Trait: Alzheimer's disease

Information

Experimental Factor Ontology ID: EFO_0000249

EFO Trait Description: A progressive, neurodegenerative disease characterized by loss of function and death of nerve cells in several areas of the brain leading to loss of cognitive function such as memory and language. [NCIT: P378]

Associated PGS

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)
PPM000053 PGS000026 (PHS) PSS000036 Desikan RS et al. (2017) Reported Trait: Alzheimer disease r (correlation between between binned quantiles of PHS-predicted and empirical age of AD onset): 0.9 APOE risk alleles (e2 and e4), age, sex, genetic PCs 1-5

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
PSS000036 Cases are patients with clinically diagnosed AD and compared to cognitively normal older individuals 17,956 individuals
[ 6,984 cases, 10,972 controls]
40.50574738249053 % Male samples
European ADGC ADGC Phase 2