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Genotyping

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.


GeneScan/Fragment Analysis Services

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.

Recommended DNA quantity for GeneScan/Fragment Analysis: 200-300 ng of DNA in a 20 µL volume.  DNA must be quantified by fluorometric method, such as Qubit or PicoGreen.


Human Cell Line Authentication (Cell ID)

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. You may learn more at the Promega Cell Line Authentication Testing page. The RTSF Genomics Core provides cell line authentication services using the Promega GenePrint® 10 System which employs simultaneous co-amplification and three-color detection of ten loci in a single reaction run on the ABI 3730xl.

Required DNA quantity: 10 µl at a concentration of 2 ng/µl.  DNA must be quantified by fluorometric method, such as Qubit or PicoGreen.


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 QuantStudio 7 Flex while our TakaraBio SmartChip qPCR system allows samples to be run in one of 14 preconfigured formats on a 5,184-well SmartChip.


Please contact the Genomics Core (gtsf@msu.edu) for more information.