| Publication Information (EuropePMC) | |
| Title | Evaluation of a Genetic Risk Score to Improve Risk Prediction for Alzheimer's Disease. |
| PubMed ID | 27340842(Europe PMC) |
| doi | 10.3233/JAD-150749 |
| Publication Date | June 1, 2016 |
| Journal | J Alzheimers Dis |
| Author(s) | Chouraki V, Reitz C, Maury F, Bis JC, Bellenguez C, Yu L, Jakobsdottir J, Mukherjee S, Adams HH, Choi SH, Larson EB, Fitzpatrick A, Uitterlinden AG, de Jager PL, Hofman A, Gudnason V, Vardarajan B, Ibrahim-Verbaas C, van der Lee SJ, Lopez O, Dartigues JF, Berr C, Amouyel P, Bennett DA, van Duijn C, DeStefano AL, Launer LJ, Ikram MA, Crane PK, Lambert JC, Mayeux R, Seshadri S, International Genomics of Alzheimer’s Project. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000025 (GRS) |
PGP000015 | Chouraki V et al. J Alzheimers Dis (2016) |
Alzheimer's disease | Alzheimer disease | 19 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000025/ScoringFiles/PGS000025.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000051 | PGS000025 (GRS) |
PSS000034| European Ancestry| 4,353 individuals |
PGP000015 | Chouraki V et al. J Alzheimers Dis (2016) |
Reported Trait: Incident Alzheimer's disease in APOE Ɛ4 carriers | HR: 1.24 [1.15, 1.34] | — | ΔC-index between models with and without GRS: 0.0112 [0.0015, 0.0208] | age at baseline, sex, education level | HRs are derived from a meta-analysis of studies (adjusted for study center, and participant relatedness) |
| PPM000052 | PGS000025 (GRS) |
PSS000035| European Ancestry| 15,334 individuals |
PGP000015 | Chouraki V et al. J Alzheimers Dis (2016) |
Reported Trait: Incident Alzheimer's disease in APOE Ɛ4 non-carriers | HR: 1.13 [1.08, 1.18] | — | ΔC-index between models with and without GRS: 0.0018 [-0.0003, 0.0039] | age at baseline, sex, education level | HRs are derived from a meta-analysis of studies (adjusted for study center, and participant relatedness) |
| PPM000050 | PGS000025 (GRS) |
PSS000033| European Ancestry| 19,687 individuals |
PGP000015 | Chouraki V et al. J Alzheimers Dis (2016) |
Reported Trait: Incident Alzheimer's disease | HR: 1.17 [1.13, 1.21] | — | ΔC-index between models with and without GRS: 0.0043 [0.0019, 0.0067] | age at baseline, sex, education level, APOE Ɛ4 status | HRs are derived from a meta-analysis of studies (adjusted for study center, and participant relatedness) |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000033 | Most of the studies used standard screening procedures based on history, medical review, screening questions, and cognitive assessments that flagged participants with potential cognitive impairment. These participants underwent complete neurological and neuropsychological evaluation. An initial decision was made regarding the presence or absence of dementia, using the DSM-IV criteria; a diagnosis of possible, probable, or definite AD was made as a second step using NINCDS-ADRDA (National Institute of Neurological Disorders and Stroke Alzheimer’s Disease and Related Disorders Association) criteria. | — | [
|
— | European | — | 8 cohorts
|
As one SNP (rs9271192) was missing in FHS, WHICAP, and Rotterdam because of poor imputation quality, an 18 SNP-based GRS was computed in these cohorts. As the samples used in this project were partially overlapping with the ones used in the original IGAP study, we ran an additional IGAP meta-analysis after excluding those and did not find significant changes in the estimations of HRs for the SNPs considered |
| PSS000034 | Most of the studies used standard screening procedures based on history, medical review, screening questions, and cognitive assessments that flagged participants with potential cognitive impairment. These participants underwent complete neurological and neuropsychological evaluation. An initial decision was made regarding the presence or absence of dementia, using the DSM-IV criteria; a diagnosis of possible, probable, or definite AD was made as a second step using NINCDS-ADRDA (National Institute of Neurological Disorders and Stroke Alzheimer’s Disease and Related Disorders Association) criteria. | — | 4,353 individuals | — | European | — | 8 cohorts
|
As one SNP (rs9271192) was missing in FHS, WHICAP, and Rotterdam because of poor imputation quality, an 18 SNP-based GRS was computed in these cohorts. As the samples used in this project were partially overlapping with the ones used in the original IGAP study, we ran an additional IGAP meta-analysis after excluding those and did not find significant changes in the estimations of HRs for the SNPs considered |
| PSS000035 | Most of the studies used standard screening procedures based on history, medical review, screening questions, and cognitive assessments that flagged participants with potential cognitive impairment. These participants underwent complete neurological and neuropsychological evaluation. An initial decision was made regarding the presence or absence of dementia, using the DSM-IV criteria; a diagnosis of possible, probable, or definite AD was made as a second step using NINCDS-ADRDA (National Institute of Neurological Disorders and Stroke Alzheimer’s Disease and Related Disorders Association) criteria. | — | 15,334 individuals | — | European | — | 8 cohorts
|
As one SNP (rs9271192) was missing in FHS, WHICAP, and Rotterdam because of poor imputation quality, an 18 SNP-based GRS was computed in these cohorts. As the samples used in this project were partially overlapping with the ones used in the original IGAP study, we ran an additional IGAP meta-analysis after excluding those and did not find significant changes in the estimations of HRs for the SNPs considered |