SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data.
BACKGROUND
Targeted 'deep' sequencing of specific genes or regions is of great interest in clinical cancer diagnostics where some sequence variants, particularly translocations and indels, have known prognostic or diagnostic significance. In this setting, it is unnecessary to sequence an entire genome, and target capture methods can be applied to limit sequencing to important regions, thereby reducing costs and the time required to complete testing. Existing 'next-gen' sequencing analysis packages are optimized for efficiency in whole-genome studies and are unable to benefit from the particular structure of targeted sequence data.


RESULTS
We developed SLOPE to detect structural variants from targeted short-DNA reads. We use both real and simulated data to demonstrate SLOPE's ability to rapidly detect insertion/deletion events of various sizes as well as translocations and viral integration sites with high sensitivity and low false discovery rate.


BACKGROUND
Binary code available at http://www-genepi.med.utah.edu/suppl/SLOPE/index.html
Abel
Haley J
HJ
Department of Internal Medicine, Division of Genetic Epidemiology, Department of Pathology, University of Utah, Salt Lake City, UT, USA. haley@genepi.med.utah.edu
Duncavage
Eric J
EJ
Becker
Nils
N
Armstrong
Jon R
JR
Magrini
Vincent J
VJ
Pfeifer
John D
JD
D016678:Genome; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014178:Translocation, Genetic