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Open Access Research article

Empirical assessment of competitive hybridization and noise in ultra high density canine tiling arrays

Cali E Willet1*, Laura Bunbury-Cruickshank1, Diane van Rooy1, Georgina Child2, Mohammad R Shariflou1, Peter C Thomson1 and Claire M Wade1

Author Affiliations

1 Faculty of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia

2 University of Sydney Veterinary Teaching Hospital, The University of Sydney, Sydney, NSW 2006, Australia

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BMC Bioinformatics 2013, 14:231  doi:10.1186/1471-2105-14-231

Published: 22 July 2013

Abstract

Background

In addition to probe sequence characteristics, noise in hybridization array data is thought to be influenced by competitive hybridization between probes tiled at high densities. Empirical evaluation of competitive hybridization and an estimation of what other non-sequence related features might affect noisy data is currently lacking.

Results

A high density array was designed to a 1.5 megabase region of the canine genome to explore the potential for probe competition to introduce noise. Multivariate assessment of the influence of probe, segment and design characteristics on hybridization intensity demonstrate that whilst increased density significantly depresses fluorescence intensities, this effect is largely consistent when an ultra high density offset is applied. Signal variation not attributable to sequence composition resulted from the reduction in competition when large inter-probe spacing was introduced due to long repetitive elements and when a lower density offset was applied. Tiling of probes immediately adjacent to various classes of repeat elements did not generate noise. Comparison of identical probe sets hybridized with DNA extracted from blood or saliva establishes salivary DNA as a source of noise.

Conclusions

This analysis demonstrates the occurrence of competitive hybridization between oligonucleotide probes in high density tiling arrays. It supports that probe competition does not generate random noise when it is maintained across a region. To prevent the introduction of noise from this source, the degree of competition should be regulated by minimizing variation in density across the target region. This finding can make an important contribution to optimizing coverage whilst minimizing sources of noise in the design of high density tiling arrays.

Keywords:
Array comparative genome hybridization; aCGH; Copy number variation; CNV; Tiling path offset; Oligonucleotide probe; Probe competition; Canis lupus