Genetic Marker Analysis

SNP genotyping

SNP genotyping is the measurement of genetic variations of single nucleotide polymorphisms (SNPs) between members of a species. The use of SNP genotyping is accelerating throughout a wide range of scientific and commercial areas including:

  • Personal genomics research and pharmacogenomics.
  • Marker-assisted breeding and genetic tracking of livestock.
  • Adventitious GMO detection and quantitation.
  • Marker-assisted selection of high-value crops.
  • Fisheries management and wildlife species tracking.
  • Genetic identification and quality control for biorepositories and service labs .

The Fluidigm BioMarkHD genotyping solution combines integrated fluidic circuit (IFC) technology with optimised instruments and robust allele-specific assays that deliver thousands of ultrahigh quality datapoints much faster, more cost-effectively and more reliably than traditional plate-based or mass spectrometry based genotyping platforms.

More recently, low cost sequencing has allowed even higher densities of SNPs to be interrogated across more samples (genotyping by sequencing). Using the Fluidigm Juno Targeted DNA Sequencing Library Preparation System, including Targeted DNA Seq Library Preparation reagents, you can produce dozens to hundreds of sample libraries daily, with each sample enriched for up to 4,800 specific amplicons covering user-defined genes or genomic loci.


Microsatellites (also known as simple sequence repeats, simple tandem repeats, variable nucleotide tandem repeats in eukaryote research; and Multiple Loci VNTR Analysis in microbial research) are widely used to determine the genotype of organisms based on naturally occurring variation. With eukaryotes, the genotypes are used in areas like population genetics, forensics and agriculture advancement. With bacteria and other microbes, MLVA is used for population genetics, to study transmission routes, sources of infection and the impact of vaccination and use of antibiotics on antibiotic resistance.

When using fluorescently labelled primers to amplify and type microsatellites on capillary sequencing instruments, GeneMarker analysis software decreases analysis set-up time, through automated correction of common genotyping problems including saturated and pull-up peaks, instrument spikes and stutter peaks. A flexible panel editor provides custom panels required for microsatellite analysis. GeneMarker® software's automated Run Wizard is designed to make analysis quick, easy, and accurate; compatible with all ABI PRISM®, Beckman CEQ™ or MegaBACE ™ genetic analysers .

When using unlabeled PCR primers that are specific to polymorphic microsatellite regions, Fragment Analyzer can be used to accurately separate and type microsatellites. Delivering the fastest run times and highest resolution of any dsDNA fragment analysis system, it provides complete size and quantification information for microsatellite fragment analysis and DNA fragment analysis with low cost unlabelled primers.


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