title: digit-a tool for detection and identification of genomic interchromosomal translocations.
abstract: Structural variations (SVs) in genomic DNA can have profound effects on the evolution of living organisms, on phenotypic variations and on disease processes. A critical step in discovering the full extent of structural variations is the development of tools to characterize these variations accurately in next generation sequencing data. Toward this goal, we developed a software pipeline named digit that implements a novel measure of mapping ambiguity to discover interchromosomal SVs from mate-pair and pair-end sequencing data. The workflow robustly handles the high numbers of artifacts present in mate-pair sequencing and reduces the false positive rate while maintaining sensitivity. In the simulated data set, our workflow recovered 96% of simulated SVs. It generates a self-updating library of common translocations and allows for the investigation of patient- or group-specific events, making it suitable for discovering and cataloging chromosomal translocations associated with specific groups, traits, diseases or population structures.
authors.affiliation: Technical University of Applied Sciences Wildau, 15745 Wildau, Germany.|Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Meier
authors.affiliation: Technical University of Applied Sciences Wildau, 15745 Wildau, Germany.|Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
authors.forename: Stefan
authors.initials: S
authors.lastname: Graw
authors.affiliation: Technical University of Applied Sciences Wildau, 15745 Wildau, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Beyerlein
authors.affiliation: Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
authors.forename: Devin
authors.initials: D
authors.lastname: Koestler
authors.affiliation: Department of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA.
authors.forename: Julian R
authors.initials: JR
authors.lastname: Molina
authors.affiliation: Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Chien
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D015723:Gene Library; D006801:Humans; D012680:Sensitivity and Specificity; D012984:Software; D014178:Translocation, Genetic