Genomic strategies to understand causes of keratoconus

Abstract

Keratoconus (KTCN) is a degenerative disorder of the eye characterized by the conical shape and thinning of the cornea. The abnormal structure of KTCN-affected cornea results in loss of visual acuity. While many studies examine how environmental factors influence disease development, finding the genetic triggers has been a major emphasis of KTCN research. This paper focuses on genomic strategies that were implemented for finding candidate genes, including linkage and association studies, and presents different approaches of mutation screening. The advantages and limitations of particular tools are discussed based on literature and personal experience. Since etiology underlying KTCN is complex, numerous findings indicating heterogeneity of genetic factors involved KTCN etiology are presented.

Keywords: Candidate gene; Complex disease; High-throughput methods; Keratoconus; Next-generation sequencing.

Fig. 1

Schematic representation of the human eye. a Representation of healthy human eye with normal corneal thickness. b Structure of the human cornea. The cornea is a complex tissue comprised of five main layers (from the anterior to posterior margin): corneal epithelium, Bowman’s membrane, stroma, Descemet’s membrane, and endothelium. c Human eye with keratoconus with characteristic thinning and cone-like bulging of the cornea

Fig. 2

Integrating biological data from multiple approaches to understand keratoconus. To understand biological processes underlying keratoconus, integrated analysis of various biological aspects may be required. The figure summarizes information on numerous areas, including DNA sequence (genome), epigenetic modifications (epigenome), RNA transcripts (transcriptome), proteins (proteome), metabolites (metabolome), and microorganisms (microbiome). Each element in the array contains examples of techniques and technologies that can be used to study particular biological aspects. List of abbreviations: genome-wide association study (GWAS), next-generation sequencing (NGS), whole-genome sequencing (WGS), whole-exome sequencing (WES), reverse-transcription-PCR (RT-PCR), chromatin immunoprecipitation-sequencing (ChIP-Seq), RNA sequencing (RNA-seq), whole-genome bisulfite sequencing (WGB-seq), 2-D gel electrophoresis (2-DE), enzyme-linked immunosorbent assay (ELISA), nuclear magnetic resonance (NMR), mass spectrometry (MS), gas chromatography (GC), liquid chromatography–mass spectrometry (LC–MS)