Publication: Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations.

Information

PGS Catalog Publication (PGP) ID: PGP000006
PubMed ID: 30104762
doi: 10.1038/s41588-018-0183-z

Publication Date: Aug. 13, 2018

Journal: Nat Genet

Authors: Khera AV, Chaffin M, Aragam KG, Haas ME, Roselli C, Choi SH, Natarajan P, Lander ES, Lubitz SA, Ellinor PT, Kathiresan S.

PGS Associated with PGP000006

PGS Developed By This Study

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 (PPM) ID Evaluated Score PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000022 PGS000013 (GPS_CAD) PSS000015 Khera AV et al. (2018) Reported Trait: Coronary artery disease cases 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 Khera AV et al. (2018) Reported Trait: Type 2 diabetes cases 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 Khera AV et al. (2018) Reported Trait: Breast cancer cases 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 Khera AV et al. (2018) Reported Trait: Atrial fibrillation cases 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 Khera AV et al. (2018) Reported Trait: Inflammatory bowel disease cases 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 Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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 288,978 individuals
[ 4,576 cases, 293,554 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. 157,895 individuals
[ 6,586 cases, 164,481 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). 288,978 individuals
[ 8,676 cases, 297,654 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. 288,978 individuals
[ 5,853 cases, 294,831 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. 288,978 individuals
[ 5,853 cases, 294,831 controls]
European UKB UKB Phase 2