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DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning
Published on: March 15, 2011
A simple method for comparing microarray genotype data between brain and other tissues
1The Stacey MND Laboratory, Department of Pathology D06, The University of Sydney, NSW 2006, Australia.
Journal of Neuroscience Methods
|July 23, 2008
Summary
This study presents a flexible method for analyzing single nucleotide polymorphism (SNP) data from microarrays, particularly for complex datasets involving different tissues. The approach uses Microsoft Access for tailored analysis without specialized software, aiding in comparisons and identifying genetic variations.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Microarray technology generates substantial single nucleotide polymorphism (SNP) data.
- Existing software packages may not adequately address unique datasets, such as those from multiple tissue types in case-control studies.
- Customizable analysis methods are needed for complex genomic data.
Purpose of the Study:
- To demonstrate a flexible, non-specialized software method for analyzing Affymetrix 500K GeneChip SNP data.
- To provide a customizable approach for investigators analyzing diverse SNP datasets.
- To facilitate comparisons of SNP genotypes across different tissues and sample groups.
Main Methods:
- SNP genotype data from white blood cell and brain DNA of amyotrophic lateral sclerosis patients and controls were imported into a Microsoft Access database.
- Analysis was performed using Microsoft Access queries and Visual Basic scripts.
- Both two-way and three-way genotype comparisons were conducted.
Main Results:
- The developed method successfully analyzed SNP genotype data from different tissue types.
- Database queries and Visual Basic scripts enabled flexible genotype comparisons.
- The approach is adaptable for analyzing copy number variations from SNP intensity data across multiple datasets.
Conclusions:
- A flexible and customizable method for analyzing microarray SNP data using Microsoft Access is demonstrated.
- This approach is valuable for comparing SNP data across multiple datasets, especially in cases involving different tissues or suspected somatic mosaicism.
- The method offers a viable alternative to array-dedicated software for specific analytical needs.
