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Systematic biases in DNA copy number originate from isolation procedures

Sebastiaan van Heesch1, Michal Mokry12, Veronika Boskova1, Wade Junker3, Rajdeep Mehon4, Pim Toonen1, Ewart de Bruijn1, James D Shull35, Timothy J Aitman4, Edwin Cuppen16* and Victor Guryev17*

Author Affiliations

1 Hubrecht Institute and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

2 Current affiliation: Laboratory of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Centre, Lundlaan 6, 3584 EA Utrecht, The Netherlands

3 Department of Genetics, Cell Biology and Anatomy, 985805 University of Nebraska Medical Center, Omaha, Nebraska, 68198-5805, USA

4 Medical Research Council Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK

5 Current affiliation: McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin, Madison, Wisconsin, 53706-1599, USA

6 Department of Medical Genetics, UMC Utrecht, Universiteitsweg 100, 3584 GG Utrecht, The Netherlands

7 Current affiliation: Laboratory of Genome Structure and Ageing; European Research Institute for the Biology of Ageing; RuG and UMC Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands

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Genome Biology 2013, 14:R33  doi:10.1186/gb-2013-14-4-r33

Published: 24 April 2013

Additional files

Additional file 1:

Additional data file 1 is a figure showing the genome-wide correlation between aCGH results and NGS read-depth.

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Additional file 2:

Additional data file 2 is an Excel table listing all the correlations between the aCGH data and specific genome characteristics belonging to Figure 2(replication timing, SINEs, gene density, GC content).

Format: XLS Size: 623KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

Additional data file 3 shows the relation between tissue-specific aCGH patterns and gene expression data.

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Additional file 4:

Additional data file 4 contains a figure illustrating that independent DNA isolation techniques (phenol-chloroform and a commercial column-based DNA isolation kit) have no effect on the aCGH pattern.

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Additional file 5:

Additional data file 5 is an excel table listing all putative somatic CNV regions that could be identified by comparing brain and liver tissue after either 30 min or 60 min of proteinase K treatment.

Format: XLS Size: 46KB Download file

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Additional file 6:

Additional data file 6 shows the effects of increase proteinase K treatment on the wave pattern on rat chromosome 16 (30 min versus overnight treatment). Also, it shows all time points on a genome-wide scale compared to a fully random read distribution.

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Additional file 7:

Additional data file 7 is a figure showing that NGS read coverage depends on the homogeneity of a tissue, independent of the GC content.

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Additional file 8:

Additional data file 8 provides additional genome-wide aCGH plots for the tissue and strain comparisons presented in Figure 1A.

Format: PDF Size: 7MB Download file

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