digit—a tool for detection and identification of genomic interchromosomal translocations

  • 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.

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Author:Richard Meier, Stefan GrawORCiD, Peter Beyerlein, Devin Koestler, Julian R. Molina, Jeremy Chien
Parent Title (English):Nucleic Acids Research
Document Type:Article
Year of Publication:2017
Publishing Institution:Technische Hochschule Wildau
Release Date:2017/06/06
First Page:e72
Source:Richard Meier, Stefan Graw, Peter Beyerlein, Devin Koestler, Julian R. Molina, Jeremy Chien; digit—a tool for detection and identification of genomic interchromosomal translocations. Nucleic Acids Res 2017; 45 (9): e72. doi: 10.1093/nar/gkx010
Faculties an central facilities:Fachbereich Ingenieur- und Naturwissenschaften
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 576 Genetik und Evolution
Licence (German):Creative Commons - CC BY-NC - Namensnennung - Nicht kommerziell 4.0 International
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