Publication: Evaluation of a Genetic Risk Score to Improve Risk Prediction for Alzheimer's Disease.

Information

PGS Catalog Publication (PGP) ID: PGP000015
PubMed ID: 27340842
doi: 10.3233/JAD-150749

Publication Date: June 1, 2016

Journal: J Alzheimers Dis

Authors: 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.

PGS Associated with PGP000015

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
PPM000050 PGS000025 (GRS) PSS000033 Chouraki V et al. (2016) Reported Trait: Incident Alzheimer's disease cases 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)
PPM000051 PGS000025 (GRS) PSS000034 Chouraki V et al. (2016) Reported Trait: Incident Alzheimer's disease cases 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 Chouraki V et al. (2016) Reported Trait: Incident Alzheimer's disease cases 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)

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
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. 19,687 individuals
[ 2,782 cases]
European ACT, AGES, CHS, FHS, ROSMAP, RS, 3C, WHICAP 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 ACT, AGES, CHS, FHS, ROSMAP, RS, 3C, WHICAP 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 ACT, AGES, CHS, FHS, ROSMAP, RS, 3C, WHICAP 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