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For each gene and its flanking sequence, a heatmap was generated to indicate copy number of probes assayed.
The CNstate ranges from 0 to 4: normal CN corresponds to CNstate 2; CNstates 0 and 1 indicate copy number loss; CNstates 3 and 4 correspond to copy number gain.
Black dots indicate probes with normal copy-number, green dots indicate copy-number gain, and red dots indicate copy-number loss.
We used a sliding window to identify regions where the majority of bases had a ratio < = 0.6, indicating copy number loss, or > = 1.4, indicating copy number gain.
Red colour indicates copy number gain or higher gene expression and blue colour indicates copy number loss or lower gene expression in CNV and FPKM tracks, respectively.
The amount of PCR product, dependent on ligation, indicates copy number.
The darkest boxes and thick arrows (Fig. 1) indicate copying behavior and have been added relative to the previous model.
Distribution of ratio data within each region approximated a normal curve, with the position of the peak indicating copy number.
Genotypes and copy numbers are displayed as sequential blocks of which color indicates genotype, horizontal coordinate indicates position on the chromosome and vertical coordinate indicates copy number.
Each RAR marker was coded as 0 or 1 based on the copy number status; 0 indicates no copy number variation and 1 indicates copy number change in the marker region.
Genes with z scores > = 10 were considered high-level amplifications; a z score > = 3 indicates copy number gain and < = −3 copy number loss.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com