Bioinformatic approaches to the analysis of alternative splicing variants in cancer biology
This chapter discusses the use of bioinformatic methods to analyze alternative splicing and investigate its role in cancer biology. A brief introduction to alternative splicing is followed by a discussion of methods for alternative splicing analysis. Both historical and current methods for detecting alternative splice variants are presented, including a detailed discussion of the application of microarray technology. Designs for bioinformatic approaches useful in studies of cancer biology are outlined, including those for matched and unmatched studies. These designs incorporate a general framework for alternative splice variant detection, methods for transcript abundance measurement, and limits of current technology. An example is presented from a study of alternative splice variants in medulloblastomas which illustrates the complex yet significant differences that can be detected between tissues when alternative splicing is considered.
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