Question: loss of function prediction
0
gravatar for RT
5.4 years ago by
RT340
European Union
RT340 wrote:

Hello everyone,

I am using snpeff for variant annotation and effect prediction. For my genes of interest, I am looking for the disrupted gene models in the population (snp data for 50 individuals). Loss of function analysis or gene disruption is done based on SNPeff criteria's- loss of start, stop gain etc. Few of the positions are heterozygous. My question is how should I treat these positions? Suppose for a heterozygous position C/G, G causes an early stop codon. We don't know which allele is expressed or dominating? So for these cases, I am concluding that the gene model is broken. Is this correct to say?

Thanks.

snpeff disrupted gene models • 2.1k views
ADD COMMENTlink modified 5.4 years ago by Devon Ryan95k • written 5.4 years ago by RT340
0
gravatar for Devon Ryan
5.4 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

Well, it "might" be broken. You can get dosage compensation to correct for the non-functional allele, but the only way to find that out is to do the RNAseq and/or Western blot.

ADD COMMENTlink written 5.4 years ago by Devon Ryan95k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1614 users visited in the last hour