Genetic Data

Genetic factors play an important role in Alzheimer’s disease and a key aim of the ADNI is providing the opportunity to combine genetics with imaging and clinical data to help investigate mechanisms of the disease. Genotyping and sequencing data have been generated for ADNI 1, ADNI GO and ADNI 2 subjects and are available to ADNI investigators. A summary of the available data is shown below.  Please see the Genetic Data Methods section for more information about the Illumina Genotyping Assays.

Summary of Available Sequencing Data

ADNI 1 GWAS ADNI GO/2 GWAS ADNI WGS
Genotyping Platform Illumina Human610-Quad BeadChip Illumina HumanOmniExpress BeadChip Illumina Omni 2.5M (WGS Platform)
Number of SNPs 620,901 SNP &
CNV Markers
730,525 SNP &
CNV Markers
#SNPs: ~3.7 million
#Indels: ~700,000
#SVs: ~3,500
Patients Diagnosis Groups NC, MCI, AD NC, EMCI, MCI,
LMCI, AD
NC, MCI, AD
Number of Subjects 818 432 818
File format CSV, PLINK CSV VCF (version 4.1)

Summary of Available Genotyping Data

Type Overview File Format
APOE
Genotyping
The epsilon 4 allele of APOE is the strongest known genetic risk factor for AD with a two- to three-fold increased risk for AD in people with one epsilon 4 allele rising to about 12-fold in those with two alleles. APOE genotyping was performed at the time of participant enrollment and included in the ADNI database. The two SNPs (rs429358, rs7412) that define the epsilon 2, 3, and 4 alleles, are not on the Human610-Quad BeadChip, and therefore were genotyped using DNA extracted by Cogenics from a 3 mL aliquot of EDTA blood. CSV
TOMM40 PolyT Variant Genotyping of the risk gene, TOMM40 (translo-case of outer mitochondrial membrane 40), was performed by Polymorphic DNA Technologies. Support for the PolyT assays was generously provided by Allen Roses of Duke University. The ADNI Genetics Core and NCRAD supported DNA preparation. Michael Lutz of Duke University provided bioinformatics expertise. CSV

 

Whole Genome Sequencing (WGS)

In July 2012 the Brin-Wojcicki Foundation and the Alzheimer’s Association donated funds to support whole genome sequencing (WGS) of 818 ADNI participants (at the time, 128 with AD, 415 with MCI, 267 controls and 8 of uncertain diagnosis). Samples were sent to Illumina where non-CLIA WGS, as well as Illumina Omni 2.5M genome-wide association study (GWAS) single nucleotide polymorphism (SNP) arrays, were performed on each sample and completed in the spring of 2013. Basic quality control checks were then performed and others continue to be performed.

WGS SNPs data is currently already available to authorized ADNI investigators from within the ADNI Archive. Many users will find this adequate to their needs. Because the actual raw data amounts to over 150TB, it cannot be reasonably distributed over the internet. However, if users wish to re-call variants or realign the reads using other toolkits, they may request access to the entire WGS raw dataset.

For more information please see the Whole Genome Sequencing (WGS) Data Access webpage.

Genome-Wide Association Studies

Genome-wide association studies (GWAS) employ tests of association between markers, called single nucleotide polymorphisms (SNPs), and a phenotype of interest. Findings from case-control GWAS and other types of genetic association studies can provide targets for examining quantitative phenotypes derived from ADNI imaging and other biomarker data sets. GWAS data is available for download to qualified researchers.

For more information see the paper, “Alzheimer’s Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans.” Saykin AJ, et al. Alzheimers Dement. 2010 May;6(3):265-73. doi: 10.1016/j.jalz.2010.03.013. PMID: 20451875

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