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Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

Gro Nilsen12, Knut Liestøl12, Peter Van Loo34, Hans Kristian Moen Vollan567, Marianne B Eide28, Oscar M Rueda9, Suet-Feung Chin9, Roslin Russell9, Lars O Baumbusch5, Carlos Caldas109, Anne-Lise Børresen-Dale56 and Ole Christian Lingjærde125*

  • * Corresponding author: Ole Christian Lingjærde ole@ifi.uio.no

  • † Equal contributors

Author Affiliations

1 Biomedical Informatics, Dept of Informatics, University of Oslo, Oslo, Norway

2 Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway

3 Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

4 Dept of Human Genetics, VIB and University of Leuven, Leuven, Belgium

5 Dept of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway

6 Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway

7 Dept of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital Radiumhospitalet, Oslo, Norway

8 Dept of Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway

9 Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Dept of Oncology, University of Cambridge, Li Ka-Shing Centre, Cambridge, UK

10 Cambridge Breast Unit, Addenbrookes Hospital and Cambridge National Institute for Health Research Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK

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BMC Genomics 2012, 13:591  doi:10.1186/1471-2164-13-591

Published: 4 November 2012

Additional files

Additional file 1:

This pdf-file contains a formal description of the iterative PCF-based Winsorization algorithm.

Format: PDF Size: 108KB Download file

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Additional file 2:

This pdf-file contains a description of the three data sets used in this paper.

Format: PDF Size: 253KB Download file

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Additional file 3:

This pdf-file describes a comparison of segmentations performed by CBS and PCF on a MicMa sample.

Format: PDF Size: 246KB Download file

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