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Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays

Nature Protocols volume 4, pages 1722–1736 (2009)Cite this article

Abstract

Array painting is a technique that uses microarray technology to rapidly map chromosome translocation breakpoints. Previous methods to map translocation breakpoints have used fluorescence in situ hybridization (FISH) and have consequently been labor-intensive, time-consuming and restricted to the low breakpoint resolution imposed by the use of metaphase chromosomes. Array painting combines the isolation of derivative chromosomes (chromosomes with translocations) and high-resolution microarray analysis to refine the genomic location of translocation breakpoints in a single experiment. In this protocol, we describe array painting by isolation of derivative chromosomes using a MoFlo flow sorter, amplification of these derivatives using whole-genome amplification and hybridization onto commercially available oligonucleotide microarrays. Although the sorting of derivative chromosomes is a specialized procedure requiring sophisticated equipment, the amplification, labeling and hybridization of DNA is straightforward, robust and can be completed within 1 week. The protocol described produces good quality data; however, array painting is equally achievable using any combination of the available alternative methodologies for chromosome isolation, amplification and hybridization.

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Figure 1: A schematic outlining the steps of an array paint experiment.
Figure 2: Images of chromosome preparation and staining.
Figure 3: A schematic detailing the flow sorting of the derivative chromosomes resulting from a translocation between chromosomes 3 and 20, t(3;20)(q13.2;p12.2).
Figure 4: Bivariate flow karyotype of chromosomes from a normal male human lymphoblastoid cell line, GM7016A.
Figure 5: Agarose gel electrophoresis (1.5%) of amplified derivative chromosome products.
Figure 6: Array paint of derivative chromosomes A and B on a Agilent 244k whole genome array.

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Acknowledgements

The labeling procedure described in Steps 39–43 was originally developed by Heike Fiegler28 and slightly modified for this protocol. We acknowledge Diana Rajan and Leong Siew Hong for proofreading and checking this protocol. We thank John Crolla (Wessex Regional Genetics Laboratory) for supplying the t(3;20) cell line used in Figure 3. This work was supported by the Wellcome Trust [Grant no. WT077008].

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Authors and Affiliations

  1. Human Genetics, Sulston Laboratories, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK

    Susan M Gribble, Bee Ling Ng, Elena Prigmore, Tomas Fitzgerald & Nigel P Carter

Authors
  1. Susan M Gribble
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  2. Bee Ling Ng
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  3. Elena Prigmore
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  4. Tomas Fitzgerald
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Contributions

S.M.G. and B.L.N. contributed equally in writing this paper; E.P. verified the protocol and proofread this paper; T.F. contributed to figures; N.P.C. originally developed this procedure and supervised this study.

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Correspondence to Susan M Gribble.

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Gribble, S., Ng, B., Prigmore, E. et al. Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays. Nat Protoc 4, 1722–1736 (2009). https://doi.org/10.1038/nprot.2009.183

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