Tuesday, April 3, 2012

Eliminating Highly Polymorphic Genes from Whole Exome Sequencing

Whole exome sequencing yields thousands of variants for each individual sequenced.  Many of these variants are in genes that are highly polymorphic or in regions that do not sequence well and therefore would not be of interest when searching for a disease-causing variant.  This is because any frequently mutated gene containing many deleterious variants will have a low probability of containing the disease-causing mutation.  Also, if the gene is in a region that does not sequence well then a high number of variants will be often reported.  When you find such variants, this would be considered a false positive.   There is a big interest in detecting these false positive signals and eliminating these variants from the list reported back from whole exome sequencing.  

A paper was just published this month in Human Mutation describing a way to do this.  They published several lists of genes for researchers to use in their own projects.  The researchers hypothesize these genes will not contain the disease-causing mutation.   This list of genes could be an incredibly useful tool to filter out highly polymorphic genes or genes that simply do not sequence well.

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