CNV Radar: an improved method for somatic copy number alteration characterization in oncology

BMC Bioinformatics
David SoongMichael Schaffer

Abstract

Cancer associated copy number variation (CNV) events provide important information for identifying patient subgroups and suggesting treatment strategies. Technical and logistical issues, however, make it challenging to accurately detect abnormal copy number events in a cost-effective manner in clinical studies. Here we present CNV Radar, a software tool that utilizes next-generation sequencing read depth information and variant allele frequency patterns, to infer the true copy number status of genes and genomic regions from whole exome sequencing data. Evaluation of CNV Radar in a public multiple myeloma dataset demonstrated that CNV Radar was able to detect a variety of CNVs associated with risk of progression, and we observed > 70% concordance with fluorescence in situ hybridization (FISH) results. Compared to other CNV callers, CNV Radar showed high sensitivity and specificity. Similar results were observed when comparing CNV Radar calls to single nucleotide polymorphism array results from acute myeloid leukemia and prostate cancer datasets available on TCGA. More importantly, CNV Radar demonstrated its utility in the clinical trial setting: in POLLUX and CASTOR, two phase 3 studies in patients with relapsed or refractory mu...Continue Reading

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Citations

Oct 16, 2020·Blood Cancer Journal·Phuc H HoangRichard S Houlston
Aug 19, 2021·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Keisuke SawadaJun-Ichi Tamaru

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Methods Mentioned

BETA
exome sequencing
PCR
exome-sequencing
exome-seq

Software Mentioned

Radar
ExpressionAnalysis
Partek Genomics Suite
Genome Analysis Toolkit ( GATK )
CoNIFER
Genome Analysis Tool Kit
CNV
CNVkit
CNV Radar
GATK

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