LOH determination from panel data

Question

[ghernandezv]

Hi everyone!

I'm analyzing data from a patient using a panel of selected genes. I found one clearly pathogenic mutant but found no second apparent mutation (the inheritance of the disease is recessive) and I thought about the possibility of a LOH to explain what I'm seeing in this patient.

It is possible to study the LOH of data coming from a pane with Rl? I have a vcf file and I think I could retrieve the fastq.

Thanks in advance!!!

Gonzalo

[German.M.Demidov]

other copy of the gene may be methylated or there could be CNV there - so not necessarily ROH is causative

but you may detect it with PLINK