When working with NIPT results, I saw that all NIPT results also had GC content calculated before analyze the results. I have searched but found no answer about the affect of GC content on NIPT results. Can anyone explained for me please? Thank you
NIIPT can be performed in various variations and for different purposes. Is it chromosome abnormalities test in your case? If so, extreme GC biases lead to decreased sequence coverage.
Yes, I'm working with chromosome anoploid. So if the GC does not meet the threshold, its mean that all comes from high signal region?
It is more difficult to quantify DNA in extreme GC regions so they may show increased/decreased coverage despite the absence of underlying aneuploidy. However if you actually work with really large genomic windows (standard for low-pass WGS that is used for aneuploidy detection), say, 50KB, it won't be that of a problem, there is not so many extreme GC windows at this scale.
Filtering them or not is your choice, which depends on desired sensitivity, specificity, size of the desired detectable variants.
Thank you very much
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy