Center for Autoimmune Genomics and Etiology (CAGE)

In collaboration with the Division of Human Genetics, CAGE can facilitate high-throughput custom SNP and whole-genome genotyping on the Illumina platform using the sophisticated iScan System.

The four-sample HumanOmni1-Quad BeadChip contains 1.2 million markers that deliver dense genome-wide coverage. 

The HumanOmni1S-8 (Omni1S) BeadChip allows investigators to supplement the Omni1 data by genotyping an additional 1.25 million variants.  Together the Omni1 and the Omni1S contain 2 million to 2.5 million total variants (targeting MAF> 2.5 percent).  Using the iScan, this eight-sample BeadChip includes the latest known variants discovered in the 1,000-genome project.

The ImmunoChip comprises 196,000 assays for genotyping individual single nucleotide polymorphisms.  The SNPs selected on the ImmunoChip represent 185 different loci that have been associated with diverse autoimmune diseases.  Of these loci, 35 are specifically associated with SLE, being added by John Harley, MD, PhD, on behalf of the International Consortium on the Genetics of Systemic Lupus Erythematosus (SLEGEN), from the known results as of February 2010.  The chip also contains a dense representation of SNPs at the MHC (6p21.3), a region carrying disease susceptibility genes in many of the autoimmune diseases.  The MHC provides the strongest association with SLE (and many other immune-mediated diseases in the genome-wide association studies in Europeans, Southeast Asians and African Americans).  SNPs on the ImmunoChip have been selected from the latest data, which include the variants discovered by sequencing subjects of the 1,000-genomes project.  A major advantage of the ImmunoChip is its modest cost.   

The re-sequencing strategy comprehensively identifies genetic variants at any given locus, including low-frequency variants.  Thus, the ImmunoChip provides a comprehensive assessment of loci implicated in autoimmune disease. 

DNA methylation plays a critical role in the regulation of gene expression and is known to be an essential mechanism for guiding normal cellular development and maintaining tissue identities.  Illumina’s HumanMethylation27 BeadChip interrogates 27,578 CpG loci covering more than 14,000 genes at single-nucleotide resolution. This high-density panel lets researchers profile up to 12 samples in parallel.