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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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Citation and License

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

Published: 24 April 2013

Abstract

Background

The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal.

Results

While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing.

Conclusion

These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.

Keywords:
Copy number variation; DNA isolation; Technological bias; Tissue specificity