CONAN - Search

CONAN (COpy Number ANalysis) is a copy number analysis tool which searches for LOH (loss of heterozygosity), Homozygous Deletions and Amplifications across the COSMIC dataset. All samples analysed with PICNIC or ASCAT (where the total copy number and minor allele copy number are known) are searched.

CONAN replaces the old version at http://www.sanger.ac.uk/genetics/CGP/conan which is no longer available. The new version uses minimum coordinate ranges for copy number segments (high confidence) which gives more reliable results than the previous version which used maximum coordinate ranges (lower confidence). The new version also uses the GRCh37 coordinate system.

The search can be for a gene symbol, ensembl gene id or a region in the format chr:start-end eg 22:15000001-15005000.

Two output options are available for results. 'Graphical View' will list data in tables and link through to CNV ChromoView where the CNVs are plotted by genome position. 'Export View' saves data to a CSV file with the following columns:

SAMPLE,TISSUE,CHROMOSOME,SEGMENT_START,SEGMENT_END,TOTAL_COPY_NUMBER,MINOR_COPY_NUMBER,CLASSIFICATION

Where the classification column will show one the following: AMP (amplification), HD (homeozygous deletion) or LOH (loss of heterozygosity)

Definitions

Minor Allele: the number of copies of the least frequent allele eg if ABB, minor allele = A ( 1 copy) and major allele = B ( 2 copies).

Copy Number: the sum of the major and minor allele counts eg if ABB, copy number = 3.

Amplification

Where the entire gene footprint, or region is covered by one or more copy number segments each with copy number greater than 7

Homozygous Deletion

Where both alleles are deleted for part or all of a coding region within the gene footprint. Coding regions are defined from COSMIC gene annotations.

LOH (loss of heterozygosity)

Where one allele is deleted across the entire gene footprint and the total copy number is 7 or less ie not amplified. The gene footprint must be covered by a single copy number segment ie there is no change in copy number state within the gene footprint

CONAN - Gene View

This table shows a list of possible gene names for a CONAN search. This page only appears if the search could not find a unique gene name the the search term. Click a gene name to start a CONAN search.

CONAN - Table View

This table shows the results of a CONAN search. Copy number feature counts broken down by tissue are shown in the table. To view all the samples counted for any copy number feature/tissue combination, select the count and click 'Go'.

CONAN - Sample View

This table shows all the samples with the selected copy number feature/tissue type in the gene or genomic region of interest. Clicking the feature type in the last column links to the CNV ChromoView page showing a table and plot of all the copy number variants.