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  Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing

Chen, W., Ullmann, R., Langnick, C., Menzel, C., Wotschofsky, Z., Hu, H., et al. (2010). Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing. European Journal of Human Genetics. doi:10.1038/ejhg.2009.211.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7C49-C Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7C4A-A
Genre: Journal Article
Alternative Title : Eur J Hum Genet

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Chen, Wei1, Author              
Ullmann, Reinhard2, Author              
Langnick, Claudia, Author
Menzel, Corinna3, Author
Wotschofsky, Zofia4, Author              
Hu, Hao1, Author              
Döring, Andreas, Author
Hu, Yuhui1, Author              
Kang, Hui5, Author              
Tzschach, Andreas1, Author              
Hoeltzenbein, Maria3, Author
Neitzel, Heidemarie, Author
Markus, Susanne, Author
Wiedersberg, Eberhard, Author
Kistner, Gerd, Author
van Ravenswaaij-Arts, Conny M. A., Author
Kleefstra, Tjitske, Author
Kalscheuer, Vera M.6, Author              
Ropers, Hans-Hilger1, Author              
Affiliations:
1Dept. of Human Molecular Genetics (Head: Hans-Hilger Ropers), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433549              
2Molecular Cytogenetics (Reinhard Ullmann), Dept. of Human Molecular Genetics (Head: Hans-Hilger Ropers), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479645              
3Max Planck Society, ou_persistent13              
4Dept. of Developmental Genetics (Head: Bernhard G. Herrmann), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433548              
5Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
6Chromosome Rearrangements and Disease (Vera Kalscheuer), Dept. of Human Molecular Genetics (Head: Hans-Hilger Ropers), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479642              

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Free keywords: Breakpoint mapping, Next-generation sequencing technology, Paired-end sequencing
 Abstract: Characterisation of breakpoints in disease-associated balanced chromosome rearrangements (DBCRs), which disrupt or inactivate specific genes, has facilitated the molecular elucidation of a wide variety of genetic disorders. However, conventional methods for mapping chromosome breakpoints, such as in situ hybridisation with fluorescent dye-labelled bacterial artificial chromosome clones (BAC-FISH), are laborious, time consuming and often with insufficient resolution to unequivocally identify the disrupted gene. By combining DNA array hybridisation with chromosome sorting, the efficiency of breakpoint mapping has dramatically improved. However, this can only be applied when the physical properties of the derivative chromosomes allow them to be flow sorted. To characterise the breakpoints in all types of balanced chromosome rearrangements more efficiently and more accurately, we performed massively parallel sequencing using Illumina 1G analyser and ABI SOLiD systems to generate short sequencing reads from both ends of DNA fragments. We applied this method to four different DBCRs, including two reciprocal translocations and two inversions. By identifying read pairs spanning the breakpoints, we were able to map the breakpoints to a region of a few hundred base pairs that could be confirmed by subsequent PCR amplification and Sanger sequencing of the junction fragments. Our results show the feasibility of paired-end sequencing of systematic breakpoint mapping and gene finding in patients with disease-associated chromosome rearrangements.

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Language(s): eng - English
 Dates: 2010
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
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Title: European Journal of Human Genetics
  Alternative Title : Eur J Hum Genet
Source Genre: Journal
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Pages: - Volume / Issue: - Sequence Number: - Start / End Page: - Identifier: ISSN: 1018-4813