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.
Author: | Richard Meier, Stefan GrawORCiD, Peter Beyerlein, Devin Koestler, Julian R. Molina, Jeremy ChienORCiD |
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URN: | urn:nbn:de:kobv:526-opus4-9697 |
DOI: | https://doi.org/10.1093/nar/gkx010 |
ISSN: | 1362-4962 |
Parent Title (English): | Nucleic Acids Research |
Document Type: | Article |
Language: | English |
Year of Publication: | 2017 |
Publishing Institution: | Technische Hochschule Wildau |
Release Date: | 2017/06/06 |
Volume: | 45 |
Issue: | 9 |
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 |