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a Plasmid DNA p88-D-21 was quantitated spectrophotometrically, and dilutions containing the indicated copy number of target sequence were added to each polymerase chain reaction (PCR) assay.
The main idea is that for each manually annotated region, one can check whether an algorithm predicts the indicated copy number or breakpoints in that region.
f Plasmid DNA pISR-Dfrag-D6 was quantitated spectrophotometrically, and dilutions containing the indicated copy number of target sequence were added to each PCR assay.
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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.
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.
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.
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