Mitochondrial DNA variant discovery in Normal-tension glaucoma patients by next-generation sequencing

Investigative Ophthalmology and Visual Science

Volumn 55, Issue 2, 2014, Pages 986-992

  Jeoung, Jin Wook ^a   Seong, Moon Woo ^a   Park, Sung Sup ^a   Kim, Dong Myung ^a   Kim, Seok Hwan ^b   Park, Ki Ho ^a  

^a Seoul National University Hospital   (South Korea)

^b Seoul National University   (South Korea)

Author keywords

Genetic variation; Mitochondria; Mitochondrial DNA; Normal tension glaucoma

Indexed keywords

ADENOSINE TRIPHOSPHATE; CYTOCHROME B; CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA;

ADULT; AMINO ACID SUBSTITUTION; ARTICLE; ATP6 GENE; ATP8 GENE; BIOINFORMATICS; CLINICAL ARTICLE; CONTROLLED STUDY; COX1 GENE; COX3 GENE; CYTB GENE; DNA EXTRACTION; DNA LIBRARY; DNA SEQUENCE; FEMALE; GENE FREQUENCY; GENE MUTATION; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; HETEROPLASMY; HUMAN; LOW TENSION GLAUCOMA; MALE; MIDDLE AGED; ND2 ND6 GENE; PHENOTYPE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNR1 GENE; RNR2 GENE;

GENETIC VARIATION; MITOCHONDRIA; MITOCHONDRIAL DNA; NORMAL-TENSION GLAUCOMA;

DNA, MITOCHONDRIAL; FEMALE; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION STUDIES; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LOW TENSION GLAUCOMA; MALE; MIDDLE AGED; NADH DEHYDROGENASE; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; RISK FACTORS;

EID: 84896710467     PISSN: 01460404     EISSN: 15525783     Source Type: Journal    
DOI: 10.1167/iovs.13-12968     Document Type: Article

References (46)

