Question: What is the importance of probe no and segmentation mean in Copy Number Variation data
gravatar for akij
3.4 years ago by
akij100 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 • 1.7k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by akij100

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):

ADD REPLYlink written 3.4 years ago by Fabio Marroni2.6k

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

ADD REPLYlink written 3.4 years ago by akij100
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