Motivation
Next generation sequencing technologies have been decreasing the costs and increasing the world-wide capacity for sequence production at an unprecedented rate, making the initiation of large scale projects aiming to sequence almost 2000 genomes [1]. Structural variation detection promises to be one of the key diagnostic tools for cancer and other diseases with genomic origin. In this paper, we study the problem of detecting structural variation events in two or more sequenced genomes through high throughput sequencing . We propose to move from the current model of (1) detecting genomic variations in single next generation sequenced (NGS) donor genomes independently, and (2) checking whether two or more donor genomes indeed agree or disagree on the variations (in this paper we name this framework Independent Structural Variation Discovery and Merging - ISV&M), to a new model in which we detect structural variation events among multiple genomes simultaneously.
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The 1000 Genomes Project Consortium: Nature 467, 1061–1073 (2010)
Hormozdiari, F., Alkan, C., Eichler, E., Sahinalp, S.C.: Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. Genome Research 19: 1270–1278 (2009)
Hormozdiari, F., Hajirasouliha, I., Dao, P., Hach, F., Yorukoglu, D., Alkan, C., Eichler, E.E., Sahinalp, S.: Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 26(12), i350–i357 (2010)
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© 2011 Springer-Verlag Berlin Heidelberg
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Hormozdiari, F., Hajirasouliha, I., McPherson, A., Eichler, E.E., Sahinalp, S.C. (2011). Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. In: Bafna, V., Sahinalp, S.C. (eds) Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science(), vol 6577. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-20036-6_11
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DOI: https://doi.org/10.1007/978-3-642-20036-6_11
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-20035-9
Online ISBN: 978-3-642-20036-6
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