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Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2
Description:
EXCAVATOR2 is a read count (RC) based tool that exploits all
the reads produced by Whole Exome Sequencing (WES) and Targeted
Sequencing (TS) experiments to detect Copy Number Variants (CNV)
with a genome-wide resolution. Copy Number Variants are structural
rearrangements involving DNA segments of at least 50bp that can be
present with an altered copy number compared to the reference
genome. They are one of the main sources of genomic variation in
humans contributing to phenotypic variation but are also associated
with many classes of diseases, from neurological disorders to
cancer. Various computational methods have been developed for the
detection of CNVs starting from NGS data are based on the read count
(RC) approach. EXCAVATOR2 exploits all reads produced by targeted
sequencing experiments using probes enrichment kits and, combining
signals from In- and Off-Target, it enhances the identification of
genomic CNVs, particularly in exon-rich regions, and to be more
accurate in breakpoints detection. It can be effectively employed
for the identification of CNVs in small as well as large-scale
re-sequencing studies with best performance, and so maximizing the
utility of exome sequencing data in genetic and cancer studies.
Lastly, it is of particular interest that all WES/TS experiments can
be re-analysed using our method with the beneficial effect to
identify CNVs affecting non-coding genomic regions.
We are investigating the feasibility of our method on cancer genomic
data, with specific focus on tumour heterogeneity and classification
for clinical purpose, and on the identification of non-coding
alterations associated with mendelian disorders.
Source code and datasets
The source code, supplementary files and user manual are available at the Sourceforgenet repository
Citation
Please consider citing the following paper if you found a resource useful:
- Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2
Romina D'Aurizio, Tommaso Pippucci, Lorenzo Tattini, Betti Giusti, Marco Pellegrini, Alberto Magi
Nucleic Acids Research, Volume 44, Issue 20, 16 November 2016, Page e154, https://doi.org/10.1093/nar/gkw695
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Styled and mantained by:
M. Elena Renda
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