1. Sommer A, Tielsch JM, Katz J, et al. Racial differences in the cause-specific prevalence of blindness in east Baltimore. N Engl J Med. 1991;325:1412-1417.
2. Klein BE, Klein R, Sponsel WE, et al. Prevalence of glaucoma. The Beaver Dam Eye Study. Ophthalmology. 1992;99:1499-1504.
3. Quigley HA, Vitale S. Models of open-angle glaucoma prevalence and incidence in the United States. Invest Ophthalmol Vis Sci. 1997;38:83-91.
4. Michelson G, Groh MJ. Screening models for glaucoma. Curr Opin Ophthalmol. 2001;12:105-111.
5. Goldberg I, Hollows FC, Kass MA, Becker B. Systemic factors in patients with low-tension glaucoma. Br J Ophthalmol. 1981;65:56-62.
6. Barron MJ, Griffiths P, Turnbull DM, Bates D, Nichols P. The distributions of mitochondria and sodium channels reflect the specific energy requirements and conduction properties of the human optic nerve head. Br J Ophthalmol. 2004;88:286-290.
7. Abu-Amero KK, Morales J, Bosley TM. Mitochondrial abnormalities in patients with primary open-angle glaucoma. Invest Ophthalmol Vis Sci. 2006;47:2533-2541.
8. Ju WK, Liu Q, Kim KY, et al. Elevated hydrostatic pressure triggers mitochondrial fission and decreases cellular ATP in differentiated RGC-5 cells. Invest Ophthalmol Vis Sci. 2007; 48:2145-2151.
9. Matullo G, Di Gaetano C, Guarrera S. Next generation sequencing and rare genetic variants: from human population studies to medical genetics. Environ Mol Mutagen. 2013;54: 518-532.
10. Mathieson I, McVean G. Differential confounding of rare and common variants in spatially structured populations. Nat Genet. 2012;44:243-246.
11. Gravel S, Henn BM, Gutenkunst RN, et al. Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A. 2011;108:11983-11988.
12. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet. 1999;23:147.
13. Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248-249.
14. Finnila S, Lehtonen MS, Majamaa K. Phylogenetic network for European mtDNA. Am J Hum Genet. 2001;68:1475-1484.
15. Accetturo M, Santamaria M, Lascaro D, et al. Human mtDNA site-specific variability values can act as haplogroup markers. Hum Mutat. 2006;27:965-974.
16. Allingham RR, Liu Y, Rhee DJ. The genetics of primary openangle glaucoma: a review. Exp Eye Res. 2009;88:837-844.
17. Izzotti A, Longobardi M, Cartiglia C, Sacca SC. Mitochondrial damage in the trabecular meshwork occurs only in primary open-angle glaucoma and in pseudoexfoliative glaucoma. PLoS One. 2011;6:e14567.
18. Osborne NN. Pathogenesis of ganglion "cell death" in glaucoma and neuroprotection: focus on ganglion cell axonal mitochondria. Prog Brain Res. 2008;173:339-352.
19. Huoponen K, Lamminen T, Juvonen V, Aula P, Nikoskelainen E, Savontaus ML. The spectrum of mitochondrial DNA mutations in families with Leber hereditary optic neuroretinopathy. Hum Genet. 1993;92:379-384.
20. Lamminen T, Huoponen K, Sistonen P, et al. mtDNA haplotype analysis in Finnish families with leber hereditary optic neuroretinopathy. Eur J Hum Genet. 1997;5:271-279.
21. Wallace DC. Mitochondrial DNA sequence variation in human evolution and disease. Proc Natl Acad Sci U S A. 1994;91: 8739-8746.
22. Chol M, Lebon S, Benit P, et al. The mitochondrial DNA G13513A MELAS mutation in the NADH dehydrogenase 5 gene is a frequent cause of Leigh-like syndrome with isolated complex I deficiency. J Med Genet. 2003;40:188-191.
23. Richter C, Park JW, Ames BN. Normal oxidative damage to mitochondrial and nuclear DNA is extensive. Proc Natl Acad Sci U S A. 1988;85:6465-6467.
24. Wei YH, Lu CY, Lee HC, Pang CY, Ma YS. Oxidative damage and mutation to mitochondrial DNA and age-dependent decline of mitochondrial respiratory function. Ann N Y Acad Sci. 1998;854:155-170.
25. Croteau DL, Stierum RH, Bohr VA. Mitochondrial DNA repair pathways. Mutat Res. 1999;434:137-148.
26. Melki R, Lefort N, Brezin AP, Garchon HJ. Association of a common coding polymorphism (N453S) of the cytochrome P450 1B1 (CYP1B1) gene with optic disc cupping and visual field alteration in French patients with primary open-angle glaucoma. Mol Vis. 2005;11:1012-1017.
27. Pasquale LR, Loomis SJ, Kang JH, et al. CDKN2B-AS1 genotypeglaucoma feature correlations in primary open-angle glaucoma patients from the United States. Am J Ophthalmol. 2013;155: 342-353.
28. van der Walt JM, Nicodemus KK, Martin ER, et al. Mitochondrial polymorphisms significantly reduce the risk of Parkinson disease. Am J Hum Genet. 2003;72:804-811.
29. Takasaki S. Mitochondrial SNPs associated with Japanese centenarians, Alzheimer's patients, and Parkinson's patients. Comput Biol Chem. 2008;32:332-337.
30. Rollins B, Martin MV, Sequeira PA, et al. Mitochondrial variants in schizophrenia, bipolar disorder, and major depressive disorder. PLoS One. 2009;4:e4913.
31. Kokaze A, Ishikawa M, Matsunaga N, et al. Combined effect of longevity-associated mitochondrial DNA 5178 C/A polymorphism and coffee consumption on the risk of hyper-LDL cholesterolemia in middle-aged Japanese men. J Hum Genet. 2010;55:577-581.
32. Sawabe M, Tanaka M, Chida K, et al. Mitochondrial haplogroups A and M7a confer a genetic risk for coronary atherosclerosis in the Japanese elderly: an autopsy study of 1,536 patients. J Atheroscler Thromb. 2011;18:166-175.
33. Kong GY, Van Bergen NJ, Trounce IA, Crowston JG. Mitochondrial dysfunction and glaucoma. J Glaucoma. 2009;18:93-100.
34. Kujoth GC, Hiona A, Pugh TD, et al. Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging. Science. 2005;309:481-484.
35. Navarro A, Boveris A. The mitochondrial energy transduction system and the aging process. Am J Physiol Cell Physiol. 2007; 292:C670-686.
36. Lascaratos G, Garway-Heath DF, Willoughby CE, Chau KY, Schapira AH. Mitochondrial dysfunction in glaucoma: understanding genetic influences. Mitochondrion. 2012;12:202-212.
37. Tanaka M, Gong JS, Zhang J, Yoneda M, Yagi K. Mitochondrial genotype associated with longevity. Lancet. 1998;351:185-186.
38. Matsunaga H, Tanaka Y, Tanaka M, et al. Antiatherogenic mitochondrial genotype in patients with type 2 diabetes. Diabetes Care. 2001;24:500-503.
39. Xu L, Hu Y, Chen B, et al. Mitochondrial polymorphisms as risk factors for endometrial cancer in southwest China. Int J Gynecol Cancer. 2006;16:1661-1667.
40. Li XY, Guo YB, Su M, Cheng L, Lu ZH, Tian DP. Association of mitochondrial haplogroup D and risk of esophageal cancer in Taihang Mountain and Chaoshan areas in China. Mitochondrion. 2011;11:27-32.
41. Zheng S, Qian P, Li F, et al. Association of mitochondrial DNA variations with lung cancer risk in a Han Chinese population from southwestern China. PLoS One. 2012;7:e31322.
42. Tanaka M, Cabrera VM, Gonzalez AM, et al. Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res. 2004;14:1832-1850.
43. Lee HY, Yoo JE, Park MJ, Chung U, Kim CY, Shin KJ. East Asian mtDNA haplogroup determination in Koreans: haplogrouplevel coding region SNP analysis and subhaplogroup-level control region sequence analysis. Electrophoresis. 2006;27: 4408-4418.
44. Lightowlers RN, Chinnery PF, Turnbull DM, Howell N. Mammalian mitochondrial genetics: heredity, heteroplasmy and disease. Trends Genet. 1997;13:450-455.
45. Taylor RW, Turnbull DM. Mitochondrial DNA mutations in human disease. Nat Rev Genet. 2005;6:389-402.
46. Wadhwa SD, Higginbotham EJ. Ethnic differences in glaucoma: prevalence, management, and outcome. Curr Opin Ophthalmol. 2005;16:101-106.