Question: Detecting CNV can't cover aneuploidy situation
gravatar for CY
2.9 years ago by
United States
CY470 wrote:

CNV detection in cancer sample can be done based on either mapping distance of paired-end reads or read depth. However, The mapping distance strategy is not able to detect CNV in case of aneuploidy, right? Because aneuploidy produces CNV while the mapping distance of paired-end reads on each chromosome still remain unchanged. Does this mean the read depth strategy is better since it cover both situation? Can someone share some insight?

cnv sequence next-gen • 728 views
ADD COMMENTlink modified 2.9 years ago by WouterDeCoster43k • written 2.9 years ago by CY470
gravatar for WouterDeCoster
2.9 years ago by
WouterDeCoster43k wrote:

Read depth is very noisy due to amplification biases, general uneven amplification and random sampling from a library. So it's definitely not the holy grail of CNV calling methods. As often, the most powerful methods combine read depth, mapping distance and split reads to get the most reliable calls.

ADD COMMENTlink written 2.9 years ago by WouterDeCoster43k

Maybe important to add that in whole-exome data, because you only sequence 1-2% of the genome, you don't see most of the breakpoints directly. So you are pretty much left with read-pileups.

Then there is unfortuantely a huge variance in quality of whole-exome data. Great sequencing centers get coverage now fairly even and you get clean somatic copy number calls out of high quality data. Garbage in, garbage out.

ADD REPLYlink written 2.9 years ago by markus.riester490
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