Mapping translocation breakpoints by next-generation sequencing.
Chen W,
Kalscheuer V,
Tzschach A,
Menzel C,
Ullmann R,
Schulz MH,
Erdogan F,
Li N,
Kijas Z,
Arkesteijn G,
Pajares IL,
Goetz-Sothmann M,
Heinrich U,
Rost I,
Dufke A,
Grasshoff U,
Glaeser B,
Vingron M,
Ropers HH.
Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. wei@molgen.mpg.de
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 [PubMed - indexed for MEDLINE]
PMCID: PMC2493403