Abstract
BackgroundOne of the most important somatic aberrations, copy number variations (CNVs) in tumor genomes is believed to have a high probability of harboring oncotargets. Detection of somatic CNVs is an essential part of cancer genome sequencing analysis, but the accuracy is usually limited due to various factors. A post-processing procedure including manual review and refinement of CNV segments is often needed in practice to achieve better accuracy.ResultscnvCurator is a user-friendly tool with functions specifically designed to facilitate the process of interactively visualizing and editing somatic CNV calling results. Different from other general genomics viewers, the index and display of CNV calling results in cnvCurator is segment central. It incorporates multiple CNV-specific information for concurrent, interactive display, as well as a number of relevant features allowing user to examine and curate the CNV calls.ConclusionscnvCurator provides important and practical utilities to assist the manual review and edition of results from a chosen somatic CNV caller, such that curated CNV segments will be used for down-stream applications.
Highlights
One of the most important somatic aberrations, copy number variations (CNVs) in tumor genomes is believed to have a high probability of harboring oncotargets
Upon manual review we found this segment contain a sub-segment of copy number loss, as supported by three lines of evidences: 1) decreasing read depth in tumor over normal, as shown in the tracks of read depth and the track of logR ratio of tumor to normal; 2) the corresponding change of B Allele Frequency (BAF) pattern as shown in the BAF track; 3) as shown in Fig. 3, the breakpoints of this sub-segment are in the exact position separating the soft-clipped part from the matched part of multiple split reads in the tumor bam, but not in the normal bam
Normal; 2) there is no clear change of BAF pattern as shown in the BAF track; 3) the breakpoint positions are not supported by either split reads or discordant read pairs
Summary
One of the most important somatic aberrations, copy number variations (CNVs) in tumor genomes is believed to have a high probability of harboring oncotargets. Detection of somatic CNVs is an essential part of cancer genome sequencing analysis, but the accuracy is usually limited due to various factors. A post-processing procedure including manual review and refinement of CNV segments is often needed in practice to achieve better accuracy. CNV is one of the most important somatic aberrations, and has been identified as the driver event in many cancer types [1, 4, 5]. Accurate detection of CNVs from massive amounts of raw NGS data of the cancer genome requires sophisticated computational algorithms, with read depth, B Allele Frequency (BAF), split reads, and discordant read pairs derived from sequence read mapping as the primary input [7]. A number of computational methods have been developed to identify CNVs using NGS data [7, 8]. The concordance of different CNV calling tools is especially low in real applications [10,11,12], suggesting that caution and care are needed to interpret and report the calling results, and additional post-processing might be needed to achieve maximum accuracy
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