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GenoCensus™: Analysis and Visualisation of Genomic Copy Number Variation
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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