Services

SNP Genotyping Methods

1. SNP genotyping is performed using MALDI-TOF (Matrix-assisted laser desorption ionization-time of flight) mass spectrometry as the main approach.

2. SNP genotyping performed using Affymetrix GeneChip MegAllele System

1. SNP analysis using Sequenom Mass Spectrometry

SNP genotyping by MALDI-TOF mass spectrometry is performed using the Sequenom mass spectrometry system. Our service includes primer and assay design through to production of genotypes. All steps involved are highly automated and are tracked using a laboratory management system with bar-coding. In this method, multiplexed PCR and then a minisequencing reaction are performed in a single well. The size of reaction products is determined directly by MALDI-TOF mass spectrometry, yielding genotype information. Multiplexing permits determination of up to 12 SNPs in a single well of a 384 well plate. Specialized equipment for this work includes a Biomek multi-pipettor robot, a Multimek multi-pipettor robot, a nanoliter plotting robot for spotting the extension products onto chips, and the mass spectrometer.

SAMPLE SUBMISSION

Project Design and Quality Control
To ensure quality in our service we aim to work closely with investigators. After an initial discussion about experimental design, primer and assay design will be carried out by our experienced staff. Possibly, a second discussion may be required to discuss assay options for any SNPs which assays cannot be designed for. Following this it is the decision of the investigator whether to continue genotyping on the customer supplied test samples. 

Submission of Samples for SNP analysis using Mass Spectrometry

• Submit 394 well PCR plate/s and the Ext primers and the request form to 1-202BSBE

Rates - click here for link to rates

2. SNP analysis using Affymetrix GeneChip

ParAllele has developed a novel technology based on the concept of Molecular Inversion Probes that enables up to 20,000 SNPs to be scored in a single assay. This unprecedented level of multiplexing is made possible through exquisite enzymological specificity using a unimolecular interaction that is insensitive to cross-reactivity amongst multiple probe molecules. The technology has been demonstrated to exhibit high accuracy while enabling a high rate of conversion of individual SNPs into working multiplexed assays. For more details about Molecular Inversion Probes, please visit ParAllele  publications page.

SAMPLE SUBMISSION

Project Design and Quality Control
To ensure quality in our service we aim to work closely with investigators. Samples are run as a set of 24 (2 controls and 22 test samples) per set. To have the best call accuracy and conversion rate minimum of 72 individual samples are required.

  Submission of Samples for SNP analysis using Mass Spectrometry

• Genomic DNA (unamplified) is submitted - 2.0 µg for 3K to 5K SNPs. 4.0 µg for 6K to 10K SNPs.< 50 ng

Rates – Please inquire