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Genome Res. 2008 Jul;18(7):1143-9. doi: 10.1101/gr.076166.108. Epub 2008 Mar 7.

Mapping translocation breakpoints by next-generation sequencing.

Author information

1
Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. wei@molgen.mpg.de

Abstract

Balanced chromosome rearrangements (BCRs) can cause genetic diseases by disrupting or inactivating specific genes, and the characterization of breakpoints in disease-associated BCRs has been instrumental in the molecular elucidation of a wide variety of genetic disorders. However, mapping chromosome breakpoints using traditional methods, such as in situ hybridization with fluorescent dye-labeled bacterial artificial chromosome clones (BAC-FISH), is rather laborious and time-consuming. In addition, the resolution of BAC-FISH is often insufficient to unequivocally identify the disrupted gene. To overcome these limitations, we have performed shotgun sequencing of flow-sorted derivative chromosomes using "next-generation" (Illumina/Solexa) multiplex sequencing-by-synthesis technology. As shown here for three different disease-associated BCRs, the coverage attained by this platform is sufficient to bridge the breakpoints by PCR amplification, and this procedure allows the determination of their exact nucleotide positions within a few weeks. Its implementation will greatly facilitate large-scale breakpoint mapping and gene finding in patients with disease-associated balanced translocations.

PMID:
18326688
PMCID:
PMC2493403
DOI:
10.1101/gr.076166.108
[Indexed for MEDLINE]
Free PMC Article

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