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Finding Common Regions of Alteration in Copy Number Data

  • Oscar M. Rueda
  • Ramon Diaz-Uriarte
  • Carlos Caldas
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 973)

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.

Key words

aCGH SNP Copy number alterations Copy number variation Minimal common regions 

Notes

Acknowledgments

This research was supported by Cancer Research UK and the Spanish Ministerio de Ciencia e Innovación (grant BIO2009-12458 to RDU).

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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Oscar M. Rueda
    • 1
  • Ramon Diaz-Uriarte
    • 2
  • Carlos Caldas
    • 3
    • 4
    • 5
    • 6
    • 7
  1. 1.Cancer Research UK Cambridge Research Institute, Li Ka Shing CentreCambridgeUK
  2. 2.Departamento de Bioquímica, Instituto de Investigaciones Biomédicas “Alberto Sols,”Universidad Autónoma de MadridMadridSpain
  3. 3.Department of OncologyUniversity of CambridgeCambridgeUK
  4. 4.Cancer Research UK Cambridge Research InstituteCambridgeUK
  5. 5.Cambridge Breast UnitAddenbrooke’s Hospital, Cambridge University Hospital NHS Foundation TrustCambridgeUK
  6. 6.NIHR Cambridge Biomedical Research CentreCambridgeUK
  7. 7.Cambridge Experimental Cancer Medicine CentreCambridgeUK

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