Whole-Genome Genotyping and Copy Number Variation Analysis

Since they were first developed in 2005, whole-genome genotyping (WGGT) arrays have become an important tool for discovering variants that contribute to human diseases and phenotypes. The two primary applications of this technology, genome-wide association studies (GWAS) and copy number variant (CNV) analysis, have helped researchers begin to unravel the complex genetic architecture behind diseases such as diabetes and Crohn's disease, and traits such as hair and eye color.

Illumina's WGGT Infinium BeadChips offer researchers the flexibility to genotype samples with hundreds of thousands to millions of markers that deliver dense genome-wide coverage with the most up-to-date content available from the scientific community. Markers on the BeadChips are strategically selected by Illumina scientists to  provide maximum coverage of the genome for both association testing and copy number detection.

Keep up-to-date with recent discoveries by customizing Infinium iSelect HD BeadChips with Infinium Add-On Content. Whether it comes from publically available databases or new discoveries, allows researchers to combine existing marker sets with new, unique content on a single BeadChip, increasing efficiency and cost effectiveness in study design.

The Omni Family of Microarrays

The latest generation of Infinium WGGT products is The Omni Family of Microarrays. This flexible, complimentary family of microarrays represents a revolution in array design, delivering up to 5 million makers per sample and offering an unprecedented amount of customizability. Designed from next-generation sequencing data from international projects such as the 1000 Genomes Project, Omni microarrays deliver unrivaled coverage of the genome. Access to whole-genome sequencing data provides the most complete picture of the extent of variation, allowing Illumina scientists to select the most informative markers to provide superior power to detect trait- and disease-associated variants.

Custom Mid- to High-plex Genotyping

For researchers who want to study focused genomic regions of interest, or are interested in organisms for which there are no standard products, Illumina offers a broad range of custom genotyping options. Customized iSelect BeadChips can be easily developed to fit any experimental design, allowing customers to select the ideal solution for their loci multiplexing and sample throughput requirements. Convenient online tools and Illumina representatives are available to help you design and select your markers of interest, and choose the assay and customized products to best suit your research goals.

Focused Genotyping

Focused genotyping supports a variety of applications such as candidate-gene studies in cancer, cardiovascular disease, and admixture mapping. Illumina also works closely with major animal consortia to develop genome-wide genotyping products for non-human organisms, including both animal and plant species.

Cytogenetic Analysis

Structural variability is a substantial source of genetic varia­tion that has a major influence on phenotypic variation. Cytogenetic analysis allows researchers to profile chromosomal aberrations such as amplifications, deletions, rearrangements, point mutations, copy number changes, and copy-neutral loss of heterozygosity (LOH) events.

Linkage Analysis

Linkage analysis provides researchers a powerful method for mapping the location of disease-causing loci by identifying genetic markers that are co-inherited with a phenotype of interest. Illumina's linkage analysis BeadChips present the optimal solution for identifying regions of statistically unequivocal linkage by delivering the information content, call rates, and accuracy that enable discovery of links between familial genotype and phenotype in both monogenic and polygenic disorders.

Array-Based Methylation Analysis

DNA methylation plays a critical role in the regulation of gene expression and has been implicated in the etiology of many human diseases including cancer. Methylation profiling with BeadArray technology allows researchers to analyze the effects of aberrant methylation (either hyper- or hypomethylation) for a variety of applications. Illumina has developed a robust methylation profiling platform that provides quantitative methylation measurement at the single-CpG-site level, providing the highest resolution for understanding epigenetic changes.

Transcriptome Analysis

RNA sequencing has revolutionized the exploration of gene expression. Advances in the sequencing workflow, from sample preparation through data analysis, enable rapid profiling and deep investigation of the transcriptome. With RNA sequencing, you can characterize all transcriptional activity, coding and non-coding, in any organism without a priori assumptions.

Illumina's unique combination of long and short reads, single and paired-end sequencing, strand specificity, and capacity for tens of millions to billions of reads per run allows you to...

• annotate coding SNPs
• discover transcript isoforms
• identify regulatory RNAs
• characterize splice junctions
• determine the relative abundance of transcripts

With the greatest daily output available for any sequencing system, transcript profiles can be generated in a single day. RNA sequencing reads can be aligned across splice junctions to identify isoforms, novel transcripts and gene fusions. Identify and quantify both rare and common transcripts, with over six orders of magnitude of dynamic range. Reveal the hidden world of non-coding RNA architecture without prior information.

FFPE Sample Analysis

Formalin-fixed, paraffin-embedded (FFPE) samples are preserved tissue samples that are generally associated with disease. Many of these samples represent clinical outcomes, which could provide a potential gold mine of information when linked with underlying expression profiles. FFPE samples generally contain partially degraded RNA, so transcription analysis is a challenge for many gene expression assays. By using unique PCR and labeling steps based on the proven GoldenGate chemistry, Illumina's DASL assays provide high-quality data from degraded RNA samples. The DASL assay is available in the Whole-Genome DASL Assay, a fixed content, whole-genome profiling panel.