Exome sequencing analysis of Retinitis pigmentosa

By Edgardo Lopez

Retinitis pigmentosa (RP) is a degenerative disease that is characterized by blindness and retina spots formed by pigments that blocks the cornea. This disease doesn’t show during early stages of development until you pass puberty. In a genetic aspect this disease is consider a rare disease since there are many genetic possibilities to obtain it from your parents as an autosomal dominance (adRP), autosomal recessive (arRP), X-linked (xlRP), or even transmitted as a mitochondrial or digenic trait in the most rare cases.  The RetNet database has report that there are 62 genes that are associated to RP. Some of those genes are mutations or defected variants of other genes like RHO, RPGR or USH2A to gave some examples. For a better reference of how this disease behaves, a group of scientist analyzes the frequency of mutations and genes that are responsible of RP in a population in China. Performing better analysis with emerging technique like next generation sequencing will provide a faster way to achieve a better molecular diagnostic of the disease in the patient or even on a population (like groups of families). In this study they use Whole Exome sequencing (WES) that basically is the nucleotide date obtain from the whole genome protein coding section to detect variants in 62 causative genes from 157 unrelated Chinese families with the disease. To perform the WES this group of scientist use blood samples from leukocytes of peripheral venous to obtain the genomic DNA. NimbleGen SeqCap EZ Exome system was use to obtain the Exome library from the DNA samples and Sanger sequencing also was used to confirm the gene variants that were identified by WES.

An example of a retina without the disease and with RP(picture A) and also how a person with RP sees through time(picture B). 

A

B

As a result from the WES analysis 244 candidates variants were detected from 60 of the 62 genes that are highly related to RP and 240 of those candidates were confirm also by Sanger sequencing. From the bioinformatics analysis 50% of the variants that were identified are novel to be consider potential pathogenic mutations. More that 30% of the mutations were link to heterozigocity associated with adRP, more than 40% of homozygous or compound heterozygous mutations associated with arRP, and less that 15% were hemizygous mutations associated with xlRP. The most frequent genes found in the 157 families were RHO, USH2A and RPGR that are found in adRP, arRP and xlRP.

In the following picture you can see the proportions of individual genes on the 157 families.  

For some strange cases of RP that doesn’t have that same behavior, future studies are expected to include possible pathogenic variants in noncoding regions and deletions in the whole Exome.  Using next generation sequencing helps to achieve great results in this article to determinate pathogenic mutations in RP patients that other techniques wouldn’t and approximately 50% of the population appears with the 60 genes that has been detected in previous studies of RP. This article shows a better understanding of the relationship between genotype and phenotype in a certain disease that can be implemented in many other for future medical goals.

Reference:
Yan Xu et. al. 2014 Mutation of 60 known causative genes in 157 families with retinitis pigmentosa based on exome sequencing. Journal of Human Genetics doi:10.1007/s00439-014-1460-2