Why GC-content normalization for CNV analysis?

Question

[mittu1602]

Hello all,

I am working on CNV analysis tools of which some tools perform GC-normalization on tumor samples or look for mappablity read count on tumor samples. Usually this is done in the absence of control samples.

It would be helpful if anyone can explain or share something relevant as to how GC-normalization helps in analysing copy number variation.

Thank you

Answer 1

[Jan Oosting]

There are both technical and biological reasons to do GC-content normalization.

Technically, both PCR efficiency of target sequences, and binding of probes to target sequences are related to GC content of the sequence. Especially without normal samples this is a problem.

The technical issues could be solved by testing paired normal sampled, but we still see copy number effects that show a relationship with GC-content. It appears that replication timing during the cell cycle is related to GC-content. Because the growth-fraction in tumor tissue is generally higher than in normal tissue, these effects can be seen in copy-number profiles. GC-content is easier to obtain than replication timing, which is why generally GC-content normalization is used.