli... nor PT, Kathiresan S.Show more
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:
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

PGS Developed By This Publication

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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)
PGS000013
(GPS_CAD)
PGP000006 |
Khera AV et al. Nat Genet (2018)
Coronary artery diseasecoronary artery disease6,630,150
G
D
E
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 mellitus6,917,436
G
D
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000014/ScoringFiles/PGS000014.txt.gz - Check Terms/Licenses
PGS000015
(GPS_BC)
PGP000006 |
Khera AV et al. Nat Genet (2018)
Breast cancerbreast carcinoma5,218
G
D
E
https://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 fibrillationatrial fibrillation6,730,541
G
D
E
https://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 diseaseinflammatory bowel disease6,907,112
G
D
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000017/ScoringFiles/PGS000017.txt.gz - Check Terms/Licenses
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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.

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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
PPM000022PGS000013
(GPS_CAD)
PSS000015|
European Ancestry|
288,978 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Coronary artery diseaseAUROC: 0.81 [0.81, 0.81]Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.04age; sex; Ancestry PC 1-4; genotyping chip
PPM000023PGS000014
(GPS_T2D)
PSS000017|
European Ancestry|
288,978 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Type 2 diabetesAUROC: 0.73 [0.72, 0.73]Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.029age; sex; Ancestry PC 1-4; genotyping chip
PPM000024PGS000015
(GPS_BC)
PSS000014|
European Ancestry|
157,895 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Breast cancerAUROC: 0.69 [0.68, 0.69]Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.027age; sex; Ancestry PC 1-4; genotyping chip
PPM000025PGS000016
(GPS_AF)
PSS000013|
European Ancestry|
288,978 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Atrial fibrillationAUROC: 0.77 [0.76, 0.77]Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.029age; sex; Ancestry PC 1-4; genotyping chip
PPM000026PGS000017
(GPS_IBD)
PSS000016|
European Ancestry|
288,978 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Inflammatory bowel diseaseAUROC: 0.63 [0.62, 0.64]Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.021age; sex; Ancestry PC 1-4; genotyping chip
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Evaluated Samples

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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
PSS000013Atrial fibrillation ascertainment was based on self-report of atrial fibrillation, atrial flutter, o... r 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 previouslyShow more
[
  • 4,576 cases
  • , 284,402 controls
]
EuropeanUKBUKB Phase 2
PSS000014Breast cancer ascertainment was based on self-report in an interview with a trained nurse, ICD-9 cod... es (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.Show more
[
  • 6,586 cases
  • , 151,309 controls
]
,
0.0 % Male samples
EuropeanUKBUKB Phase 2
PSS000015CAD ascertainment was based on a composite of myocardial infarction or coronary revascularization. M... yocardial 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).Show more
[
  • 8,676 cases
  • , 280,302 controls
]
EuropeanUKBUKB Phase 2
PSS000016Inflammatory bowel disease ascertainment was based on report in an interview with a trained nurse, o... r an ICD-9 code of 555.X or ICD-10 code of K51.X in hospitalization records.Show more
[
  • 5,853 cases
  • , 283,125 controls
]
EuropeanUKBUKB Phase 2
PSS000017Type 2 diabetes ascertainment was based on self-report in an interview with a trained nurse or an IC... D-10 code of E11.X in hospitalization records.Show more
[
  • 5,853 cases
  • , 283,125 controls
]
EuropeanUKBUKB Phase 2
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