CNV analyzer¶

The CNV Analyzer report builder annotates and summarizes copy number variation (CNV) calls from the CNVkit caller for tumor samples. This report builder provides an overview of CNVs discovered from tumor samples with annotation of known CNVs in similar locations previously reported in COSMIC.

Example use case¶

The user is interested in identifying CNVs in specific tumor samples, genes involved in specific CNVs, and if any CNV in this location has been previously reported in COSMIC.

Description of the algorithm¶

CNVs from tumor samples selected from subjects are joined with Ensembl gene data to get the gene range for each CNV (if available), including total gene count, genes at the start position, and genes at the end position. If the CNV has the same gene range as CNVs previously identified in COSMIC CNV reference data, the COSMIC CNVs are listed in the COSMIC columns in the output, including CNV ID, tumor ID, primary site, etc. as annotation.

Interpreting the output¶

Output columns can be filtered by selecting one of the following Perspective views (see also Column descriptions):

Default view - Shows the CNVs identified from selected tumor samples which include the candidate genes provided in the candidate_gene_report selector or candidate_gene_report_grid input fields.
All Amplifications - Displays only CNVs with a copy number greater than the min_amp_copy_number.
All Loss and Deletions - Shows only CNVs with a copy number less than “2”.
Candidate Gene Amplification - Shows CNVs that include the candidate genes provided in the candidate_gene_report_selector or candidate_gene_report_grid fields and a copy number greater than the min_amp_copy_number.
Candidate Gene Deletions - Shows CNVs that include the genes provided in the candidate_gene_report selector or candidategene_report_grid fields and a copy number less than “2”.

Detailed CNV information such as Copy_number, mutation_type, Segment_Mean, Num_Probes, CNV_length, and CNV_size is displayed in the corresponding output columns.

The gene_symbol column lists the genes included in each CNV.

The Gene_range column shows the genes at the start position and end position of the CNV.

The PN and Flag column groups can provide information about the presence of other data types that are available for both the tumor sample and the corresponding normal sample, which can be useful for a multi-omic study.

Column descriptions¶

Report output columns and descriptions¶
Group	Column	Description
Basic	Chrom, End	CNV coordinates
	PN	Sample/subject name selected individually or as part of a TCGA project as input from which the CNV is identified
CNV	gene_count	Total number of genes included in CNV length
	length	Length of the CNV in the chromosome in base pairs
	size	Length of the CNV in the chromosome in KB or MB
COSMIC	CNV_ID	Unique ID for a similar CNV (i.e., with the same gene range) reported in COSMIC
	gene_range	The first and last gene included in CNV length in COSMIC
	ID_SAMPLE	Sample ID of similar COSMIC CNV
	ID_STUDY	Study ID of similar COSMIC CNV
	ID_TUMOR	Tumor ID of similar COSMIC CNV
	MUT_TYPE	Mutation type of similar CNVs: gain or loss
	Primary_histology	Primary histology of similar CNV reported in COSMIC
	Primary_site	Primary site of tumor of similar CNV reported in COSMIC
	SAMPLE_NAME	Sample name of the similar CNV reported in COSMIC
	TOTAL_CN	Copy number count of similar CNV reported in COSMIC
Flag	CNV_normal	Logistic result whether the CNV normal sample is available
	CNV_tumor	Logistic result whether the CNV tumor sample is available
	Methy_normal	Logistic result whether the methylation normal sample is available
	Methy_tumor	Logistic result whether the methylation tumor sample is available
	miRNA_norma	Logistic result whether the miRNA normal sample is available
	miRNA_tumo	Logistic result whether the miRNA tumor sample is available
	RNAseq_normal	Logistic result whether the RNAseq normal sample is available
	RNASseq_tumor	Logistic result wether the RNAseq tumor sample is available
	WES	Logistic result whether the WES sample is available
Gene	range	First gene and list gene included in CNV length
	symbol	List of genes included in CNV length
PN	CNV_normal	Paired normal sample ID for CNV
	Methyl_normal	Paired normal sample ID for methylation
	Methyl_tumor	Tumor sample ID for methylation
	miRNA_normal	Paired normal sample ID for miRNA
	miRNA_tumor	Tumor sample ID for miRNA
	RNASeq_normal	Paired normal sample ID for RNAseq
	RNASeq_tumor	Tumor sample ID for RNAseq
	WES	Sample ID for WES
Other columns	Candidate_genes(option)	List of candidate genes included in CNV length if they were specified as candidate_gene_report_selector or candidate_gene_report_grid input parameters
	Copy_number	Total count of copies of the CNV
	Disease_type	Disease type of the Subject in which the CNV was identified
	mutation_type	Mutation type of the CNV: gain or loss
	Num_Probes	Probe counts for the CNV
	Primary_site	Primary site of the disease of the Subject
	Segment_Mean	Log2 ratio of the tumor intensity to the normal intensity, which converts to an absolute copy number by (2^seg_mean)*2
	startx	Start position of the CNV
	SubjectID	Patient ID
	TCGA_project	Tumor type in TCGA project

Perspective views¶

Perspectives subtabs focus on subsets of the columns in the Default view.

Perspectives¶
Perspective	Description
All Amplifications	Shows all amplified CNVs (if CNV is located on the Y chromosome and the copy number is greater than “1”; if CNV is not located on the Y chromosome and the copy number is greater than the value of min_amp_copy_number, which is “3” by default)
All Loss and Deletions	Shows all deleted CNVs (if CNV is located on the Y chromosome and the copy number is equal to “0”; if CNV is not located on the Y chromosome and the copy number is less than “2”)
Candidate Gene Amplifications	Shows all amplified CNVs present in candidate genes (if selected in the input parameters)
Candidate Gene Deletions	Shows all deleted CNVs in candidate genes (if selected in the input parameters)
Default view	Shows all CNVs, including amplifications and deletions