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Methods and Resources

Mapping translocation breakpoints by next-generation sequencing

¹ Max-Planck-Institute for Molecular Genetics; ² Max-Planck-Institue for Molecular Genetics; ³ Max-Planck-Insitute for Molecular Genetics; ⁴ Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University; ⁵ Department of Genetics, Hospital Universitario La Paz; ⁶ Practice of Human Genetics; ⁷ Centre of Human Genetics; ⁸ Department of Medical Genetics, Eberhard Karls University; ⁹ Institut fur Klinische Genetik, Olgahospital

Abstract Balanced chromosome rearrangements (BCRs) can cause genetic diseases by disrupting or inactivating specific genes, and the characterisation 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 hybridisation 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' (Solexa/Illumina) 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 to determine their exact nucleotide positions within few weeks. Its implementation will greatly facilitate large-scale breakpoint mapping and gene finding in patients with disease-associated balanced translocations. Solexa sequencing data have been submitted to Short Read Archive at NCBI http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?) and are accessible through accession number SRA00261. ArrayCGH data have been submitted to the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/ ) and are accessible through GEO Series accession number GSE10115. A detailed description of our statistical method can be found in supplementary method. Supplementary table lists all primer pairs used to amplify the junction fragments. Flow sorting diagrams are provides as supplementary figures.

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