Abstract
Next-generation sequencing (NGS)-based technologies are ideal for genomic analyses owing to their cost-effectiveness, unprecedented speed, and accuracy. Acceleration in examining genome, transcriptome, and epigenome has made significant impact in biomedical sciences. This review highlights the applications of high-throughput NGS technologies in improving the molecular understanding of retinal degenerative diseases (RDDs). I focus on NGS-based methods and strategies that are allowing expedited disease gene identifications, improved diagnosis, and deeper understanding of the mechanisms through which genetic variations lead to diseases.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
1000 Genomes Project Consortium, Auton A, Brooks LD et al (2015) A global reference for human genetic variation. Nature 526:68–74
Aldiri I, Xu B, Wang L et al (2017) The dynamic epigenetic landscape of the retina during development, reprogramming, and tumorigenesis. Neuron 94:550–568.e10
Chan JC, Piper DE, Cao Q et al (2009) A proprotein convertase subtilisin/kexin type 9 neutralizing antibody reduces serum cholesterol in mice and nonhuman primates. Proc Natl Acad Sci U S A 106:9820–9825
Ellingford JM, Barton S, Bhaskar S et al (2016) Whole genome sequencing increases molecular diagnostic yield compared with current diagnostic testing for inherited retinal disease. Ophthalmology 123:1143–1150
ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74
Fritsche LG, Igl W, Bailey JN et al (2016) A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. Nat Genet 48:134–143
Geerlings MJ, de Jong EK, den Hollander AI (2017) The complement system in age-related macular degeneration: a review of rare genetic variants and implications for personalized treatment. Mol Immunol 84:65–76
Gusev A, Ko A, Shi H et al (2016) Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet 48:245–252
Hoshino A, Ratnapriya R, Brooks MJ et al (2017) Molecular anatomy of the developing human retina. Dev Cell 43:763
International HapMap Consortium (2003) The International HapMap Project. Nature 426:789–796
Kolodziejczyk AA, Kim JK, Svensson V et al (2015) The technology and biology of single-cell RNA sequencing. Mol Cell 58:610–620
Lander ES, Linton LM, Birren B et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Liu MM, Zack DJ (2013) Alternative splicing and retinal degeneration. Clin Genet 84:142–149
Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11:31–46
Mo A, Luo C, Davis FP et al (2016) Epigenomic landscapes of retinal rods and cones. Elife 5:e11613
Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
Neveling K, Collin RW, Gilissen C et al (2012) Next-generation genetic testing for retinitis pigmentosa. Hum Mutat 33:963–972
Nicolae DL, Gamazon E, Zhang W et al (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 6:e1000888
O’Sullivan J, Mullaney BG, Bhaskar SS et al (2012) A paradigm shift in the delivery of services for diagnosis of inherited retinal disease. J Med Genet 49:322–326
Ratnapriya R, Swaroop A (2013) Genetic architecture of retinal and macular degenerative diseases: the promise and challenges of next-generation sequencing. Genome Med 5:84
Roadmap Epigenomics Consortium, Kundaje A, Meuleman W et al (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317–330
Roberts L, Ratnapriya R, du Plessis M et al (2016) Molecular diagnosis of inherited retinal diseases in indigenous African populations by whole-exome sequencing. Invest Ophthalmol Vis Sci 57:6374–6381
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467
Stone EM, Andorf JL, Whitmore SS et al (2017) Clinically focused molecular investigation of 1000 consecutive families with inherited retinal disease. Ophthalmology 124:1314–1331
Venter JC, Adams MD, Myers EW et al (2001) The sequence of the human genome. Science 291:1304–1351
Vervoort R, Lennon A, Bird AC et al (2000) Mutational hot spot within a new RPGR exon in X-linked retinitis pigmentosa. Nat Genet 25:462–466
Yang HJ, Ratnapriya R, Cogliati T et al (2015) Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res 46:1–30
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this paper
Cite this paper
Ratnapriya, R. (2019). Applications of Genomic Technologies in Retinal Degenerative Diseases. In: Bowes Rickman, C., Grimm, C., Anderson, R., Ash, J., LaVail, M., Hollyfield, J. (eds) Retinal Degenerative Diseases. Advances in Experimental Medicine and Biology, vol 1185. Springer, Cham. https://doi.org/10.1007/978-3-030-27378-1_46
Download citation
DOI: https://doi.org/10.1007/978-3-030-27378-1_46
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-27377-4
Online ISBN: 978-3-030-27378-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)