Covance Genomics Laboratory (CGL) offers both Illumina and Affymetrix based services for genotyping. CGL utilizes Illumina's industry-leading sequencing technology which provides the sample throughput level and high-quality data required for accurate SNP discovery and structural variation analysis studies.
CGL also offers human whole genome and targeted genotyping services using the Affymetrix DMET, Affymetrix 6.0 assay as well as the Illumina Infinium II assay in its multiple formats including iSelect and the Omni 1M Quad. We have implemented an impressive throughput capability enabled by parallel sample processing that is completely scalable to meet our client needs.
CGL offers the most comprehensive pharmacogenetic assay on the market—the Affymetrix DMET Plus microarray protocol containing known pharmacogenetic markers for drug metabolism studies. It can query 1,936 markers in 225 FDA-validated genes simultaneously and automatically translate the genotyping results into standardized star allele nomenclature. The protocol utilizes standard Affymetrix microarray equipment and has been improved with in-house automation and LIMS.
As a purpose-built, CLIA-compliant laboratory, CGL prides itself in high quality results. Of the 6,000+ samples run using DMET assay over the last two years, we've reported less than a 1% failure rate.
CGL offers human whole genome and targeted genotyping services using the Illumina Infinium II assay. The Illumina platform is based on self-assembly of oligonucleotide-coated beads onto a micro-etched silicon surface. Genomic DNA is amplified, fragmented, and then hybridized onto this array. A single base pair extension reaction allows SNP differentiation, after which the array is scanned to generate the SNP calls. The system returns >99% call rates for DNA samples of good quality, with greater than 99.9% concordance between replicate samples. The data generated by the Infinium assay can be used for association studies and also for Copy Number Abnormality/Loss of Heterozygosity (CNA/LOH) research.
CGL offers human whole genome genotyping on the Affymetrix 6.0 SNP array. This array contains >900,000 probes for SNPs and also >900,000 Copy Number Variation (CNV) probes for non-polymorphic regions. In the Affymetrix process, aliquots of genomic DNA are digested with two different restriction enzymes, amplified via size-selective PCR to reduce complexity, purified, fragmented and labeled. The labeled DNA is hybridized to Affymetrix 6.0 arrays and detected using a streptavidin-phycoerythrin assay. The Affymetrix system generally provides call rates in excess of 99% with good quality DNA.
- What are the differences between these arrays?
There are several differences between the Affymetrix and Illumina platforms, ranging from content to workflow to philosophy. Some of the major differences include:
- Workflow (PCR-based amplification for Affymetrix, Phi29-based WGA for Illumina).
- Number of features (the current Affymetrix flagship chip, the 6.0, contains ~1.8 million assays, the Illumina 1Meg array contains about 1.1 million).
- Approach to copy number analysis (Affymetrix has half its features just for copy number; Illumina uses all its features for copy number.)
- Probe selection (Affymetrix probes are more randomly placed across the genome than Illumina's, which are generally concentrated in HapMap blocks.)
- Price. Please contact CGL for the most recent pricing of the two platforms.
- Which array should I choose?
The question of which array is dependent in part on the application and the available budget. For unbiased discovery of copy number variation, Affymetrix may be more useful given its random probe placement. Illumina, with its concentration on assaying HapMap blocks can offer more power on a per SNP basis. Ultimately, discussion with a subject matter expert in population genetics can help decision making.