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| Research Services: Affymetrix whole genome DNA analysis |
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Affymetrix has a number of fixed content arrays for whole genome DNA analysis. GPCL provides service on the 10K mapping array and the Genome Wide SNP 5.0 and 6.0. This technology is appropriate for genetic association and mapping studies when custom content is not required. Please see Affymetrix.com for most complete and up to date information on product options.
The Assay Affymetrix DNA analysis chips use a selective enrichment and hybridization method to assess the genotype of thousands of loci in a single sample. Digestion with a specific restriction enzyme followed by ligation to universal adapters yields DNA fragments that can be amplified through a standard PCR reaction with a single set of primers. Following amplification and PCR clean up the DNA is enzymatically fragmented and end labeled with a proprietary biotin analog. Following hybridization of the labeled DNA to the microarray, the chip is washed and stained with a streptavidin bound florescent dye. Analysis uses the observed florescent intensity at each probe site to determine sample genotype for the locus. This technology is also used with alternative analysis to determine copy number variation within individuals and, using pooled samples, SNP distribution in populations. Scanning and Data GPCL utilizes an Affymetrix GeneChip 450 fluidics station and Affymetrix GeneChip 3000 Array Scanner with high-resolution patch and GeneChip autoloader. A high-resolution scan of the chip surface provides a digital image of the intensity of each probe. A statistical algorithm is used to determine the genotype of the individual sample from the fluorescent intensity of each probe. Sample Preparation The amount of DNA needed varies with the chip type in use. Please contact GPCL for guidance in sample preparation. |