Finding common regions of alteration in copy number data

Methods Mol Biol. 2013:973:339-53. doi: 10.1007/978-1-62703-281-0_21.

Abstract

In this chapter, we review some recent methods designed for detecting recurrent copy number regions, that is, genomic regions that show evidence of being altered in a set of samples. We analyze Affymetrix SNP6 data from 87 Her2-type breast tumors from a recent study using three different methods, showing different definitions and features of common regions: studying heterogeneity in copy number profiles, refining candidates for driver oncogenes, and consolidating broad amplifications.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Breast / metabolism
  • Breast / pathology
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / pathology
  • DNA Copy Number Variations
  • Female
  • Gene Dosage*
  • Humans
  • Oligonucleotide Array Sequence Analysis / methods*
  • Polymorphism, Single Nucleotide
  • Receptor, ErbB-2 / genetics*

Substances

  • Receptor, ErbB-2