Why GC content is important on NIPT results?
0
0
Entering edit mode
24 days ago
khanhlpbao • 0

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

NGS NIPT Sequencing • 311 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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?

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Thank you very much

ADD REPLY

Login before adding your answer.

Traffic: 2487 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6