Detection of recurrent rearrangement breakpoints from copy number data

Background: Copy number variants (CNVs), including deletions, amplifications, and other rearrangements, are common in human and cancer genomes. Copy number data from array comparative genome hybridization (aCGH) and next-generation DNA sequencing is widely used to measure copy number variants. Comparison of copy number data from multiple individuals reveals recurrent variants. Typically, the interior of a recurrent CNV is examined for genes or other loci associated with a phenotype. However, in some cases, such as gene truncations and fusion genes, the target of variant lies at the boundary of the variant. Results: We introduce Neighborhood Breakpoint Conservation (NBC), an algorithm for identifying rearrangement breakpoints that are highly conserved at the same locus in multiple individuals. NBC detects recurrent breakpoints at varying levels of resolution, including breakpoints whose location is exactly conserved and breakpoints whose location varies within a gene. NBC also identifi...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Anna M. Ritz, Pamela L. Paris, Michael Ittmann, Colin Collins, Benjamin J. Raphael
• Keywords: Biometrics, BMCBI 2011, Fusion Genes, Genes Software, Protein Phosphatase