SNP Genotyping

SNP Genotyping Service

Sample Submission Form

Sample Submission Guidelines

SNP Genotyping at Garvan Molecular Genetics

Garvan Molecular Genetics operates a MassARRAY platform from Sequenom. It allows amongst other high throughput solutions the analysis of iPLEX assays which are designed for high throughput single nucleotide polymorphism (SNP) genotyping.

The MassARRAY system is based on matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Using the speed and accuracy of the MassARRAY system, this innovative method opens new routes for high-throughput SNP genotyping in a multiplexed assay design.

The assay design allows for running up to 384 multiplexed PCRs on one chip. The multiplex level can be up to 30x, so that the total number of SNPs that can be assessed on one single chip is up to ~10,000. Multiplexing and high throughput analysis therefore brings down the price per single SNP to ~20 cents (excl. primers) allowing analysis of large cohorts of samples or SNPs.


iPLEX assay design

The method for SNP genotyping on the MassARRAY platform consists of an initial locus-specific PCR reaction, followed by single base extension using mass-modified dideoxynucleotide terminators of an oligonucleotide primer which anneals immediately upstream of the polymorphic site of interest. Using MALDI-TOF mass spectrometry, the distinct mass of the extended primer identifies the SNP allele (see: Curr. Protoc. Hum. Genet. 60:2.12.1-2.12.18. © 2009 by John Wiley & Sons Inc.)


iPLEX assay accuracy

The iPLEX chemistry is the latest version of SNP genotyping tools on the MassARRAY platform and has proven to be highly efficient and reliable. For more information, read "iPLEX™ Assay: Increased Plexing Efficiency and Flexibility for MassARRAY System Through Single Base Primer Extension with Mass-Modified Terminators".


Custom SNP Genotyping

After you have contacted us for a brief discussion of the type and scope of your project we can give you a quotation and a timeframe for result generation. Please use our sample submission form and follow our sample submission guidelines for sample submission. We will follow a strict process which has been approved by Sequenom (now called Agena Bioscience) – see "SNP Genotyping SOP". We will perform the assay design and order the primers for you, setup PCRs and spot and run the chip(s). We will generate result CSV-files which will be emailed to you.


Routine SNP Genotyping for genetic monitoring of mouse inbred strains

Garvan Molecular Genetics offers a 28 SNP panel for quality controlling inbred mouse lines routinely. The panel assesses genetic contamination in colonies containing a large number of genetically diverse mouse strains. This test is used by the Jackson Laboratory for their mouse lines and investigates 28 relevant loci which cover over 300 inbred, wild-derived, congenic, consomic and recombinant inbred strains. This SNP genotyping is performed with iPLEX chemistry on our MassARRAY platform.