Browse > Article
http://dx.doi.org/10.5734/JGM.2013.10.1.13

Strategies for Mutation Discovery in Retinitis Pigmentosa: Transition to the Next Generation  

Yoon, Chang Ki (Department of Ophthalmology, Seoul National University College of Medicine)
Yu, Hyeong Gon (Department of Ophthalmology, Seoul National University College of Medicine)
Publication Information
Journal of Genetic Medicine / v.10, no.1, 2013 , pp. 13-19 More about this Journal
Abstract
Retinitis pigmentosa (RP) is the most common hereditary retinal disorder and is characterized by progressive retinal degeneration and decline in vision. RP comprises a heterogeneous group of disorders caused by various genetic variants. Since the first discovery of the causal mutation in the RHO gene using positional cloning, numerous mutations have been detected in more than 60 loci and 50 genes. However, causal genes have not been discovered in about 50% of cases. We attempt here to review the strategies to identify causal alleles of retinitis pigmentosa. These include conventional methods as well as state-of-the-art technologies based on next-generation sequencing.
Keywords
Retinitis pigmentosa; RHO gene; Next-generation sequencing;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Shumaker JM, Metspalu A, Caskey CT. Mutation detection by solid phase primer extension. Hum Mutat 1996;7:346-54.   DOI
2 den Hollander AI, McGee TL, Ziviello C, Banfi S, Dryja TP, Gonzalez- Fernandez F, et al. A homozygous missense mutation in the IRBP gene (RBP3) associated with autosomal recessive retinitis pigmentosa. Invest Ophthalmol Vis Sci 2009;50:1864-72.   DOI
3 Dvir L, Srour G, Abu-Ras R, Miller B, Shalev SA, Ben-Yosef T. Autosomalrecessive early-onset retinitis pigmentosa caused by a mutation in PDE6G, the gene encoding the gamma subunit of rod cGMP phosphodiesterase. Am J Hum Genet 2010;87:258-64.   DOI
4 Estrada-Cuzcano A, Neveling K, Kohl S, Banin E, Rotenstreich Y, Sharon D, et al. Mutations in C8orf37, encoding a ciliary protein, are associated with autosomal-recessive retinal dystrophies with early macular involvement. Am J Hum Genet 2012;90:102-9.   DOI
5 Tabor HK, Risch NJ, Myers RM. Candidate-gene approaches for studying complex genetic traits: practical considerations. Nat Rev Genet 2002; 3:391-7.
6 Pullat J, Kusnezow W, Jaakson K, Beier M, Hoheisel JD, Metspalu A. Arrayed primer extension on in situ synthesized 5'-->3' oligonucleotides in microchannels. N Biotechnol 2008;25:133-41.   DOI
7 Ávila-Fernández A, Cantalapiedra D, Aller E, Vallespín E, Aguirre- Lambán J, Blanco-Kelly F, et al. Mutation analysis of 272 Spanish families affected by autosomal recessive retinitis pigmentosa using a genotyping microarray. Mol Vis 2010;16:2550-8.
8 Audo I, Lancelot ME, Mohand-Saïd S, Antonio A, Germain A, Sahel JA, et al. Novel C2orf71 mutations account for - 1% of cases in a large French arRP cohort. Hum Mutat 2011;32:E2091-103.   DOI
9 Jaijo T, Aller E, Garcia-Garcia G, Aparisi MJ, Bernal S, Avila-Fernández A, et al. Microarray-based mutation analysis of 183 Spanish families with Usher syndrome. Invest Ophthalmol Vis Sci 2010;51:1311-7.   DOI
10 Ostergaard E, Duno M, Batbayli M, Vilhelmsen K, Rosenberg T. A novel MERTK deletion is a common founder mutation in the Faroe Islands and is responsible for a high proportion of retinitis pigmentosa cases. Mol Vis 2011;17:1485-92.
11 Schaaf CP, Wiszniewska J, Beaudet AL. Copy number and SNP arrays in clinical diagnostics. Annu Rev Genomics Hum Genet 2011;12:25-51.   DOI
12 LaFramboise T. Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res 2009;37:4181-93.   DOI
13 Kim C, Kim KJ, Bok J, Lee EJ, Kim DJ, Oh JH, et al. Microarray-based mutation detection and phenotypic characterization in Korean patients with retinitis pigmentosa. Mol Vis 2012;18:2398-410.
