de novos incorporated into compound het model

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May 4, 2018, 6:47:10 PM5/4/18
to gemini-variation
I'm loving GEMINI as the new tool for diagnosing rare genetic diseases at the BC Children's Hospital, and really appreciate the predefined and unit-tested inheritance models. 

I have a question about the compound het inheritance models, which are used to identify candidate autosomal recessive disease genes. Specifically, I want to know if de novo mutations (DNMs) get incorporated into the compound het model. The situation I'm hoping to clarify is the following:

We have a DNM in a proband with two healthy parents. The DNM is in an autosomal recessive disease gene, and alone we are not convinced it is producing the phenotype. I am wondering if the compound het model would include this DNM to be paired with other potentially damaging het variants in the proband, perhaps a damaging variant inherited from one of the two parents. 

If this is unclear I am happy to clarify.


Brent Pedersen

May 21, 2018, 11:13:14 AM5/21/18
to Phillip Richmond, gemini-variation
Hi Phil, sorry for the delay.
currently, a DN+compound het will not be found correctly with gemini.
I need a couple of weeks to sort out all known deficiencies of the
inheritance models, including this one. I hope to have this fixed in
the next couple of months.
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