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Australian Government: National Measurement InstituteAustralian Government: National Measurement Institute
National Measurement Institute

Genotype Analysis

SNP genotyping analysis softwareXX (red), XY (blue)Genotyping refers to mapping variations in genome across individual organisms. The most common form of variation is single nucleotide polymorphisms (SNPs) which occur when a single nucleotide (A, T, C or G) in the genome sequence is changed. SNP genotyping is rapidly growing as a useful tool in many scientific disciplines including personalised medicine, plant and animal biotechnology.

Many SNPs have no known effect on cell function but scientists believe that some SNPs can predispose people to certain diseases whilst others may influence a patient’s response to a drug. To identify an association between an SNP and a particular disease or genetic trait, researchers need high throughput approaches to screen vast numbers of samples.

Researchers at NMI have implemented and validated a relatively low-cost microfluidic system for high-throughput SNP genotyping, and are now offering this service to external clients. The technology allows simultaneous analysis of 48 different SNPs across 48 individual samples using Taqman® SNP genotyping assays. The key to the efficiency of this approach is the matrix of channels, chambers and integrated valves finely patterned into layers of silicone in the microfluidic chip. The valves partition each sample / assay combination into an individual reaction chamber. Each chip comprises a total of 2 304 (48 x 48) individual reaction chambers.

As part of the validation process, researchers at NMI investigated the effect of input DNA copy number on genotyping call accuracy using well-characterised genomic DNA samples. The genotyping call for a particular SNP is the designation of homozygous (XX or YY) or heterozygous (XY). For samples with a low starting input DNA concentration, researchers at NMI incorporated and validated a multiplex specific target amplification step prior to genotyping. The principles of this validation approach can be applied to genomic sequences derived from any biological tissue.

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