The human genome is a three-billion letter string of the DNA bases A, T, C and G (the genetic code). Most of that sequence is the same in everyone. But there are many places in the genome where a single letter of the sequence sometimes differs from one person to the next. The analysis of these DNA differences between individuals has become increasingly important in medical research and diagnostics. SNP genotyping is a measurement of genetic variations of single nucleotide polymorphisms (SNPs) between individuals or cells. It is the most common form of genotyping, which is the measurement of DNA sequence variation. A SNP is a single base pair mutation at a specific locus. SNPs are involved in the etiology of many human diseases and are becoming of particular interest in pharmacogenomics or personalized medicine.

Empire Genomics offers SNP analysis services utilizing either the Sequenom or Illumina Infinium platforms. Sequenom methodology is one of the cheapest and most error free technologies for high throughput SNP typing. It uses samples arrayed in 384 well plates and allows custom genotyping of SNPs within candidate genes or genomic intervals. The technology involves PCR amplification of the region containing the SNP of interest, an optimized primer extension reaction to generate allele-specific DNA products, and chip-based mass spectrometry for separation and analysis of the DNA analytes. A single post-PCR primer extension reaction generates diagnostic products that, based on their unique mass values, allow discriminating between two alleles. The entire process has been designed for complete automation including assay development, PCR setup, post-PCR treatment, nanoliter transfer of diagnostic products onto silicon chips, serial reading of chip positions in the mass spectrometer, and final analytical interpretation. The Infinium platform from Illumina is an extremely high throughput SNP genotyping system that allows the identification and scoring of up to 2.5 million SNPs per single DNA sample. The Infinium assay relies on direct hybridization of genomic targets to array-bound sequences. Single base extension is followed by fluorescent staining, signal amplification, scanning, and analysis using the Genome Studio software. Due to the high number of SNPs that can be analyzed on infinium chips, simplicity of sample preparation, and relative ease of data analysis, this platform has been widely exploited for dozens of major studies in human genetics. These include whole genome association studies, population genetic analyses, and copy number variation investigations.

Sample Preparation

For most infinium assays 4 ul of 50 ng/ul DNA is the recommended input material. We request at least 10 ul of DNA at this concentration. Please provide clean and accurately quantified input genomic DNA. Some degradation is tolerated, but extensively degraded material may not perform well in the assay. Illumina recommends that all DNA be quantified using the PicoGreen fluorometric assay. Empire has the reagents and equipment necessary to carry out this Picogreen DNA quantitation assay, please inquire if you're interested in this option. Nanodrop readings plus gel visualization of all samples provides sufficient quality control determination for DNA to be used in the assay. Samples should be resuspended in water, 10 mM Tris 8.0, Qiagen EB (10 mM Tris 8.5), or TE.