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Ultra-high resolution array painting facilitates breakpoint sequencing
  1. S M Gribble1,*,
  2. D Kalaitzopoulos1,*,
  3. D C Burford1,*,
  4. E Prigmore1,*,
  5. R R Selzer2,
  6. B L Ng1,
  7. N S W Matthews1,
  8. K M Porter1,
  9. R Curley1,
  10. S J Lindsay1,
  11. J Baptista3,
  12. T A Richmond2,
  13. N P Carter1
  1. 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
  2. 2NimbleGen Systems, Madison, Wisconsin, USA
  3. 3Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, UK
  1. Correspondence to:
 N P Carter
 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK; npc{at}sanger.ac.uk

Abstract

Objective: To describe a considerably advanced method of array painting, which allows the rapid, ultra-high resolution mapping of translocation breakpoints such that rearrangement junction fragments can be amplified directly and sequenced.

Method: Ultra-high resolution array painting involves the hybridisation of probes generated by the amplification of small numbers of flow-sorted derivative chromosomes to oligonucleotide arrays designed to tile breakpoint regions at extremely high resolution.

Results and discussion: How ultra-high resolution array painting of four balanced translocation cases rapidly and efficiently maps breakpoints to a point where junction fragments can be amplified easily and sequenced is demonstrated. With this new development, breakpoints can be mapped using just two array experiments: the first using whole-genome array painting to tiling resolution large insert clone arrays, the second using ultra-high-resolution oligonucleotide arrays targeted to the breakpoint regions. In this way, breakpoints can be mapped and then sequenced in a few weeks.

  • CGH, comparative genomic hybridisation
  • FISH, fluorescence in situ hybridisation
  • LINE, long interspersed element
  • PCR, polymerase chain reaction
  • SINE, short interspersed element
  • array painting
  • array-CGH
  • oligonucleotide array
  • transloction breakpoints

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Footnotes

  • * These authors contributed equally to this work.

  • Published Online First 13 September 2006

  • Competing interests: None declared.

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