Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies

PLoS ONE

Volumn 9, Issue 12, 2014, Pages

  Pozo, María González Del ^a,b   Méndez Vidal, Cristina ^a,b   Bravo Gil, Nereida ^a,b   Vela Boza, Alicia ^c   Dopazo, Joaquin ^c,d   Borrego, Salud ^a,b   Antiñolo, Guillermo ^a,b,c  

^a UNIVERSITY OF SEVILLE   (Spain)

^b CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE ENFERMEDADES RARAS CIBERER   (Spain)

^c Genomics and Bioinformatics Platform of Andalusia (GBPA)   (Spain)

^d CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOMAL RECESSIVE DISORDER; CONTROLLED STUDY; EXOME; GENE MUTATION; GENE SEGREGATION; GENE SEQUENCE; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN; MOLECULAR GENETICS; OPEN READING FRAME; RETINA DYSTROPHY; RETINITIS PIGMENTOSA; SPANIARD; ADOLESCENT; ADULT; AMINO ACID SEQUENCE; CHILD; CHROMOSOME SEGREGATION; FAMILY; FEMALE; GENETICS; INHERITANCE; MALE; MIDDLE AGED; MUTATION; NUCLEOTIDE SEQUENCE; PEDIGREE;

RHODOPSIN;

ADOLESCENT; ADULT; AMINO ACID SEQUENCE; BASE SEQUENCE; CHILD; CHROMOSOME SEGREGATION; DNA MUTATIONAL ANALYSIS; EXOME; FAMILY; FEMALE; HUMANS; INHERITANCE PATTERNS; MALE; MIDDLE AGED; MOLECULAR SEQUENCE DATA; MUTATION; PEDIGREE; RETINAL DYSTROPHIES; RHODOPSIN;

EID: 85052409583     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0116176     Document Type: Article

References (32)

