Illumina Method
To address DNA strand designation and orientation, Illumina has developed a consistent and simple method to ensure uniformity in the reporting of genotype calls.
Initially, we used Illumina BeadStudio 3.2 software to generate SNP genotypes from bead intensity data. After performing sample verification and quality control bioinformatics, the genotype data for 818 ADNI participants was made available to qualified researchers. Reprocessed array data was made available in 2010 using an updated version of BeadStudio, Illumina GenomeStudio v2009.1, for all 818 samples. Although the 2010 files are highly similar to the initial release, a comparison of calls for all 620,901 markers (from the two versions of Final Reports for each sample) indicated that only nine samples had mismatches in genotypes successfully called in the two versions, and those mismatches comprised <0.01% of all markers. Finally, a new DNA source file is included in the downloads to identify whether peripheral blood (n = 731) or immortalized LCL (n = 87) derived DNA was analyzed for each genotyped sample.
For ADNI GO/ADNI 2, genotyping was performed on 85 genomic DNAs using the Illumina HumanOmniExpress BeadChip, which contains 730,525 SNP markers, according to the manufacturers protocols.
Resources:
- ADNI 1 genetic data protocols can be found in the paper, “Alzheimer’s Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans.” Saykin AJ, et al. Alzheimer’s Dement. 2010 May;6(3):265-73. doi: 10.1016/j.jalz.2010.03.013. PMID: 20451875
- Illumina Genotype Assays guide: methods in determining strand allele for Infinium Assays
- Infinium® HD Assay Super Protocol Guide
- HumanOmniExpress-24 Beadchips Data Sheet
