Over the last few years genome-wide association studies (GWAS) have successfully identified thousands of genetic variants associated with human diseases. Building on this success, the 1000 Genomes Project (1KGP) is dramatically expanding the catalog of variation for the next generation of GWAS, as it will seek to identify nearly all variants that exist at any appreciable frequency in human populations. Based on the 1kGP data, Illumina estimates that roughly 5 million markers will be needed to capture genome-wide variation down to 1% minor allele frequency (MAF) across diverse populations.
With the Omni family of microarrays, researchers can get started on next-generation GWAS now and access 50% greater coverage of common and rare variants over any other commercial array. The 2010 product roadmap for Omni microarrays allows researchers to add supplemental content to their current GWAS and progressively build up to the full 5 million variants in a step-wise manner. Illumina is developing the arrays in collaboration with leading scientists from 1KGP to select the highest-value markers. As new data are released into the public domain, supplemental arrays will be made available that include coverage of the most recent common and rare variants identified by the project.
Omni microarrays will facilitate testing of new scientific hypotheses, including the role of rare variants, copy number variants, and other non-SNP markers on diseases and traits. With intelligent tag-SNP selection, cutting-edge content, and backed by the powerful Infinium HD Assay, Omni microarrays will allow researchers to make the most of what 1KGP can offer.
Illumina's freely accessible iControlDB is an online database of genotype and phenotype data from individuals on all ILMN’s GWAS arrays that can be used as controls for association or imputation studies.
For those interested in the Omni Roadmap, Illumina has developed Infinium Multi-Use Sample Preparation kits. These kits require only a single sample amplification, which can be used and then stored for supplemental roadmap arrays as they become available. Illumina testing has shown that the samples will continue to produce high-quality data over multiple usages without any deleterious effects from storage periods. The DNA input requirement for the multi-use kit is 750ng at 50ng/μl.
Multiple Roadmap paths provide flexibility for timing and budget to help investigators effectively achieve their research goals. This allows researchers to select the path that delivers the content most relevant for their unique study.
A ground-breaking product for genomic research, the Omni2.5 is the first commercial microarray designed to be maximally powerful in the era of the 1000 Genomes Project (1kGP). This 4-sample BeadChip captures genomic variation down to 2.5% MAF, offering up to 50 % greater coverage of both common and rare variants over any previous commercial array.
It features a comprehensive marker set that delivers the highest coverage rates across Caucasian, Asian, and African populations, designed from the pilot phase of 1kGP and all three phases of HapMap. Researchers starting the roadmap with the Omni2.5 will complete the 5 million marker set with the Omni2.5S. This array will provide an additional unique set of 2.5 million markers derived from future releases of the 1kGP that will include coverage of rare variants down to 1% MAF.
The 4-sample Omni1 BeadChip provides optimized tag SNP content from all three HapMap phases, and features >300,000 markers that target high-value regions of the genome, including coverage of the MHC region and coding variants identified by the 1kGP that are known to be highly associated with human disease. Researchers starting the roadmap with the Omni1 array can add an additional ~1.2 million markers on the Omni1S, providing high coverage of low-frequency alleles down to ~2.5% MAF from the first releases 1kGP. The final 2.5 million markers will be available on the Omni2.5S, which will provide comprehensive coverage of rare alleles down to 1% MAF derived from the complete 1kGP.
Like the Omni1, the 12-sample OmniExpress BeadChip provides optimized tag SNP content from all three HapMap phases, strategically selected to capture the greatest amount of common SNP variation (> 5% MAF). Researchers starting the roadmap with this high-throughput array can add an additional ~1.2 million markers with the Omni1S. The content on the Omni1S is derived from the first releases of the 1kGP, providing high coverage of low frequency alleles down to ~2.5% MAF. The third array on this path is the Omni2.5S, which will deliver the final 2.5 million markers from the complete 1kGP, providing comprehensive coverage of rare alleles down to 1% MAF.
Both multi-use and single-use sample preparation workflows are available for each Roadmap path. Whichever workflow is selected upon entry to the Roadmap must be maintained for all supplemental arrays as well. That is, a customer cannot begin the Roadmap with a multi-use product and then add supplemental content with a single-use product, or vice versa.
In light of the 1000 Genomes Project (1kGP) data, it is now clear that all first-generation microarrays provided far less genomic coverage than perviously thought. With respect to the 1kGP data set, only Omni arrays can maintain the industry-standard, > 80% genomic coverage. Up to 5 million genome-wide tag SNPs on Omni arrays give researchers the maximum likelihood of finding true associations for a given phenotype.
New data from the 1kGP will enable researchers to explore the role of rare variation in human traits and diseases. Omni microarrays will feature comprehensive coverage of rare variants as they are made available to the scientific community, enabling new discoveries and a more complete understanding of the role of variation in human health and diseases.
Structural variation, including copy number variants (CNVs) and copy neutral variants (inversions and translocations), is a significant contributor to the genetic basis of human disease. Dense genome-wide coverage on Omni microarrays, coupled with the sensitive Infinium HD assay, offer researchers a powerful tool for structural variation analysis. Whether your studies include genotype calling, structural variation analysis, or both; Omni microarrays provide a single solution for any course of genetic research.
*Throughput based on 1 iScan, 1 Autoloader, 1 Tecan, 5-day work week. **Throughput based on 1 iScan, 1 Autoloader2, 1 Tecan, 8-hour work day.
