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Statistics and Informatics in Molecular Cancer Research$
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Carsten Wiuf and Claus L. Andersen

Print publication date: 2009

Print ISBN-13: 9780199532872

Published to Oxford Scholarship Online: September 2009

DOI: 10.1093/acprof:oso/9780199532872.001.0001

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Methods for DNA copy number derivations

Methods for DNA copy number derivations

(p.25) 2 Methods for DNA copy number derivations
Statistics and Informatics in Molecular Cancer Research

Cameron Brennan

Oxford University Press

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.

Keywords:   segmentation, copy number aberration, copy number variation, cancer genomics, tumour-derived DNA

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