MPI für molekulare Genetik / Department of Computational Molecular Biology |
|Mapping translocation breakpoints by next-generation sequencing|
|Authors:||Chen, Wei; Kalscheuer, Vera; Tzschach, Andreas; Menzel, Corinna; Ullmann, Reinhard; Schulz, Marcel Holger; Erdogan, Fikret; Na, Li; Kijas, Zofia; Arkesteijn, Ger; Pajares, Isidora Lopez; Goetz-Sothmann, Margret; Heinrich, Uwe; Rost, Imma; Dufke, Andreas; Grasshoff, Ute; Glaeser, Birgitta; Vingron, Martin; Ropers, H. Hilger|
|Date of Publication (YYYY-MM-DD):||2008-03-07|
|Title of Journal:||Genome Research|
|Journal Abbrev.:||Genome Res|
|Issue / Number:||7|
|Copyright:||© 2008, Cold Spring Harbor Laboratory Press|
|Review Status:||not specified|
|Abstract / Description:||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.|
|Comment of the Author/Creator:||Corresponding author.
E-mail firstname.lastname@example.org; fax 49-30-84131383.
[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.]
|External Publication Status:||published|
|Communicated by:||Martin Vingron|
|Affiliations:||MPI für molekulare Genetik|
|External Affiliations:||1. International Max-Planck Research School for Computational Biology and Scientific Computing, 14195 Berlin, Germany;
2. Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3508 TC Utrecht, The Netherlands;
3. Department of Genetics, Hospital Universitario La Paz, 28046 Madrid, Spain;
4. Practice of Human Genetics, 81379 Munich, Germany;
5. Centre of Human Genetics, 82152 Martinsried, Germany;
6. Department of Medical Genetics, Eberhard Karls University, 72076 Tuebingen, Germany;
7. Institut für Klinische Genetik, Olgahospital, 70176 Stuttgart, Germany.
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