The ADNI genetics study employed the Illumina 610 Quad array with more than 620,000 markers for this investigation. The research team represented a collaborative effort among the Translational Genomics Institute (TGen) of Phoenix, the National Cell Repository for Alzheimer’s Disease, University of California Irvine Brain Imaging Center, the IU Center for Neuroimaging and the 59 ADNI Acquisition Sites. The resultant genetics data may be downloaded as comma separated values (CSV) files either by individual subject or by diagnostic group.
Promising biomarkers measured in ADNI fluids:
- APOE genotyping-blood
- DNA from blood cells
- RNA from blood cells
To address DNA strand designation and orientation for both human and non-human species, Illumina has developed a consistent and simple method to ensure uniformity in the reporting of genotype calls.
The method that Illumina has developed uses the top (TOP) and bottom (BOT) designations based on the poly- morphism itself, or the contextual surrounding sequence. This document provides a description of the TOP/BOT method, as well as the generalized nomenclature of “Allele A” and “Allele B” within the Illumina genotyping system. Beginning in mid-2005, dbSNP also adopted this TOP/BOT nomenclature and has included this designation for all SNP entries.
TOMM40 PolyT Variant Data
Genotyping 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.
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