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Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms
A G Lynch1, M J Dunning, M Iddawela
1University of Cambridge/Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK. andy.lynch@cancer.org.uk
Statistical Methods in Medical Research
|January 21, 2009
Summary
Illumina
Area of Science:
- Genomics
- Microarray Technology
- Bioinformatics
Background:
- Illumina's GoldenGate is a flexible two-channel microarray platform for interrogating genomic locations.
- It shares desirable properties with BeadArrays, including probe arrangement and sample processing capabilities.
Purpose of the Study:
- To review common adaptations of the GoldenGate platform.
- To examine associated analysis methods.
- To illustrate improvements over default analysis using example datasets.
Main Methods:
- Review of existing literature on GoldenGate adaptations.
- Analysis of example datasets to compare methods.
- Comparative analysis of default versus improved analytical approaches.
Main Results:
- Identified various common adaptations of the GoldenGate platform.
- Detailed analysis methods for each adaptation.
- Demonstrated potential improvements in data analysis through examples.
Conclusions:
- The GoldenGate platform offers flexibility in genomic analysis.
- Default analysis methods may not fully exploit the platform's capabilities.
- Improved analytical strategies can enhance data interpretation from GoldenGate assays.
