Exome sequencing analysis in three Bedouin families with Keratoconus

Abstract

Purpose : 1 in 2000 people are affected by Keratoconus (KT). Despite its prevalence within the general population, researchers have been unable to identify a confirmed genetic cause of KT. It has been documented that Keratoconus seems to occur more frequently and aggressively in Israel and Saudi Arabia. In order to identify a genetic cause of KT, we performed exome sequencing in three Bedouin families with a family history of KT.

Methods : We obtained a total of 16 samples from 3 Bedouin families with a history of KT. These samples were genotyped using an Affymetrix Genome-Wide SNP 5.0 microarray. Using MERLIN, we analyzed the SNP data for regions consistent with segregation within each of the families under both dominant and recessive models of inheritance. The SNP data was also analyzed for regions of autozygosity using PLINK to identify regions of the genome shared between the affected family members in each of the families. One KT sample from each of the families was chosen for exome sequencing. Variants were filtered based upon predicted function, variant quality, population prevalence, and commonly called unfounded variants (based upon our local set of 1000+ exomes) to create a final variant list. The variant list was annotated with corneal expression (http://genome.uiowa.edu/otdb) to assist in prioritizing potential candidates.

Results : No plausible variants were identified within the three families in genes previously reported to cause KT. In addition, no single gene with plausible disease-causing variants was shared across all three families. We identified a few genes with variants that are shared between two of the three families. Upon further inspection, however, variants in these genes were identified as technical artifacts. We also identified three regions of autozygosity that are shared between the three families. However, analysis of these regions failed to provide strong candidate genes or plausible mutations.

Conclusions : Our data supports the genetic heterogeneity of KT even within relatively isolated populations. As we proceed with our analysis, we will focus on variants within each of the families. We are also working with our collaborator in Israel to ascertain additional family members from our KT families, and to ascertain additional families with KT. This will allow us to further narrow the intervals of the genome in search of the causative mutations.

This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.