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Detection of internal exon deletion with exon Del.

Guo Y, Zhao S, Lehmann BD, Sheng Q, Shaver TM, Stricker TP, Pietenpol JA, Shyr Y - BMC Bioinformatics (2014)

Bottom Line: Such deletions have potentially significant biological meaning, and they are often too short to be considered copy number variation.Further comparisons with multiple sequencing-based CNV tools showed that ExonDel is capable of detecting unique IEDs not found by other CNV tools.ExonDel is an efficient way to screen for novel and known IEDs using exome sequencing data.

View Article: PubMed Central - PubMed

Affiliation: Vanderbilt Ingram Cancer Center, Center for Quantitative Sciences, 2220 Pierce Ave, 549 Preston Research Building, Nashville, TN 37232, USA. yan.guo@vanderbilt.edu.

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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Further validation of exon deletion on NOTCH1 was obtained using RT-PCR.
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Fig3: Further validation of exon deletion on NOTCH1 was obtained using RT-PCR.

Mentions: The 16 cell line datasets were processed in house using standard sequencing processing pipeline. The complete raw quality control results can be seen in Additional file 1: Table S1. Alignment was done using BWA [10] against the HG19 human genome reference. Statistics of alignments can be viewed in Additional file 2: Table S2. Using ExonDel to screen for IED on the 16 cell line samples, we identified both novel and known exon deletions were observed. We were able to validate the previously described deletion of exons 3 to 27 in NOTCH1 in cell line HCC1599 and identify a similar deletion in cell line MDA-MB-157. This previously unidentified IED of exons 2 to 27 is similar to the deletion in HCC1599 and those described in murine T-ALL [4, 5]. To verify these findings we performed RNAseq on these cell lines. Figure 2 depicts the sequencing depth coverage using Integrative Genomics Viewer for both DNA exome and RNAseq data for each of the cell lines. For comparison, we included a cell line without the NOTCH1 deletion (HS578T) in Figure 2. Exons 3-27 and 2-27 are clearly deleted in HCC1599 and MDA-MB-157 respectively but remain intact in HS578T cells. These deletions are further confirmed with RT-PCR (Figure 3).Figure 2


Detection of internal exon deletion with exon Del.

Guo Y, Zhao S, Lehmann BD, Sheng Q, Shaver TM, Stricker TP, Pietenpol JA, Shyr Y - BMC Bioinformatics (2014)

Further validation of exon deletion on NOTCH1 was obtained using RT-PCR.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4288651&req=5

Fig3: Further validation of exon deletion on NOTCH1 was obtained using RT-PCR.
Mentions: The 16 cell line datasets were processed in house using standard sequencing processing pipeline. The complete raw quality control results can be seen in Additional file 1: Table S1. Alignment was done using BWA [10] against the HG19 human genome reference. Statistics of alignments can be viewed in Additional file 2: Table S2. Using ExonDel to screen for IED on the 16 cell line samples, we identified both novel and known exon deletions were observed. We were able to validate the previously described deletion of exons 3 to 27 in NOTCH1 in cell line HCC1599 and identify a similar deletion in cell line MDA-MB-157. This previously unidentified IED of exons 2 to 27 is similar to the deletion in HCC1599 and those described in murine T-ALL [4, 5]. To verify these findings we performed RNAseq on these cell lines. Figure 2 depicts the sequencing depth coverage using Integrative Genomics Viewer for both DNA exome and RNAseq data for each of the cell lines. For comparison, we included a cell line without the NOTCH1 deletion (HS578T) in Figure 2. Exons 3-27 and 2-27 are clearly deleted in HCC1599 and MDA-MB-157 respectively but remain intact in HS578T cells. These deletions are further confirmed with RT-PCR (Figure 3).Figure 2

Bottom Line: Such deletions have potentially significant biological meaning, and they are often too short to be considered copy number variation.Further comparisons with multiple sequencing-based CNV tools showed that ExonDel is capable of detecting unique IEDs not found by other CNV tools.ExonDel is an efficient way to screen for novel and known IEDs using exome sequencing data.

View Article: PubMed Central - PubMed

Affiliation: Vanderbilt Ingram Cancer Center, Center for Quantitative Sciences, 2220 Pierce Ave, 549 Preston Research Building, Nashville, TN 37232, USA. yan.guo@vanderbilt.edu.

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.

Show MeSH
Related in: MedlinePlus