A simple method for comparing microarray genotype data between brain and other tissues

A number of software packages are currently available to analyse the large amounts of single nucleotide polymorphism (SNP) data generated using microarrays. However, for less usual datasets, such as those involving DNA from different types of tissue in cases and controls, investigators need a program that can be tailored to their particular needs. The purpose of this study was to demonstrate a flexible method of analysing SNP data derived from Affymetrix 500K GeneChips without the need for an array-dedicated software package. SNP genotype calls from white cell and brain DNA samples from patients with amyotrophic lateral sclerosis and controls were imported into a Microsoft Access((R)) database and analysed in two ways. The first used database "queries" designed through the Access graphical user interface. The second involved scripts written with the Visual Basic software that is supplied with Access. Both the queries and scripts performed simple two-way comparisons as well as three-way comparisons between genotypes, which is vital when comparing genotypes in different tissues in cases and controls. A similar method could be used to compare copy number changes derived from SNP intensities between multiple datasets. This flexible method can easily be customised by the investigator and would be of use in comparing microarray SNP data between multiple datasets, in particular where somatic mosaicism was suspected.

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