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CenterForMedicalGeneticsGhent / WisecondorX

WisecondorX — An evolved WISECONDOR
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Finding microdeletions #35

Closed GreeshmaThulasi closed 5 years ago

GreeshmaThulasi commented 5 years ago

Hi, I have data of patient with a known microdeletion (DiGeorge). The patient is mildly affected and is pregnant and hence done NIPT for finding the chance of Digeorge in their fetus. I have the cfDNA BAM file of 8 million reads. I tried to look at the microdeletion and got a z-score of -33.

22 19000001 21400000 -0.7799 -33.09683751274384 This is evident that there is a deletion at the desired location.

But my question is how to distinguish whether it is of maternal deletion or fetal deletion?

Seeking your response Greeshma Thulasi

leraman commented 5 years ago

You can always make an educated guess based on the fetal DNA fraction. The certainty of this guess would increase with the fetal fraction. That being said, using sWGS data only, you can actually never make an accurate prediction whether the fetus is affected for this microdeletion, because of its maternal presence. In theory, you'll need an additional experimental procedure, like CVS or amniocentesis.

GreeshmaThulasi commented 5 years ago

Thanks for the reply. So the deletion or duplication of the fetus is predicted on the assumption that the mother is normal. Right?

leraman commented 5 years ago

With NIPT, yes.