In TCGA Copy number variation (CNV) data there is a column with title Num_Probes. What is the meaning of probe number with respect to the sample data below?

Chromosome  Start   End Num_Probes  Segment_Mean
1   61735   62152   4   1.1973
1   62920   12777697    6514    2.2882

According to wikipedia, probes are usually 100-1000 bases long. Then does it mean in the first row above that, it took 4 probes to identify the region(61735 - 62152). In that case what would be the meaning of Segment_Mean?


1 Answer 1


The data you posted looks like it was produced by GISTIC, a program commonly used by TCGA to detect copy number changes. Assuming the data really is GISTIC-produced, my understanding is that "Segment_Mean" refers to the average Log2 Ratio of the probes in that particular segment. Looks like the copy-number of your 4-probe segment in your example is slightly less than half the copy-number of the longer segment.

You can also try using the GISTIC Google-Group to learn more.

  • $\begingroup$ 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 important than 1st CNV region? I don't understand the importance of segmentation here. $\endgroup$ Jul 20, 2017 at 11:55
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    $\begingroup$ Simplistic Answer: higher segment mean == higher copy number. The number for probes for each region probably doesn't matter. Also, a difference of 0.1 between each regions' segment mean probably doesn't matter much either. $\endgroup$
    – Slavatron
    Jul 20, 2017 at 20:23

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