Genotyping - Arrays

Staff within Edinburgh Genomics have contributed to the design and testing of the Illumina and Affymetrix HD bovine SNP chips, and are developing the Affymetrix HD chicken and salmon arrays.

Genotyping is the process of measuring diferences in the genotype of individuals within a population and associating those differerences with traits of interest.  The specific genotypes measured are called markers and can be any feature which is reliably and reproducibly identified within an organism's genome. The most specific genotyping platforms measure changes in individual bases - single nucleotide polymorphisms.

Modern high throughput genotyping is most commonly carried out using array-based platforms, and Edinburgh Genomics operates both major platforms, Illumina and Affymetrix.

Second and third generation sequencing technologies raise the possibility of measuring genotypes using sequencing (genotyping by sequence or GBS).  This can be done by assaying the whole genome, or by reduced-representation techniques such as RAD sequencing.

 

Applications
 

For large scale genome wide association studies (GWAS) in organisms with a genome sequence, the most cost effective platform remains the SNP chip.  Both Illumina and Affymetrix produce a range of off-the-shelf products for many important biomedical and agricultural species, and we encourage our collaborators to talk to us to help choose the most appropriate platform.

For organisms where no SNP chip is available, we are experienced in collaborating with scientists and the platform providers to develop a new SNP chip. In these cases, we would sequence a range of interesting individuals from the species in question,  call SNPs and provide these to the platform provider who can design and build the SNP chip.  Scientists within Edinburgh Genomics have experience of designing SNP chips for cattle, chicken and salmon.

Where collaborators already have a smaller set of SNPs or markers which they wish to screen in individuals throughout a population, we can work with you to design the most appropriate assay, such as a custom, focused SNP chip.

It is also now possible to carry out genotyping by sequence, either by sequencing whole genomes or by reduced representation techniques such as RAD sequencing. These approaches are ideal for organisms with no genome sequence, no SNP chip, or when more information is required beyond that which is available on currently available assays.

If cost is not an issue, then genotyping-by-sequencing has several advantages, foremost of which is the potential to discover variation in your population that is not part of a predefined SNP assay.

 

Our technologies
 

Edinburgh Genomics offers both major SNP chip platforms, Illumina and Affymetrix, and can assist with research involving thousands of high density (HD) arrays, or with small scale projects involving custom focused arrays. We also have experience in more traditional genotypings, such as the use of microsatellites.

The Illumina Infinium assay offers a flexible platform for analysing a large number of SNPs.  The Infinium assay is available as a range of standard SNP sets from 5,000 up to 1 .1 million SNPs in one single assay. Many species are available in the economical SNP 50 format and further details can be found from the Illumina website for custom and focussed assays or Illumina's range of higher density human assays. High density (> 500k SNPs) arrays are also available for a range of important biomedical and agricultural species.

We also offer Affymetrix GeneChip SNP genotyping, which offers researchers a fast, economic and powerful SNP-based genetic mapping tool.  We are one of the only labs in Europe with an Affymetrix GeneTitan system, a highly automated, ultra-highthroughput genotyping system which can process 192 high density SNP arrays in just a few hours.

Staff within Edinburgh Genomics have contributed to the design and testing of the Illumina and Affymetrix HD bovine SNP chips, and are developing the Affymetrix HD chicken and salmon arrays.