Mapping translocation breakpoints by next-generation sequencing
- Wei Chen1,9,
- Vera Kalscheuer1,
- Andreas Tzschach1,
- Corinna Menzel1,
- Reinhard Ullmann1,
- Marcel Holger Schulz1,2,
- Fikret Erdogan1,
- Na Li1,
- Zofia Kijas1,
- Ger Arkesteijn3,
- Isidora Lopez Pajares4,
- Margret Goetz-Sothmann5,
- Uwe Heinrich6,
- Imma Rost6,
- Andreas Dufke7,
- Ute Grasshoff7,
- Birgitta Glaeser8,
- Martin Vingron1, and
- H. Hilger Ropers1
- 1 Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
- 2 International Max-Planck Research School for Computational Biology and Scientific Computing, 14195 Berlin, Germany;
- 3 Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3508 TC Utrecht, The Netherlands;
- 4 Department of Genetics, Hospital Universitario La Paz, 28046 Madrid, Spain;
- 5 Practice of Human Genetics, 81379 Munich, Germany;
- 6 Centre of Human Genetics, 82152 Martinsried, Germany;
- 7 Department of Medical Genetics, Eberhard Karls University, 72076 Tuebingen, Germany;
- 8 Institut für Klinische Genetik, Olgahospital, 70176 Stuttgart, Germany
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.
Footnotes
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↵9 Corresponding author.
↵9 E-mail wei{at}molgen.mpg.de; fax 49-30-84131383.
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[Supplemental material is available online at www.genome.org. Solexa sequencing data have been submitted to the Short Read Archive at NCBI (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?) and are accessible through accession no. SRA000261. ArrayCGH data have been submitted to the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession no. GSE10115.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.076166.108.
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- Received January 14, 2008.
- Accepted March 4, 2008.
- Copyright © 2008, Cold Spring Harbor Laboratory Press