DNENRICH - question re the gene recurrence statistic

[Chey Loveday]

Hi there,

 

I have read your paper and the info on the DNENRICH website and have a question that would really appreciate some clarification on.

 

I have a bunch of data from a relatively large cohort (n=500) of child-parent trios with a relatively heterogeneous phenotype. I’ve identified de novos in four unrelated individuals across three paralagous genes. I know that this observation unequivocally implicates these mutations as being causal. However, I would like to formally assess the probability of obtaining this result by chance. Is it possible to use the gene recurrence test to calculate this? Does it make sense to use your software for this type of calculation?

 

My background is more biological than statistical, so please do forgive me if I’m asking what is an obvious question!

 

Many thanks in advance for your consideration.

 

Chey

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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[Menachem Fromer]

Hi Chey,

Thanks for the question. This indeed  is exactly what the software was intended to do.

You'd need to define some sets of genes to be tested.

For example, in your case, you'd have to define a .set file stating that those genes are all among a set of some paralogous genes.

More generally, if you clustered all genes into sets of paralogous genes (say 100 sets of 2 or more genes that are paralogues), you can then test for having more than expected mutation numbers within particular paralagous gene functions.

Conceptually, these sets of genes would be no different than a .set file grouping genes into their sub-cellular compartment or enzymatic function, etc...

Best,

Menachem

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