Paper Info
Title
Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions.
Abstract
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.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.
Year
DOI
Venue
2011
10.1093/bioinformatics/btr169
Bioinformatics
Keywords
Field
DocType
high accuracy,cnv identification,tandem copy number variation,repeat-rich region,multiple mapping position,efficient algorithm,high-throughput sequencing technique,new opportunity,current generation,dramatic effect,active area,copy number variation,genomics,algorithms,dna
Copy-number variation,Computer science,Algorithm,Genomics,Bioinformatics,Reference genome
Journal
Volume
Issue
ISSN
27
11
1367-4811
Citations 
PageRank 
References 
3
0.59
5
Authors
4
Name
Order
Citations
PageRank
Dan He113312.54
Farhad Hormozdiari211611.73
Nicholas A. Furlotte3172.26
Eleazar Eskin41790170.53