Digit—a tool for detection and identification of genomic interchromosomal translocations. Issue 9 (28th January 2017)

• Record Type: Journal Article
• Authors: Meier, Richard; Graw, Stefan; Beyerlein, Peter; Koestler, Devin; Molina, Julian R.; Chien, Jeremy
• Is Part Of: Nucleic acids research. Volume 45:Issue 9(2017)
• Page Start: e72
• Page End: e72
• Publication Date: 2017-01-28
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkx010
• Languages: English
• ISSNs: 0305-1048

Abstract

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.