Ultra-high resolution array painting facilitates breakpoint sequencing
- S M Gribble1,*,
- D Kalaitzopoulos1,*,
- D C Burford1,*,
- E Prigmore1,*,
- R R Selzer2,
- B L Ng1,
- N S W Matthews1,
- K M Porter1,
- R Curley1,
- S J Lindsay1,
- J Baptista3,
- T A Richmond2,
- N P Carter1
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- 2NimbleGen Systems, Madison, Wisconsin, USA
- 3Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, UK
- Correspondence to: N P Carter Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK;
- Received 18 June 2006
- Accepted 3 August 2006
- Revised 21 July 2006
- Published Online First 13 September 2006
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
↵* These authors contributed equally to this work.
Published Online First 13 September 2006
Competing interests: None declared.