Question: What is the importance of probe no and segmentation mean in Copy Number Variation data
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gravatar for akij
23 months ago by
akij90
akij90 wrote:

I was given to do some statistical analysis on Copy number variation(CNV) data of some cancer types from TCGA. Should I consider probe number and segmentation mean in the calculation? In my understanding, chromosome and start, end numbers and gain/loss are important. Is it important to know how many probe numbers were used or what is the segmentation mean of certain CNV i.e if a a sample has a CNV gain at 12792599 - 13278863 with probe no 100 and segmentation mean 0.4 and if another sample also has a CNV gain at the same position 12792599 - 13278863 with probe no 200 and segmentation mean 0.5, does this mean 2nd CNV region is more or less important than 1st CNV region? I never seen any article to use probe number and segmentation mean in their calculation though. Some example data

 Sample                                  Chromosome Start   End Num_Probes  Segment_Mean
    AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   61735   12785720    6509    0.0628
    AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   12792599    13278863    57  -0.5061
    AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   13326062    25256850    7563    0.0667
    AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   25266637    25336819    32  0.6428
    AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   25336853    57755402    18550   0.0636
    AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   57757884    69368291    8418    0.1007
    AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   69375800    84595696    9774    0.0659
sequencing cnv • 1.1k views
ADD COMMENTlink modified 23 months ago • written 23 months ago by akij90
1

Both number of probes and segment mean are important. You might read the official DNAcopy tutorial to start (in several plot the segment mean is plotted): https://bioconductor.org/packages/release/bioc/vignettes/DNAcopy/inst/doc/DNAcopy.pdf

ADD REPLYlink written 23 months ago by Fabio Marroni2.2k

Thanks for the reply. Could you tell me what exactly probe no and segmentation_mean actually means?

ADD REPLYlink written 23 months ago by akij90
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