Methods for DNA copy number derivations
Chromosomal aberrations are a common form of mutation in cancer. Copy number profiling of tumour-derived DNA has proven to be a productive starting point for identifying novel cancer-relevant genes and molecularly-defined tumour subclasses. Generating and interpreting copy number draws on intuitively simple ideas which are complicated when reduced to practice. This chapter presents a range of issues relevant to choosing a profiling platform, designing custom arrays, reducing noise, and identifying artefacts or population polymorphisms which can mimic cancer aberrations. Specific methods and examples highlight the problems of segmentation/change-point determination, multi-sample analysis, hierarchical clustering, and high-resolution mapping of intragenic copy number aberrations.
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