Genotyping
The GSL offers a variety of genotyping and SNP validation services:
Whole-genome SNP mapping arrays are the most common genotyping microarrays and are most often used for association or linkage studies. Recent designs can query around 1 million SNPs, delivering a high-resolution picture of a subject's genotype. In addition, this resolution may be taken advantage of to provide a genome-wide copy number analysis. The genome-wide mapping approach is best used with large studies of hundreds of samples or more, since finding high-confidence results usually requires high numbers of cases and controls.
Illumina HumanOmni1-Quad BeadChip
The HumanOmni1-Quad BeadChip contains over 1 million markers, including markers derived from the 1,000 Genomes Project and all three HapMap phases. In addition, the Chip includes 10K SNPs targeting four 1Mb regions known to be associated with human diseases; over 31K non-synonymous SNPs, as well as SNPs targeting new coding variants. These Chips have a median spacing of 1.2 kb to enhance CNV identification. This BeadVhip is multiplexed, providing 4 arrays per slide.
Affymetrix Genome-Wide Human SNP Array 6.0
This array features more than 1.8 million markers for genomic variation, including more than 900K SNPs and 946K probes for assessing copy number. This density of SNP coverage provides a nearly saturated view of the genome, with SNPs uniformly distributed to simplify linkage analysis, association, and copy number studies.
Affymetrix Axiom
The Axiom Genotyping Solution offers the highest throughput available for genome-wide association studies and candidate gene association studies. It utilizes the GeneTitan instrument to process up to 750 samples per week. The Axiom Genome-Wide Human Array Plates contain more than 560K SNPs and more than 6K indels and are available in Caucasian, Asian, and African versions to maximize genomic coverage of common and novel SNPs in specific populations. Array Plates are customizable with SNPs from a proprietary database of validated genomic markers.
Querying a known panel of SNPs, MNPs, or indels is often done following a whole-genome SNP mapping experiment that resulted in identification of significant SNPs to be verified with additional samples. The GSL offers two platforms to meet these needs: the Illumina GoldenGate Assay and the BioTrove OpenArray Genotyping System.
Illumina GoldenGate Genotyping Assay
The GoldenGate Genotyping Assay can interrogate 96, or from 384 to 1536 SNPs simultaneously. Standard panels exist for human and mouse content, but Custom Panels can be designed for other species. Panels are deployed on 32-, 16-, and 12-sample Universal BeadChips or the 96-sample Universal Array Matrix.
BioTrove OpenArray
The BioTrove (now Applied Biosystems) OpenArray plate consists of 3072 through-holes that can be loaded with reagents to perform individual 33nl real-time PCR reactions. The configuration of the through-holes allows the research to interrogate many samples against a large number of assays in a flexible format, with both the number of samples and assays capable of being altered to fit research plans. OpenArray plates can utilize either Syber Green I chemistry (SYG Real-Time qPCR) or Applied Biosystems TaqMan chemistry (DLP Real-Time qPCR). Plates can be fully customized with any of the 4.5 million assays targeting SNPs, insertion-deletions of up to six bases, and Multiple Nucleotide Polymorphisms (MNPs).
The GSL offers real-time PCR services for validation of gene expression or genotyping results using either Taqman technology or SYBR Green I technology. TaqMan chemistry uses a fluorogenic probe to allow detection of a specific PCR product as it accumulates over PCR cycles. SYBR Green I dye detects double-stranded DNA (PCR product) as it accumulates during PCR cycles. Applied Biosystems has a nice discussion of the advantages and disadvantages of each chemistry
The GSL recommends 4 technical replicates for each probe and sample to provide maximum confidence in RT-PCR results. Over 4.5 million pre-designed TaqMan SNP Genotyping Assays are available that support detection of SNPs, indels of up to six bases, and MNPs. For pre-designed assays, a 40X concentration of the assay is provided which allows 1500 reactions. TaqMan Copy Number Assays are also available and include genes, known CNVs, and extragenic/non-gene regions.
