Interpretation of TCGA CNV data

Question

[goletrus]

Hi,

TCGA level 3 data contains CNVs given as values -2, -1, 0, +1 or +2. The -2 and +2 correspond possible homozygous deletion or high-level gain, respectively. The cBio portal FAQ says that "-1 is a shallow loss (possibly heterozygous deletion)" and "1 indicates a low-level gain". On the other hand, the cBio portal omits the -1 and 1 CNVs when calculating total alterations in a gene. Are these -1 and 1 values biologically meaningful signs of alterations or should they be omitted?

Thank you for your help already in advance!

Answer 1

[raunakms]

TCGA level 3 data is the normalized segmentation values where the value 0 means diploid state of the chromosome. Any positive value means amplification and negative means deletion. We must remember that in a copy-number gain or loss event, a large segment of chromosome (or even whole chromosome) is amplified or deleted which often contains multiple genes. The CNV normalized values -1 or 1 are the low confidence events which could often be an artifact. These values can sometimes introduce noise during analysis so usually only high confidence values are used.

[H.Hasani]

Hi,

I used Firehose to download Gistic2 results. I have Level4 and the tables typically range between [-1.26300, 4.56500 ], I couldn't find any documentation explaining these numbers? i.e. I thought GISTIC ranges between -2 & 2? could you please help?