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Prioritisation of structural variant calls in cancer genomes

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ABSTRACT

Sensitivity of short read DNA-sequencing for gene fusion detection is improving, but is hampered by the significant amount of noise composed of uninteresting or false positive hits in the data. In this paper we describe a tiered prioritisation approach to extract high impact gene fusion events from existing structural variant calls. Using cell line and patient DNA sequence data we improve the annotation and interpretation of structural variant calls to best highlight likely cancer driving fusions. We also considerably improve on the automated visualisation of the high impact structural variants to highlight the effects of the variants on the resulting transcripts. The resulting framework greatly improves on readily detecting clinically actionable structural variants.

No MeSH data available.


EML4-ALK inversion fusion.(A) shows the effect of the fusion and (B) the read evidence for the event at both breakpoints.
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fig-6: EML4-ALK inversion fusion.(A) shows the effect of the fusion and (B) the read evidence for the event at both breakpoints.

Mentions: In Fig. 5 an interchromosomal translocation resulting in a fusion between ROS1 and SLC34A2 is shown. If multiple genes are overlapping the breakpoints NGB allows choosing the most relevant gene for the researcher. Another example for the EML4-ALK fusion that results from an inversion is shown if Fig. 6.


Prioritisation of structural variant calls in cancer genomes
EML4-ALK inversion fusion.(A) shows the effect of the fusion and (B) the read evidence for the event at both breakpoints.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5382922&req=5

fig-6: EML4-ALK inversion fusion.(A) shows the effect of the fusion and (B) the read evidence for the event at both breakpoints.
Mentions: In Fig. 5 an interchromosomal translocation resulting in a fusion between ROS1 and SLC34A2 is shown. If multiple genes are overlapping the breakpoints NGB allows choosing the most relevant gene for the researcher. Another example for the EML4-ALK fusion that results from an inversion is shown if Fig. 6.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Sensitivity of short read DNA-sequencing for gene fusion detection is improving, but is hampered by the significant amount of noise composed of uninteresting or false positive hits in the data. In this paper we describe a tiered prioritisation approach to extract high impact gene fusion events from existing structural variant calls. Using cell line and patient DNA sequence data we improve the annotation and interpretation of structural variant calls to best highlight likely cancer driving fusions. We also considerably improve on the automated visualisation of the high impact structural variants to highlight the effects of the variants on the resulting transcripts. The resulting framework greatly improves on readily detecting clinically actionable structural variants.

No MeSH data available.