14 Gonzalez-del Pozo M, Borrego S, Barragan I, Pieras JI, Santoyo J, Matamala N, et al. Mutation screening of multiple genes in Spanish patients with autosomal recessive retinitis pigmentosa by targeted resequencing. PLoS One 2011;6:e27894.   DOI
15 Kannabiran C, Singh H, Sahini N, Jalali S, Mohan G. Mutations in TULP1, NR2E3, and MFRP genes in Indian families with autosomal recessive retinitis pigmentosa. Mol Vis 2012;18:1165-74.
16 Hartong DT, Berson EL, Dryja TP. Retinitis pigmentosa. Lancet 2006;368: 1795-809.   DOI
17 Retinal Information Network website. http://www.sph.uth.tmc.edu/ retnet/
18 Ferrari S, Di Iorio E, Barbaro V, Ponzin D, Sorrentino FS, Parmeggiani F. Retinitis pigmentosa: genes and disease mechanisms. Curr Genomics 2011;12:238-49.   DOI
19 Daiger SP, Bowne SJ, Sullivan LS. Perspective on genes and mutations causing retinitis pigmentosa. Arch Ophthalmol 2007;125:151-8.   DOI
20 Farrar GJ, Kenna P, Jordan SA, Kumar-Singh R, Humphries MM, Sharp EM, et al. A three-base-pair deletion in the peripherin-RDS gene in one form of retinitis pigmentosa. Nature 1991;354:478-80.   DOI
21 Royer-Pokora B, Kunkel LM, Monaco AP, Goff SC, Newburger PE, Baehner RL, et al. Cloning the gene for an inherited human disorder- -chronic granulomatous disease--on the basis of its chromosomal location. Nature 1986;322:32-8.   DOI
22 Blanton SH, Heckenlively JR, Cottingham AW, Friedman J, Sadler LA, Wagner M, et al. Linkage mapping of autosomal dominant retinitis pigmentosa (RP1) to the pericentric region of human chromosome 8. Genomics 1991;11:857-69.   DOI
23 Chakarova CF, Hims MM, Bolz H, Abu-Safieh L, Patel RJ, Papaioannou MG, et al. Mutations in HPRP3 , a third member of pre-mRNA splicing factor genes, implicated in autosomal dominant retinitis pigmentosa. Hum Mol Genet 2002;11:87-92.   DOI
24 Lander ES, Botstein D. Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children. Science 1987;236: 1567-70.   DOI
25 Bandah-Rozenfeld D, Collin RW, Banin E, van den Born LI, Coene KL, Siemiatkowska AM, et al. Mutations in IMPG2 , encoding interphotoreceptor matrix proteoglycan 2, cause autosomal-recessive retinitis pigmentosa. Am J Hum Genet 2010;87:199-208.   DOI
26 Bandah-Rozenfeld D, Mizrahi-Meissonnier L, Farhy C, Obolensky A, Chowers I, Pe'er J, et al. Homozygosity mapping reveals null mutations in FAM161A as a cause of autosomal-recessive retinitis pigmentosa. Am J Hum Genet 2010;87:382-91.   DOI
27 Rehman AU, Morell RJ, Belyantseva IA, Khan SY, Boger ET, Shahzad M, et al. Targeted capture and next-generation sequencing identifies C9orf75 , encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79. Am J Hum Genet 2010;86:378-88.   DOI
28 Nikopoulos K, Gilissen C, Hoischen A, van Nouhuys CE, Boonstra FN, Blokland EA, et al. Next-generation sequencing of a 40 Mb linkage interval reveals TSPAN12 mutations in patients with familial exudative vitreoretinopathy. Am J Hum Genet 2010;86:240-7.   DOI
29 Collin RW, Safieh C, Littink KW, Shalev SA, Garzozi HJ, Rizel L, et al. Mutations in C2orf71 cause autosomal-recessive retinitis pigmentosa. Am J Hum Genet 2010;86:783-8.   DOI
30 Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008;456:53-9.   DOI
31 Antonarakis SE, Beckmann JS. Mendelian disorders deserve more attention. Nat Rev Genet 2006;7:277-82.   DOI
32 Stenson PD, Ball EV, Howells K, Phillips AD, Mort M, Cooper DN. The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics. Hum Genomics 2009;4:69-72.   DOI
33 Kryukov GV, Pennacchio LA, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet 2007;80:727-39.   DOI
34 Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 2010;42:30-5.   DOI
35 Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, et al. Carrier testing for severe childhood recessive diseases by nextgeneration sequencing. Sci Transl Med 2011;3:65ra4.
