Exome sequencing study of 20 patients with high myopia

PeerJ
Ling WanXiaoming Chen

Abstract

High myopia is a common ocular disease worldwide. To expand our current understanding of the genetic basis of high myopia, we carried out a whole exome sequencing (WES) study to identify potential causal gene mutations. A total of 20 individuals with high myopia were exome sequenced. A novel filtering strategy combining phenotypes and functional impact of variants was applied to identify candidate genes by multi-step bioinformatics analyses. Network and enrichment analysis were employed to examine the biological pathways involved in the candidate genes. In 16 out of 20 patients, we identified 20 potential pathogenic gene variants for high myopia. A total of 18 variants were located in myopia-associated chromosomal regions. In addition to the novel mutations found in five known myopia genes (ADAMTS18, CSMD1, P3H2, RPGR, and SLC39A5), we also identified pathogenic variants in seven ocular disease genes (ABCA4, CEP290, HSPG2, PCDH15, SAG, SEMA4A, and USH2A) as novel candidate genes. The biological processes associated with vision were significantly enriched in our candidate genes, including visual perception, photoreceptor cell maintenance, retinoid metabolic process, and cellular response to zinc ion starvation. Systematic mutati...Continue Reading

References

Oct 18, 2003·American Journal of Human Genetics·Dror SharonEliot L Berson
Apr 14, 2004·Archives of Ophthalmology·John H KempenUNKNOWN Eye Diseases Prevalence Research Group
Jul 9, 2004·Human Mutation·Ronald J E PenningsHannie Kremer
Aug 17, 2005·Ophthalmic & Physiological Optics : the Journal of the British College of Ophthalmic Opticians (Optometrists)·Seang-Mei SawWei-Han Chua
May 26, 2006·Proceedings of the National Academy of Sciences of the United States of America·M E J Newman
Aug 29, 2006·Investigative Ophthalmology & Visual Science·Maria García-HoyosCarmen Ayuso
Oct 27, 2006·Investigative Ophthalmology & Visual Science·Mohamed DiraniPaul N Baird
Feb 28, 2007·Investigative Ophthalmology & Visual Science·Diana ValverdeCarmen Ayuso
Apr 20, 2007·Glycobiology·Mary C Farach-Carson, Daniel D Carson
Sep 2, 2008·Investigative Ophthalmology & Visual Science·Margarida C LopesChristopher J Hammond
Dec 17, 2008·Human Molecular Genetics·Artur V CideciyanKrzysztof Palczewski
Mar 28, 2009·Investigative Ophthalmology & Visual Science·Yi-Ju LiTerri L Young
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Dec 17, 2009·Archives of Ophthalmology·Susan VitaleFrederick L Ferris
Apr 7, 2010·Progress in Retinal and Eye Research·Wolfgang BergerJohn Neidhardt
Aug 14, 2010·Human Molecular Genetics·Jamie K Teer, James C Mullikin
Jun 23, 2011·PLoS Genetics·Yi ShiZhenglin Yang
Sep 3, 2011·American Journal of Human Genetics·Shikma MordechaiOhad S Birk
May 9, 2012·Lancet·Ian G MorganSeang-Mei Saw
May 7, 2013·American Journal of Human Genetics·Khanh-Nhat Tran-VietTerri L Young
May 11, 2013·Investigative Ophthalmology & Visual Science·Yabin ChenQingjiong Zhang
Jun 19, 2014·The New England Journal of Medicine·Leslie G Biesecker, Robert C Green
Jul 6, 2014·American Journal of Human Genetics·Seunggeung LeeXihong Lin
Oct 14, 2014·F1000Research·Guanming WuLincoln Stein
Nov 25, 2014·Nucleic Acids Research·Xueqiu JianXiaoming Liu
Dec 23, 2014·Acta Ophthalmologica·Preeti GuptaChing-Yu Cheng
Mar 6, 2015·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Hui GuoKun Xia
Aug 28, 2015·Progress in Molecular Biology and Translational Science·Qingjiong Zhang

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Citations

Nov 28, 2020·The British Journal of Ophthalmology·Razek G CoussaIan C Han
Mar 13, 2021·Advances in Medical Sciences·Joanna SwierkowskaMarzena Gajecka
Apr 4, 2021·Genes·Cristina Alvarez-PeregrinaMiguel Ángel Sánchez-Tena
Jul 6, 2021·Frontiers in Cell and Developmental Biology·Yang LiuWen-Juan Zhuang
Jul 25, 2021·Journal of Cellular and Molecular Medicine·Shanshan DongZhengmao Hu

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Datasets Mentioned

BETA
GSE94437
GSE41102

Methods Mentioned

BETA
exome sequencing
RNA-seq
Whole Genome Sequencing
GTPase
genotyping

Software Mentioned

Cytoscape
BWA
Platypus
MutationAssessor
MutationTaster
GATK
VEP
CADD
samtools
LRT

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