Mapping translocation breakpoints by next-generation sequencing

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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. ©2008 by Cold Spring Harbor Laboratory Press.

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Chen, W., Kalscheuer, V., Tzschach, A., Menzel, C., Ullmann, R., Schulz, M. H., … Ropers, H. H. (2008). Mapping translocation breakpoints by next-generation sequencing. Genome Research, 18(7), 1143–1149. https://doi.org/10.1101/gr.076166.108

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