Polygenic Score (PGS) ID: PGS000025

Predicted Trait
Reported Trait Alzheimer's Disease
Mapped Trait(s) Alzheimer's disease (EFO_0000249)
Released in PGS: Oct. 14, 2019

Score Details

Score Construction
PGS Name GRS
Variants
Original Genome Build GRCh37
Number of Variants 19
Development Method
Name log-OR weighted sum of risk allele dosages
Parameters Top SNP in each locus (+- 500kb around top SNP) reaching genome-wide significance, excluding APOE. Recoded the odds ratios (OR) from the IGAP meta-analysis so they would all indicate an increased risk of AD and used the log(OR)and corresponding alleles to compute a weighted sum of risk allele dosages. applied an additional transformation so that one unit of the GRS would be interpreted as one additional risk allele.
PGS Source
PGS Catalog Publication (PGP) ID PGP000015
Citation (link to publication) Chouraki V et al. J Alzheimers Dis (2016)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002245
EuropePMC: 24162737
55,134 individuals European

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 ID
(PPM ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000052 PSS000035 PGP000015
Chouraki V et al. (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)
PPM000051 PSS000034 PGP000015
Chouraki V et al. (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)
PPM000050 PSS000033 PGP000015
Chouraki V et al. (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)

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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.
[
  • 2,782 cases
]
European 8 cohorts
  • 3C
  • ,ACT
  • ,AGES
  • ,CHS
  • ,FHS
  • ,ROSMAP
  • ,RS
  • ,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 8 cohorts
  • 3C
  • ,ACT
  • ,AGES
  • ,CHS
  • ,FHS
  • ,ROSMAP
  • ,RS
  • ,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 8 cohorts
  • 3C
  • ,ACT
  • ,AGES
  • ,CHS
  • ,FHS
  • ,ROSMAP
  • ,RS
  • ,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