The RTSF Genomics Core at Michigan State University offers a number of options for genotyping services. The available platforms and technologies encompass a wide range of sample and assay set sizes allowing analysis of a handful to millions of loci simultaneously.
DNA Fingerprinting and Genotyping Applications
Amplified Fragment Length Polymorphism (AFLP)
AFLP is a powerful DNA fingerprinting technique that can be used for plants and bacteria based on the selective amplification of restriction fragments from a total digest of genomic DNA.
Short Tandem Repeats (STR)
STR analysis is an important complement to both the length and sequence-based DNA typing systems used for human identification. Due to their small size STRs are often used successfully to analyze samples containing minute amounts and degraded DNA that cannot be typed using conventional methods. STRs are commonly used for forensic applications determining population genotype frequencies.
DNA Quantity Required: 200-300ng of DNA in a 20uL volume.
Short tandem repeat (STR) loci are among the most informative polymorphic markers in the human genome. Additionally, STR profiles help to ensure the quality and integrity of human cell lines within the scientific community as mandated by the NIH. The RTSF Genomics Core provides cell identification services using the ProMega Cell ID System which employs simultaneous co-amplification and three-color detection of ten loci in a single reaction run on the ABI 3730xl.
DNA Quantity Required: 10ul at a concentration of 2 ng/ul.
TaqMan probe based Genotyping
TaqMan® 5'-nuclease assay chemistry provides a fast and simple way to get single nucleotide polymorphism (SNP) genotyping results. Each TaqMan® SNP Genotyping Assay includes two allele-specific TaqMan® MGB probes containing distinct fluorescent dyes and a PCR primer pair to detect specific SNP targets. Assays are run on one of two systems depending on the throughput required. Smaller sets can be run in a 384 well format on our ABI 7900ht while our WaferGen system allows samples to be run in one of 14 preconfigured formats on it 5,184 well SmartChip.
Illumina Infinium Beadchips
The Infinium platform is the largest high throughput genotyping chip on the market allowing identification of up to 4.3 million SNPs per sample. This platform is ideal for genome wide association studies, population genetic and copy number variation investigations. Several pre-configured Infinium chips are currently available for biomedical and agricultural applications. Custom content for non-model organisms is also available. The RTSF Genomics Core works in conjunction with the Potato Breeding program for MSU agricultural genotyping projects using the Illumina iScan.
Please contact the Genomics Core for more information.