Fig 1.
Quantitative stacked histograms using 96 HCC samples on Affymetrix 500K Human Mapping Array data from [1].
A) Frequency of CNV and cn-LOH events along the genome. The left axis indicates the frequency of gains or losses among the 96 samples and the legend below indicates the number of copy number gains or losses from the reference baseline. The black line indicates the frequency of cn-LOH along the genome in negative ordinates. B) Frequency of homozygous/heterozygous CNVs along the genome. Copy-neutral events / gains and losses are respectively displayed in positive and negative ordinates.
Fig 2.
Quantitative stacked histograms produced by aCNViewer showing the frequency of CNVs and cn-LOH along the genome in HCCs.
Quantitative stacked histograms generated using A) 96 freely available HCC Affymetrix 500K Human Mapping Array data [1], B) 243 HCC WES experiments from [2] and C) 317 pooled HCCs from both SNP and WES experiment data.
Fig 3.
Overview of the different steps handled by aCNViewer.
aCNviewer can process Affymetrix and Illumina SNP arrays as well as NGS data. LRR and BAF files are obtained after processing SNP raw data by PennCNV for Affymetrix and a threshold quantile normalization (tQN) for Illumina and subsequent use of ASCAT for CNV and cn-LOH detection. For NGS data, paired tumoral and non-tumoral whole exome/genome sequencing bam data are converted into seqz format and processed by Sequenza for CNV detection. aCNViewer converts CNV data into a CNV matrix with the window size defined by the user and which is subsequently used to compute dendrograms and heatmaps. Quantitative stacked histograms can be generated using the same matrix or a matrix of segments at base resolution (default behaviour). Text files are also available through GISTIC [33] providing a robust statistical way to select recurrent CNVs.
Fig 4.
Hierarchical clustering of HCCs from [1] according to BCLC staging and based on CNVs.
A) Dendrogram representation. B) Bi-dimensional heatmap. A 2Mb window length is used for computation. The chromosomes of each window are shown on the right and the BCLC staging of each tumor is given on top of the bi-dimensional heatmap.
Table 1.
aCNViewer main options.