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. CNVs can also be detected from next generation sequencing (NGS) data. CNVs can be detected by a variety of laboratory methodologies including conventional cytogenetics, fluorescence in situ hybridisaton (FISH) and single nucleotide polymorphism (SNP) array. For example, patients with chronic lymphocytic leukaemia with a copy number loss at the TP53 locus have inferior outcomes when treated with chemoimmunotherapy 1 and should preferentially be treated with non-chemotherapy based approaches 2. ĭetection of copy number variations (CNVs) is an important and clinically relevant part of characterizing the genomic aberrations in patients with malignancy.
CNspector is written in R and the source code is available for download under the GP元 Licence from.
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 a web-based clinical variant browser tailored to the clinical application of next generation sequencing for CNV assessment. 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. We illustrate the utility of CNspector at different genomic scales across a variety of sample types in a range of case studies. 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. 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. However, clinical assessment of copy number variations (CNVs) and large-scale structural variations (SVs) is still challenging. 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.