1. Hartong DT, Berson EL, Dryja TP (2006) Retinitis pigmentosa. Lancet 368: 1795-1809.
2. Daiger SP, Bowne SJ, Sullivan LS (2007) Perspective on genes and mutations causing retinitis pigmentosa. Arch Ophthalmol 125: 151-158.
3. Humphries P, Farrar GJ, Kenna P, McWilliam P (1990) Retinitis pigmentosa: genetic mapping in Xlinked and autosomal forms of the disease. Clin Genet 38: 1-13.
4. Ayuso C, Garcia-Sandoval B, Najera C, Valverde D, Carballo M, et al. (1995) Retinitis pigmentosa in Spain. The Spanish Multicentric and Multidisciplinary Group for Research into Retinitis Pigmentosa. Clin Genet 48: 120-122.
5. den Hollander AI, Black A, Bennett J, Cremers FP (2010) Lighting a candle in the dark: advances in genetics and gene therapy of recessive retinal dystrophies. J Clin Invest 120: 3042-3053.
6. Avila-Fernandez A, Cantalapiedra D, Aller E, Vallespin E, Aguirre-Lamban J, et al. (2010) Mutation analysis of 272 Spanish families affected by autosomal recessive retinitis pigmentosa using a genotyping microarray. Mol Vis 16: 2550-2558.
7. Neveling K, den Hollander AI, Cremers FP, Collin RW (2013) Identification and analysis of inherited retinal disease genes. Methods Mol Biol 935: 3-23.
8. Daiger S, Sullivan L, Bowne S (2013) Genes and mutations causing retinitis pigmentosa. Clin Genet.
9. Gonzalez-del Pozo M, Borrego S, Barragan I, Pieras JI, Santoyo J, et al. (2011) Mutation screening of multiple genes in Spanish patients with autosomal recessive retinitis pigmentosa by targeted resequencing. PLoS One 6: e27894.
10. Barragan I, Borrego S, Pieras JI, Gonzalez-del Pozo M, Santoyo J, et al. (2010) Mutation spectrum of EYS in Spanish patients with autosomal recessive retinitis pigmentosa. Hum Mutat 31: E1772-1800.
11. Mendez-Vidal C, Gonzalez-Del Pozo M, Vela-Boza A, Santoyo-Lopez J, Lopez-Domingo FJ, et al. (2013) Whole-exome sequencing identifies novel compound heterozygous mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa. Mol Vis 19: 2187-2195.
12. Gonzalez-Del Pozo M, Mendez-Vidal C, Santoyo-Lopez J, Vela-Boza A, Bravo-Gil N, et al. (2014) Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet-Biedl family. Mol Genet Genomic Med 2: 124-133.
13. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249.
14. Kumar P, Henikoff S, Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: 1073-1081.
15. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D (2010) MutationTaster evaluates diseasecausing potential of sequence alterations. Nat Methods 7: 575-576.
16. Ferre F, Clote P (2005) DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Res 33: W230-232.
17. Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PE (2008) Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Hum Mutat 29: 6-13.
18. Reese MG, Berkeley Drosophila Genome Project (1997) Splice Site Prediction by Neural Network.
19. Reese MG, Eeckman FH, Kulp D, Haussler D (1997) Improved splice site detection in Genie. J Comput Biol 4: 311-323.
20. Venselaar H, Te Beek TA, Kuipers RK, Hekkelman ML, Vriend G (2010) Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics 11: 548.
21. Xu Y, Guan L, Shen T, Zhang J, Xiao X, et al. (2014) Mutations of 60 known causative genes in 157 families with retinitis pigmentosa based on exome sequencing. Hum Genet.
22. Jinda W, Taylor TD, Suzuki Y, Thongnoppakhun W, Limwongse C, et al. (2014) Whole exome sequencing in Thai patients with retinitis pigmentosa reveals novel mutations in six genes. Invest Ophthalmol Vis Sci 55: 2259-2268.
23. Vervoort R, Lennon A, Bird AC, Tulloch B, Axton R, et al. (2000) Mutational hot spot within a new RPGR exon in X-linked retinitis pigmentosa. Nat Genet 25: 462-466.
24. Maugeri A, van Driel MA, van de Pol DJ, Klevering BJ, van Haren FJ, et al. (1999) The 2588G-.C mutation in the ABCR gene is a mild frequent founder mutation in the Western European population and allows the classification of ABCR mutations in patients with Stargardt disease. Am J Hum Genet 64: 1024-1035.
25. Lewis RA, Shroyer NF, Singh N, Allikmets R, Hutchinson A, et al. (1999) Genotype/Phenotype analysis of a photoreceptor-specific ATP-binding cassette transporter gene, ABCR, in Stargardt disease. Am J Hum Genet 64: 422-434.
26. Shroyer NF, Lewis RA, Allikmets R, Singh N, Dean M, et al. (1999) The rod photoreceptor ATPbinding cassette transporter gene, ABCR, and retinal disease: from monogenic to multifactorial. Vision Res 39: 2537-2544.
27. Nishiguchi KM, Rivolta C (2012) Genes associated with retinitis pigmentosa and allied diseases are frequently mutated in the general population. PLoS One 7: e41902.
28. Bell C, Converse CA, Hammer HM, Osborne A, Haites NE (1994) Rhodopsin mutations in a Scottish retinitis pigmentosa population, including a novel splice site mutation in intron four. Br J Ophthalmol 78: 933-938.
29. Reig C, Alvarez AI, Tejada I, Molina M, Arostegui E, et al. (1996) New mutation in the 39-acceptor splice site of intron 4 in the rhodopsin gene associated with autosomal dominant retinitis pigmentosa in a Basque family. Hum Mutat 8: 93-94.
30. al-Maghtheh M, Kim RY, Hardcastle A, Inglehearn C, Bhattacharya SS (1994) A 150 bp insertion in the rhodopsin gene of an autosomal dominant retinitis pigmentosa family. Hum Mol Genet 3: 205-206.
31. Whitehead JL, Bell C, Converse CA, Hammer HM, Haites NE (1998) Rhodopsin splice site sequence changes in retinitis pigmentosa and their effect at the mRNA level. Hum Mutat Suppl 1: S295-297.
32. Weiss ER, Osawa S, Shi W, Dickerson CD (1994) Effects of carboxyl-terminal truncation on the stability and G protein-coupling activity of bovine rhodopsin. Biochemistry 33: 7587-7593.