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GenoCensus ™ :  Analysis and  Visualisation of Genomic Copy Number Variation E'Krame Ayari, Abdel Benajjou, Jean-Paul Sara...
Identification of recurrent gain/loss patterns on chromosome 11 among many tumour samples. (courtesy CIT, LNCC, Paris) Com...
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GenoCensus™: Analysis and Visualisation of Genomic Copy Number Variation

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GenoCensus™: Analysis and Visualisation of Genomic Copy Number Variation.

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GenoCensus™: Analysis and Visualisation of Genomic Copy Number Variation

  1. 1. GenoCensus ™ : Analysis and Visualisation of Genomic Copy Number Variation E'Krame Ayari, Abdel Benajjou, Jean-Paul Saraiva, Stephanie Maillard, Pierre Lindenbaum, Emmanuel Martin, Philippe Gesnouin, Frederic Tores and Peter Brooks IntegraGen SA, Evry France <ul><li>GenoCensus ™ is a stand-alone Java program for Unix or Windows that processes files of numerical data generated from analysis of microarray images. </li></ul><ul><li>The program invokes BioConductor R modules for some tasks. </li></ul><ul><li>IntegraGen has developed 500 kb resolution BAC arrays (IntegraChip ™ ) with 5244 clones and by default the program uses annotations of chromosomal locations that are specific for these BAC clones. </li></ul><ul><li>Preliminary experiments indicate that BAC arrays are capable of detecting lower levels of mosaicism than high density oligonucleotide arrays. </li></ul><ul><li>IntegraChip ™ manufacture is sufficiently robust to permit inter-slide “single colour” analysis. </li></ul>Cy5 : Test DNA Cy3 : Reference DNA Spot replicates: 4 replicate spots per clone: 2 spots in each block, each block in 2 zones block 5244 BAC clones Median of 0.5 Mb between clones. <ul><li>Numerous controls including Cot DNA and Rice BACs. </li></ul><ul><li>Each block has 2 dilution series of pools of BACs for internal QC of normalization. </li></ul>Clone identity by end sequencing Data processing options are easily modified to adapt the analysis to different experimental contexts. IntegraChip ™ provides high signal to noise ratios and homogeneous low ratios for autosomal clones. Thus low levels of mosaicism are readily detected. The figure reveals that about 10% of the cells in a stem cell culture have 3 copies of chromosome 12. zones IntegraChip ™ V7 Whole genome coverage Stem Cell Heterogeneity Summary Click-drag zooming functionality. GenoCensus ™ whole genome view 0.5 Mb median resolution 20% euchromatin coverage Image analysis GenoCensus ™ Array Image (TIFF) GenePix R - Spot Segmentation Image analysis gpr file flat file (txt) Filters (intensity, background, replicate variation…) Normalisation (Block Lowess) Group replicates Gain/Loss Regions (CBS BioConductor R module DNA Copy) Genomic position profiles GenoCensus ™ processes array image numerical data such as from GenePix (Axon) gpr files. The next revision of GenoCensus will include image analysis with the BioConductor module SpotSegmentation. . . . . Chromosomal profiles can be viewed with or without cytogenetic bands. This example shows a dye reversal from a “trio design”. Plotting average ratios of the dye swap is an option. Dye Swap Trios
  2. 2. Identification of recurrent gain/loss patterns on chromosome 11 among many tumour samples. (courtesy CIT, LNCC, Paris) Comparison of BAC arrays with Illumina HapMap 317k arrays IntegraGen’s full service Illumina platform enabled comparison of the 2 platforms with identical DNA samples. Illumina’s gain/loss calling algorithm obliges compromises between resolution and calling of false positives. The distinction between the region of loss is more pronounced with the IntegraChip ™ BAC array, implying that the BAC array will provide a greater sensitivity to detect low levels of mosaicism. Pink bars: regions called as losses by Illumina software. The deletion includes both regions. The interruption is coincident with a CNV. Detection of tumour DNA aberrations in the presence of a large excess of DNA from normal cells. Tumour DNA with multiple gains and losses. Regions of gain and loss beyond the user-specified threshold are tabulated for export. Currently we use Circular Binary Segmentation by invoking the BioConductor module “DNA Copy”. Other algorithms can be readily integrated into the Java program. Hot links connect directly to the Toronto TCAG browser to determine if the region contains documented CNVs or segmental duplications. Inter-array analysis of copy number changes. Tumour DNA heterogeneity Recurrent patterns in tumour DNA Calling regions of gains and losses

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