title: Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions.
abstract: BACKGROUND
  Structural variations and in particular copy number variations (CNVs) have dramatic effects of disease and traits. Technologies for identifying CNVs have been an active area of research for over 10 years. The current generation of high-throughput sequencing techniques presents new opportunities for identification of CNVs. Methods that utilize these technologies map sequencing reads to a reference genome and look for signatures which might indicate the presence of a CNV. These methods work well when CNVs lie within unique genomic regions. However, the problem of CNV identification and reconstruction becomes much more challenging when CNVs are in repeat-rich regions, due to the multiple mapping positions of the reads.
  
  
  RESULTS
  In this study, we propose an efficient algorithm to handle these multi-mapping reads such that the CNVs can be reconstructed with high accuracy even for repeat-rich regions. To our knowledge, this is the first attempt to both identify and reconstruct CNVs in repeat-rich regions. Our experiments show that our method is not only computationally efficient but also accurate.
authors.affiliation: Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Dan
authors.initials: D
authors.lastname: He
authors.forename: Farhad
authors.initials: F
authors.lastname: Hormozdiari
authors.forename: Nicholas
authors.initials: N
authors.lastname: Furlotte
authors.forename: Eleazar
authors.initials: E
authors.lastname: Eskin
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping; D004247:DNA / Q000737:chemistry; D056915:DNA Copy Number Variations; D023281:Genomics / Q000379:methods; D051379:Mice; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004247:DNA