Genome Wide Association Products:
HumanCNV370-Quad Genotyping BeadChip: This BeadChip contains over 317,000 tag SNPs derived from the Phase I HapMap data, supplemented with and additional 52,167 markers designed to target copy number variant (CNV) regions of the genome. The BeadChip contains a higher desity of tag SNPs in regions of the genome that are within 10 kb of a gene or in evolutionarily conserved regions. Additionally there are about 8,000 nsSNPs, and all of the SNPs from the MHC panels. This product is optimized for Caucasian populations, and will work almost as well on Asian populations. For more details, click here and here. For a list of SNPs, click here.
HumanHap610-Quad Genotyping BeadChip: This product contains tag SNPs for the HapMap Phase I+II and includes greater coverage for CHB+JPT and YRI populations. It also includes more than 7,000 nsSNPs, SNPs from the MHC region, mitochondria and regions of known copy number variation. For more information, click here. For a list of SNPs, click here.
Human1M-Duo BeadChip: This product genotypes one million SNPs on a single chip. All of the SNPs from the 650Y product are included on this product, with additional SNPs added to increase coverage across the genome and to enhance coverage in specific regions. This means there are more than 550,000 SNPs within 10kb of a gene region and includes more than 23,000 non-synonomous SNPs. Average spacing across the genome is 2.7 kb. Additional SNPs and non-SNP features have been added to look at more than 3,000 regions in the Database of Genomic Variants (DGV), as well as other reported CNV regions not found in the DGV. The MHC region is covered with 10,000 SNPs, and there are 163 mitochondrial SNPs on the chip. For more information, click here. For a list of SNPs, click here.
LOH/Copy Number: Any of these products can used to look at LOH and copy number using Illumina's BeadStudio Genotyping Module. We do not do this analysis for you. If you would like to look at the data in this manner, you must purchase BeadStudio, which is available at a reduced cost through the SNP Center, for Hopkins investigators only. For more information on this type of analysis, a datasheet from Illumina is available here.
Affymetrix SNP Array 6.0: This product features 1.8 million genetic markers, including 900,000+ SNPs and about 950,000 copy number variation probes. Contains the SNPs from the previous 5.0 chip, with added Tag SNPs and mitochondrial SNPs. This product cannot be used with whole genome amplified DNA. For more information, click here.
Analysis software: If you wish to use Illumina's Bead Studio software to analyze your data, licenses are available for internal JHU customers for $2,000 each. This does not include the methylation module.