| 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. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000017 (GPS_IBD) |
PGP000006 | Khera AV et al. Nat Genet (2018) |
Inflammatory bowel disease | inflammatory bowel disease | 6,907,112 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000017/ScoringFiles/PGS000017.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 | |
| 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 | |
| PGS000015 (GPS_BC) |
PGP000006 | Khera AV et al. Nat Genet (2018) |
Breast cancer | breast carcinoma | 5,218 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000015/ScoringFiles/PGS000015.txt.gz | |
| 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 |
|
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 | — |
|
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 | — | [
|
— | 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. | — | [ ,
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). | — | [
|
— | 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. | — | [
|
— | 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. | — | [
|
— | European | — | UKB | UKB Phase 2 |