digit - a tool for detection and identification of genomic interchromosomal translocations
Title:
digit - a tool for detection and identification of genomic interchromosomal translocations
Authors:
Richard Meier TH ; Stefan Graw TH ; Peter Beyerlein TH ; Devin Koestler ; Julian R. Molina ; Jeremy Chien
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.
Year:
2017
Publication type:
Journal article
Journal:
Nucleic Acids Research
ISSN:
1362-4962
Number:
9
Volume:
45
Pages:
e72
Language:
English
Document status:
Open access
PubListerURL:
https://publister.bib.th-wildau.de/publister/public/publication/2256
Meier, R., Graw, S., Beyerlein, P., Koestler, D., Molina, J., & Chien, J. (2017). digit - a tool for detection and identification of genomic interchromosomal translocations Nucleic Acids Research. 45 (9), e72.
@article{2256,
author = {Meier, Richard and Graw, Stefan and Beyerlein, Peter and Koestler, Devin and Molina, Julian R. and Chien, Jeremy},
title = {digit - a tool for detection and identification of genomic interchromosomal translocations},
journal = {Nucleic Acids Research},
year = {2017},
volume = {45},
number = {9},
pages = {e72},
publisher = {Oxford University Press},
doi = {10.1093/nar/gkx010},
}