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Genomic Identification of Significant Targets in Cancer

Hi,

I search a lot but I just more confuse. I was wondering if someone could help me understand the differences between GISTIC data and Log2 ratio for copy number alteration in tumor cells? Do they come from the same data and are sort of different interpretations or they are totally different.

I would be appreciated if you could help me out.

Best,

cnv r gistic genome
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updated by Ram Ram • written by g_draculla • g_draculla

1 answer

The Log2Ratio is simply a comparison of the coverage in the tumor compared to the coverage in the normal sample. It simply tells you whether a region is duplicated or deleted in the tumor. It is actually the log2 of the ratio between these two values, so a L2R of 0.5 means that the number of reads covering the region is the doble in the tumor compared to the normal.

The GISTIC scores are actually calculated using a more complex algorithm, taking into account the background mutation rate, the location of the region with the respect to the chromosome arms, etc.. See the original GISTIC2 paper, and in particular figure 1, for more details.

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

I'd add that the log2 ratio is calculated per-tumor, while the GISTIC algorithm takes a cohort of samples and finds regions that are amplified or deleted more frequently than expected by chance across that population.

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updated by Ram Ram • written by Chris Miller Chris Miller

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