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Yutao Liu, Khaled Abu-Amero, Yelena Bykhovskaya, Arthur Zimmerman, Abdulrahman Al-Muammar, Xiaohui Li, Jerome I Rotter, R Rand Allingham, Michael A Hauser, Yaron S Rabinowitz; The Role of Rare Coding Variants in Keratoconus-associated Candidate Genes using Exome Sequencing. Invest. Ophthalmol. Vis. Sci. 2015;56(7 ):2995.
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© ARVO (1962-2015); The Authors (2016-present)
Keratoconus (KC) is a corneal ectatic disease in which the cornea develops a conical shape due to localized cornea thinning, inducing irregular astigmatism, high myopia, and marked vision impairment. Genetic factors play a significant role in KC pathogenesis. Our study aims to evaluate the role of rare coding variants in KC-associated genes in multiplex families affected by KC.
We have performed whole exome sequencing in 104 individuals (77 cases/27 controls) from 40 families using Roche NimbleGen SeqCap EZ Exome Library v3.0 with a 64Mb sequence capture followed by sequencing on Illumina HiSeq 2000. Reads were aligned to human reference genome NCBI build 37 using BWA. Potential PCR duplicate reads were removed with Picard and variants were called with GATK and annotated with SnpEff using annotations from Ensembl. Using Ingenuity Variant Analysis software, the frequency of rare variants in KC-related genes were examined in cases and controls in these families. These genes include COL4A3, COL5A1, COL8A2, VSX1, miR-184, LOX, FNDC3B, MPDZ, NFIB, RXRA, ZEB1, FOXO1, BANP, and ZNF469. We require the variants be present only in cases, not in controls. The frequency of the variants should be less than 1% in 1000Genomes, NHLBI ESP database, or public Complete Genomics database.
We have identified a total of 37 rare missense coding variants in 11 KC-associated genes (COL8A2, COL4A3, FNDC3B, LOX, MPDZ, NFIB, COL5A1, ZEB1, FOXO1, VSX1, and ZNF469). Sixteen of them are predicted to be at least possibly damaging by SIFT or PolyPhen program. These functional variants are present in 16 KC cases from 13 different families. These mutations include a frameshift (p.S275Fs*11) in VSX1, p.G3R in COL8A2, two variants in COL5A1 (p.R65Q and p.G899S), three variants in COL4A3 (p.R229W, p.T629M, and p.Q1495R), four variants in ZNF469 (p.N195K, p.P2490H, p.G2971V, and p.R3426Q), and five variants in MPDZ (p.R1997Q, p.V581F, p.I220L, p.R133H, and p.G132S). We are in the process of checking their segregation patterns within these families.
We have identified a number of rare functional candidates in KC-associated genes that are unique to the KC cases only. Our finding suggests the potential contribution of these potential functional candidates in the pathogenesis of KC. This represents the first comprehensive large scale screening of coding variants in KC-associated genes to date.
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