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Mapping translocation breakpoints by next-generation sequencing

By Wei Chen, Vera Kalscheuer, Andreas Tzschach, Corinna Menzel, Reinhard Ullmann, Marcel Holger Schulz, Fikret Erdogan, Na Li, Zofia Kijas, Ger Arkesteijn, Isidora Lopez Pajares, Margret Goetz-Sothmann, Uwe Heinrich, Imma Rost, Andreas Dufke, Ute Grasshoff, Birgitta Glaeser, Martin Vingron and H. Hilger Ropers

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

Topics: Methods
Publisher: Cold Spring Harbor Laboratory Press
OAI identifier: oai:pubmedcentral.nih.gov:2493403
Provided by: PubMed Central
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