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Detection of novel tandem duplication with next-generation sequencing

Published: 01 August 2011 Publication History

Abstract

Detection of structural variations is an important problem. With the next generation sequencing technology, it is relatively easier to obtain a set of paired-end short reads from an individual (the donor). By aligning these reads onto a reference genome (the reference), we are able to detect some of the structural variations that exist between the donor and the reference. A number of tools were developed in this direction. However, these tools are not able to detect all types of variations. In particular, they do not perform well for the detection of tandem duplications which are found to be associated with some diseases. In this paper, we try to solve this problem and developed algorithm to identify novel tandem duplications that exist in donor and vice versa. Experimental results on both simulated and real datasets showed that our solutions are effective.

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cover image ACM Conferences
BCB '11: Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
August 2011
688 pages
ISBN:9781450307963
DOI:10.1145/2147805
  • General Chairs:
  • Robert Grossman,
  • Andrey Rzhetsky,
  • Program Chairs:
  • Sun Kim,
  • Wei Wang
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Published: 01 August 2011

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  1. novel tandem duplication detection
  2. structural variations

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