A BAC clone fingerprinting approach to the detection of human genome rearrangements

Martin Krzywinski¹ , Ian Bosdet¹ , Carrie Mathewson¹ , Natasja Wye¹ , Jay Brebner² , Readman Chiu¹ , Richard Corbett¹ , Matthew Field¹ , Darlene Lee¹ , Trevor Pugh¹ , Stas Volik² , Asim Siddiqui¹ , Steven Jones¹ , Jacquie Schein¹ , Collin Collins² and Marco Marra¹

¹BC Cancer Agency Genome Sciences Centre, West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6

²Cancer Research Institute, University of California at San Francisco, San Francisco, California, USA 94143-0808

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Genome Biology 2007, 8:R224doi:10.1186/gb-2007-8-10-r224


Published:	22 October 2007

Subject areas: Bioinformatics, Genetics

Abstract

We present a method, called fingerprint profiling (FPP), that uses restriction digest fingerprints of bacterial artificial chromosome clones to detect and classify rearrangements in the human genome. The approach uses alignment of experimental fingerprint patterns to in silico digests of the sequence assembly and is capable of detecting micro-deletions (1-5 kb) and balanced rearrangements. Our method has compelling potential for use as a whole-genome method for the identification and characterization of human genome rearrangements.