Whole Genome Association
Overview
In an effort to uncover genomic causes of disease, many investigators are using the power of whole genome association assays to genotype large numbers of SNPs in a very timely manner. Large association studies have employed these techniques to investigate the genome. The CGF offers two high multiplex fixed content genotyping platforms.
Illumina® Infinium®II Assay (Fixed Panel Products)
Recommended Use
Illumina's Infinium®II Genotyping assay offers a flexible BeadChip design and high-density architecture to allow for large-scale interrogation of variations in the human genome. The size of the Infinium®II BeadChip assays range from 240,000 to 650,000 loci with a 1 million loci chip to be available in the near future. The loci in the Infinium assays are tag SNPs derived from the International HapMap Project. The newest Chip design includes content for investigating copy number variations as well.
Process
Once received, the fixed panel product will be checked for performance (if required) using a portion of the HapMap control panel.
Requirements
Samples must pass all Sample Handling and Pre-Genotyping QC criteria before they are considered for genotyping. Study samples must have 1250 ng of total genomic DNA at a concentration of at least 10 ng/ul as determined by PicoGreen® ("QDNA") to be included in genotyping. Whole genome amplified samples are not able to be used in this product. Samples are run in batches of 24 samples. Additional sample qualification based on phenotypic evaluation of the study will be performed and the PI will be informed of the results (see Pre-Genotyping QC section).
Pricing on these projects is total sample size and product type dependent. Please contact the CGF for specific pricing information.
Reporting
Due to the size and complexity of the resulting data files, the CGF Analysis team will assist the investigator in the retrieval and export of genotyping data.
Affymetrix® GeneChip® Arrays (Fixed Panel Product)
Recommended Use
The Affymetrix® GeneChip® array fixed panel products are used for genome-wide association studies and detection of copy number variation. The Mapping 100K Set provides the high genomic coverage with a mean marker distance of 26 kb, giving researchers more power to detect changes in chromosomal copy number. The Mapping 500K Array Set uses the same proven assay as the GeneChip® Mapping 10K Array and Mapping 100K Set. More information about the SNPs in these assays is available.
Process
Once received, the fixed panel product will be checked for performance (if required) using a portion of the HapMap control panel. All assays in the panel will be validated prior to the genotyping of study samples.
Requirements
Samples must pass all Sample Handling and Pre-Genotyping QC criteria before they are considered for genotyping. Each assay uses 500 ng of total genomic DNA at a concentration of 50 ng/ul as determined by PicoGreen® to be included in the genotyping project. Whole genome amplified samples are not able to be used in this product. Additional sample qualification based on phenotypic evaluation of the study will be performed and the PI will be informed of the results (see Pre-Genotyping QC section).
Pricing on these projects is total sample size and product type dependent. Please contact the CGF for specific pricing information.
Reporting
Due to the size and complexity of the resulting data files, the CGF Analysis team will assist the investigator in the retrieval, archiving and export of genotyping data.
