Question: Detecting CNV can't cover aneuploidy situation
gravatar for CY
22 months ago by
United States
CY330 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 • 558 views
ADD COMMENTlink modified 22 months ago by WouterDeCoster39k • written 22 months ago by CY330
gravatar for WouterDeCoster
22 months ago by
WouterDeCoster39k 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 22 months ago by WouterDeCoster39k

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 22 months ago by markus.riester400
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