36 Bowne SJ, Humphries MM, Sullivan LS, Kenna PF, Tam LC, Kiang AS, et al. A dominant mutation in RPE65 identified by whole-exome sequencing causes retinitis pigmentosa with choroidal involvement. Eur J Hum Genet 2011;19:1074-81.   DOI
37 Khateb S, Zelinger L, Ben-Yosef T, Merin S, Crystal-Shalit O, Gross M, et al. Exome sequencing identifies a founder frameshift mutation in an alternative exon of USH1C as the cause of autosomal recessive retinitis pigmentosa with late-onset hearing loss. PLoS One 2012;7:e51566.   DOI
38 Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nat Rev Genet 2009;10:241-51.
39 Zuchner S, Dallman J, Wen R, Beecham G, Naj A, Farooq A, et al. Wholeexome sequencing links a variant in DHDDS to retinitis pigmentosa. Am J Hum Genet 2011;88:201-6.   DOI
40 Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. Nat Biotechnol 2009;27:455-7.   DOI
41 Siemiatkowska AM, Arimadyo K, Moruz LM, Astuti GD, de Castro- Miro M, Zonneveld MN, et al. Molecular genetic analysis of retinitis pigmentosa in Indonesia using genome-wide homozygosity mapping. Mol Vis 2011;17:3013-24.
42 Blanco-Kelly F, García-Hoyos M, Cortón M, Avila-Fernández A, RiveiroAlvarez R, Gimenez A, et al. Genotyping microarray: mutation screening in Spanish families with autosomal dominant retinitis pigmentosa. Mol Vis 2012;18:1478-83.
43 Aguirre-Lamban J, Riveiro-Alvarez R, Garcia-Hoyos M, Cantalapiedra D, Avila-Fernandez A, Villaverde-Montero C, et al. Comparison of highresolution melting analysis with denaturing high-performance liquid chromatography for mutation scanning in the ABCA4 gene. Invest Ophthalmol Vis Sci 2010;51:2615-9.   DOI
44 Erali M, Wittwer CT. High resolution melting analysis for gene scanning. Methods 2010;50:250-61.   DOI
45 Reed GH, Kent JO, Wittwer CT. High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 2007;8:597-608.   DOI
46 De Leeneer K, Coene I, Poppe B, De Paepe A, Claes K. Rapid and sensitive detection of BRCA1/2 mutations in a diagnostic setting: comparison of two high-resolution melting platforms. Clin Chem 2008;54:982-9.   DOI
47 Sergouniotis PI, Li Z, Mackay DS, Wright GA, Borman AD, Devery SR, et al. A survey of DNA variation of C2orf71 in probands with progressive autosomal recessive retinal degeneration and controls. Invest Ophthalmol Vis Sci 2011;52:1880-6.   DOI
48 Sellner LN, Taylor GR. MLPA and MAPH: new techniques for detection of gene deletions. Hum Mutat 2004;23:413-9.   DOI
49 Aller E, Jaijo T, Garcia-Garcia G, Aparisi MJ, Blesa D, Diaz-Llopis M, et al. Identification of large rearrangements of the PCDH15 gene by combined MLPA and a CGH: large duplications are responsible for Usher syndrome. Invest Ophthalmol Vis Sci 2010;51:5480-5.   DOI
50 Rose AM, Mukhopadhyay R, Webster AR, Bhattacharya SS, Waseem NH. A 112 kb deletion in chromosome 19q13.42 leads to retinitis pigmentosa. Invest Ophthalmol Vis Sci 2011;52:6597-603.   DOI
51 Metzker ML. Emerging technologies in DNA sequencing. Genome Res 2005;15:1767-76.   DOI
52 Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437:376-80.
53 Ronaghi M, Karamohamed S, Pettersson B, Uhlén M, Nyrén P. Realtime DNA sequencing using detection of pyrophosphate release. Anal Biochem 1996;242:84-9.   DOI
54 Ronaghi M, Uhlen M, Nyren P. A sequencing method based on realtime pyrophosphate. Science 1998;281:363, 365.
55 Metzker ML. Sequencing in real time. Nat Biotechnol 2009;27:150-1.   DOI
56 Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends Genet 2008;24:142-9.   DOI
57 Chaisson MJ, Brinza D, Pevzner PA. De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res 2009;19:336-46.