Genome Wide Association Products:
Human660W-Quad Genotyping BeadChip: This chip features more than 550,000 tag SNPs derived from HapMap release 23. It also contains more than 100,000 markers designed to target regions of common copy number variation in multiple populations. It maintains more than 99% of the content of the previous 610-Quad BeadChip. For a list of SNPs and CNV information, please click here (zipped txt).
HumanOmniExpress BeachChip:
The HumanOmniExpress genotypes 700,000+ SNPs, gleaned from all three HapMap phases. It is primarily targeted for Caucasian and Asian populations, with genomic coverage of 0.91 at r2 > 0.8 in these populations. It also supports CNV applications, with a 4.0 kb mean distance between CNVs across the genome. The SNP list has a 95% overlap with the HumanOmni-1 Quad.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.
HumanOmni1-Quad BeadChip: The HumanOmni1 is the latest in products with more than 1 million SNPs. This product is Illumina's latest chip with greater than 1,000,000 SNPs. It contains markers for more than 11,000 CNV regions, with a 1.5 kb median marker spacing within those regions. It also features new content from the 1,000 Genomes project--55,000 non-synonymous & splice site SNPs, 18,000 SNPs in four 1Mb regions with GWAS signals for three or more disease traits. SNPs in other smaller regions with known GWAS signals. The chip contains other high value SNPs as well, such as indels, mRNA splice sites, ADME genes, mitochondrial, ABO blood typing and MHC region among others.
LOH/Copy Number: Any of these products can used to look at LOH and copy number using Illumina's GenomeStudio 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 GenomeStudio, 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.
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.