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A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples

Alex Lisovich16, Uma R Chandran16, Maureen A Lyons-Weiler256, William A LaFramboise256, Ashley R Brown6, Regina I Jakacki7, Ian F Pollack368 and Robert W Sobol469*

Author Affiliations

1 Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA

2 Department Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA

3 Department of Neurosurgery, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh, Pittsburgh, PA 15213, USA

4 Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA

5 Clinical Genomics Facility, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA

6 University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA, 15213, USA

7 Division of Pediatric Hematology/Oncology, Children's Hospital of Pittsburgh, Pittsburgh, PA, 15213, USA

8 Department of Pediatric Neurosurgery, Children's Hospital of Pittsburgh, Pittsburgh, PA, 15213, USA

9 Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, 15213, USA

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BMC Medical Genomics 2011, 4:14  doi:10.1186/1755-8794-4-14

Published: 26 January 2011

Additional files

Additional File 1:

Definitions, additional methods, a description of the paired tumor/normal data set, Heat Maps, Segmentation plots and a comparison of raw CN and segmentation results. The file contains: a) A set of definitions for some terms used throughout the text. b) A detailed method for the Affymetrix 250K Sty assay for formalin fixed, paraffin embedded tissue (FFPET) samples. c) Information on the paired tumor/normal data set used. d) References Cited in the Additional file. e) Heat Maps for the (1) in-lab FFPE normals reference, (2) the VN reference based on in-lab FFPE normals data set and (3) VN reference based on HapMap data set. f) Segmentation plots for the (1) in-lab FFPE normals reference, (2) the VN reference based on in-lab FFPE normals data set and (3) VN reference based on HapMap data set. g) A figure showing a comparison of raw CN and segmentation results (Affymetrix 6.0 array) for a renal carcinoma sample on Chr.2 utilizing three different sources of the reference signal.

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