SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing (MPseq)

Publication date: Available online 2 December 2017 Source:Cancer Genetics Author(s): Sarah H. Johnson, James B. Smadbeck, Stephanie A. Smoley, Athanasios Gaitatzes, Stephen J. Murphy, Faye R. Harris, Travis M. Drucker, Roman M. Zenka, Beth A. Pitel, Ross A. Rowsey, Nicole L. Hoppman, Umut Aypar, William R. Sukov, Robert B. Jenkins, Andrew L. Feldman, Hutton M. Kearney, George Vasmatzis Mate-pair sequencing (MPseq), using long-insert, paired-end genomic libraries, is a powerful next-generation sequencing-based approach for the detection of genomic structural variants. SVAtools is a set of algorithms to detect both chromosomal rearrangements and large (>10kb) copy number variants (CNVs) in genome-wide MPseq data. SVAtools can also predict gene disruptions, gene fusions, and characterize the genomic structure of complex rearrangements. To illustrate the power of SVAtools' junction detection methods to provide comprehensive molecular karyotypes, MPseq data was compared against a set of samples previously characterized by traditional cytogenetic methods. Karyotype, FISH and chromosomal microarray (CMA), performed for 29 patients in a clinical laboratory setting, collectively revealed 285 breakpoints in 87 rearrangements. The junction detection methods of SVAtools detected 87% of these breakpoints compared to 48%, 42% and 57% for karyotype, FISH and CMA respectively. Breakpoint resolution was also reported to 1 kb or less and additional genomic rearrangeme...
Source: Cancer Genetics - Category: Cancer & Oncology Source Type: research