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. 2014 Oct 16;15(1):332.
doi: 10.1186/1471-2105-15-332.

Detection of internal exon deletion with exon Del

Yan Guo  1 , Shilin Zhao, Brian D Lehmann, Quanhu Sheng, Timothy M Shaver, Thomas P Stricker, Jennifer A Pietenpol, Yu Shyr
Affiliations

Detection of internal exon deletion with exon Del

Yan Guo et al. BMC Bioinformatics. .

Abstract

Background: Exome sequencing allows researchers to study the human genome in unprecedented detail. Among the many types of variants detectable through exome sequencing, one of the most over looked types of mutation is internal deletion of exons. Internal exon deletions are the absence of consecutive exons in a gene. Such deletions have potentially significant biological meaning, and they are often too short to be considered copy number variation. Therefore, to the need for efficient detection of such deletions using exome sequencing data exists.

Results: We present ExonDel, a tool specially designed to detect homozygous exon deletions efficiently. We tested ExonDel on exome sequencing data generated from 16 breast cancer cell lines and identified both novel and known IEDs. Subsequently, we verified our findings using RNAseq and PCR technologies. Further comparisons with multiple sequencing-based CNV tools showed that ExonDel is capable of detecting unique IEDs not found by other CNV tools.

Conclusions: ExonDel is an efficient way to screen for novel and known IEDs using exome sequencing data. ExonDel and its source code can be downloaded freely at https://github.com/slzhao/ExonDel.

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Figures

Figure 1
Figure 1
Using data from all 16 samples, we show that depth drops for exons with low and high GC content.
Figure 2
Figure 2
Verification of NOTCH1 deletions found by ExonDel. The mapping results of both exome sequencing and RNAseq data support the large deletion in NOTCH1. RNAseq data further proves that such deletions can be carried through transcription to RNA.
Figure 3
Figure 3
Further validation of exon deletion on NOTCH1 was obtained using RT-PCR.
Figure 4
Figure 4
Comparison between ExonDel and other CNV calling tools. (A) The length distribution of the deletion detected by all tools; (B) The number of deletions detected using all tools at window size 1.
See this image and copyright information in PMC

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