CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing

John F Markham,Stephen Fox,Jason Ellul,Piers Blombery,Michael Dickinson,Satwica Yerneni,Richard Lupat,Amit Kumar,Ella R Thompson,Anthony T Papenfuss,Huei San Leong,Andrew Fellowes,Wasanthi De Silva,Jason Li,Georgina L Ryland

doi:10.1038/s41598-019-42858-8

Abstract

Next Generation Sequencing is now routinely used in the practice of diagnostic pathology to detect clinically relevant somatic and germline sequence variations in patient samples. However, clinical assessment of copy number variations (CNVs) and large-scale structural variations (SVs) is still challenging. While tools exist to estimate both, their results are typically presented separately in tables or static plots which can be difficult to read and are unable to show the context needed for clinical interpretation and reporting. We have addressed this problem with CNspector, a multi-scale interactive browser that shows CNVs in the context of other relevant genomic features to enable fast and effective clinical reporting. We illustrate the utility of CNspector at different genomic scales across a variety of sample types in a range of case studies. We show how CNspector can be used for diagnosis and reporting of exon-level deletions, focal gene-level amplifications, chromosome and chromosome arm level amplifications/deletions and in complex genomic rearrangements. CNspector is a web-based clinical variant browser tailored to the clinical application of next generation sequencing for CNV assessment. We have demonstrated the utility of this interactive software in typical applications across a range of tissue types and disease contexts encountered in the context of diagnostic pathology. CNspector is written in R and the source code is available for download under the GPL3 Licence from https://github.com/PapenfussLab/CNspector.

Highlights

Generation Sequencing is routinely used in the practice of diagnostic pathology to detect clinically relevant somatic and germline sequence variations in patient samples
In order to demonstrate the utility of CNspector across a range of sample types in clinical practice we present patient samples sequenced from both formalin-fixed paraffin embedded (FFPE) and fresh frozen tissue, from somatic and germline samples and with and without target enrichment
For all patient samples presented, relevant DNA library characteristics are summarized in SI Table 1, bait-based enrichment where applicable, is summarized in SI Table 2 and bioinformatics details for generation of copy number (CN) and www.nature.com/scientificreports other genomic features are described in SI Section S1

Summary

Introduction

Generation Sequencing is routinely used in the practice of diagnostic pathology to detect clinically relevant somatic and germline sequence variations in patient samples. While tools exist to estimate both, their results are typically presented separately in tables or static plots which can be difficult to read and are unable to show the context needed for clinical interpretation and reporting We have addressed this problem with CNspector, a multi-scale interactive browser that shows CNVs in the context of other relevant genomic features to enable fast and effective clinical reporting. CNVs can be detected from generation sequencing (NGS) data This is important because sequence variant detection using NGS is increasingly being utilized in the clinical diagnostic laboratory in order to improve diagnosis, refine prognosis and enhance therapeutic decision making. The analysis of copy number data generated by assays that are typically designed for the detection of sequence variants can be used to further enhance clinical decision making.

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Results

Discussion

Conclusion