Toward a mtDNA locus-specific mutation database using the LOVD platform

Human Mutation

Volumn 33, Issue 9, 2012, Pages 1352-1358

  Elson, Joanna L ^a,b   Sweeney, Mary G ^c   Procaccio, Vincent ^d   Yarham, John W ^a   Salas, Antonio ^e   Kong, Qing Peng ^f   van der Westhuizen, Francois H ^g   Pitceathly, Robert D S ^c   Thorburn, David R ^h   Lott, Marie T ⁱ   Wallace, Douglas C ⁱ   Taylor, Robert W ^a   Mcfarland, Robert ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

^c NATIONAL HOSPITAL FOR NEUROLOGY AND NEUROSURGERY   (United Kingdom)

^d INSERM   (France)

^e UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^f KUNMING INSTITUTE OF ZOOLOGY   (China)

^g NORTH WEST UNIVERSITY   (South Africa)

^h MURDOCH CHILDREN'S RESEARCH INSTITUTE   (Australia)

ⁱ UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Haplogroup; Human variome project; LOVD; MtDNA; Mutation

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; DATA BASE; DISORDERS OF MITOCHONDRIAL FUNCTIONS; GENE LOCUS; GENE MUTATION; GENETIC DISORDER; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; INFORMATION STORAGE; NEUROLOGIC DISEASE; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; PROGNOSIS; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DNA MUTATIONAL ANALYSIS; DNA, MITOCHONDRIAL; GENETIC LOCI; GENOME, HUMAN; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MITOCHONDRIAL DISEASES; MUTATION; OXIDATIVE PHOSPHORYLATION; PHENOTYPE; SOFTWARE;

EID: 84865184872     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22118     Document Type: Article

References (51)

1. Achilli A, Olivieri A, Pala M, Hooshiar Kashani B, Carossa V, Perego UA, Gandini F, Santoro A, Battaglia V, Grugni V, et al. 2011. Mitochondrial DNA backgrounds might modulate diabetes complications rather than T2DM as a whole. PLoS 6:e21029.
2. Achouitar S, Mohamed M, Gardeitchik T, Wortmann SB, Sykut-Cegielska J, Ensenauer R, de Baulny HO, Õunap K, Martinelli D, de Vries M, et al. 2011. Nijmegen paediatric CDG rating scale: a novel tool to assess disease progression. J Inherit Metab Dis 34:923-927. Epub 2011 May 4.
3. Anderson S, Bankier AT, Barrell BG, Debruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, et al. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
4. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147.
5. Bandelt HJ, Achilli A, Kong QP, Salas A, Lutz-Bonengel S, Sun C, Zhang YP, Torroni A, Yao YG. 2005. Low "penetrance" of phylogenetic knowledge in mitochondrial disease studies. Biochem Biophys Res Commun 333:122-130.
6. Bandelt HJ, Salas A, Bravi CM. 2006. What is a 'novel' mtDNA mutation-and does 'novelty' really matter? J Hum Genet 51:1073-1082. Epub 2006 Oct 5.
7. Bandelt HJ, Salas A, Taylor RW, Yao YG. 2009. Exaggerated status of "novel" and "pathogenic" mtDNA sequence variants due to inadequate database searches. Hum Mutat 30:191-6.
8. Bandelt HJ, Yao YG, Salas A. 2008. The search of 'novel' mtDNA mutations in hypertrophic cardiomyopathy: MITOMAPping as a risk factor. Int J Cardiol. 126:439-42.
9. Bandelt HJ, Yao YG, Salas A, Kivisild T, Bravi CM. 2007. High penetrance of sequencing errors and interpretative shortcomings in mtDNA sequence analysis of LHON patients. Biochem Biophys Res Commun. 352:283-91.
10. Brandon MC, Lott MT, Nguyen KC, Spolim S, Navathe SB, Baldi P, Wallace DC. 2005. MITOMAP: a human mitochondrial genome database - 2004 update. Nucleic Acids Research 33:D611-D613.
11. Cassereau J, Chevrollier A, Bonneau D, Verny C, Procaccio V, Reynier P, Ferre M. 2011. A locus-specific database for mutations in GDAP1 allows analysis of genotype-phenotype correlations in Charcot-Marie-Tooth diseases type 4A and 2K. Orphanet 6:87.
12. Coskun P, Wyrembak J, Schriner S, Chen HW, Marciniack C, Laferla F, Wallace DC. 2012. A mitochondrial etiology of Alzheimer and Parkinson disease. Biochim Biophys Acta. 1820:553-564.
13. Cree LM, Samuels DC, Lopes S, Rajasimha HK, Wonnapinij P, Mann JR, Dahl HHM, Chinnery PF. 2008. A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes. Nat Genet 40:249-254.
14. Dimauro S, Schon EA. 2001. Mitochondrial DNA mutations in human disease. A J Med Genet 106:18-26.
15. Elliott HR, Samuels DC, Eden JA, Relton CL, Chinnery PF. 2008. Pathogenic mitochondrial DNA mutations are common in the general population. Am J Hum Genet 83:254-260.
16. Elson JL, Andrews RM, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. 2001. Analysis of European mtDNAs for recombination. Am J Hum Genet 68:145-153.
17. Elson JL, Herrnstadt C, Preston G, Thal L, Morris CM, Edwardson JA, Beal MF, Turnbull DM, Howell N. 2006. Does the mitochondrial genome play a role in the etiology of Alzheimer's disease? Hum Genet. 119:241-54. Epub 2006 Jan 12.
18. Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT. 2001. LOVD v.2.0: the next generation in gene variant databases. Hum Mutat 32:557-563.
19. Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT. 2011. LOVD v.2.0: the next generation in gene variant databases. Hum Mutat 32:557-563.
20. He YP, Wu J, Dressman DC, Iacobuzio-Donahue C, Markowitz SD, Velculescu VE, Diaz LA, Kinzler KW, Vogelstein B, Papadopoulos N. 2010. Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. Nature 464:610-U175.
21. Holt IJ, Harding AE, Morganhughes JA. 1988. Deletions of muscle mitochondrial-dna in patients with mitochondrial myopathies. Nature 331:717-719.
22. Kogelnik AM, Lott MT, Brown MD, Navathe SB, Wallace DC. 1996. MITOMAP: A human mitochondrial genome database. Nucleic Acids Res 24:177-179.
23. Kong QP, Bandelt HJ, Sun C, Yao YG, Salas A, Achilli A, Wang CY, Zhong L, Zhu CL, Wu SF, et al. 2006. Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Hum Mol Genet 15:2076-86. Epub 2006 May 19.
24. Kong QP, Yao YG, Sun C, Zhu CL, Zhong L, Wang CY, Cai WW, Xu XM, Xu AL, Zhang YP. 2004. Phylogeographic analysis of mitochondrial DNA haplogroup F2 in China reveals T12338C in the initiation codon of the ND5 gene not to be pathogenic. J Hum Genet 49:414-23.
25. Li M, Schönberg A, Schaefer M, Schroeder R, Nasidze I, Stoneking M. 2010. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet 87:237-249.
26. McFarland R, Clark KM, Morris AAM, Taylor RW, Macphail S, Lightowlers RN, Turnbull DM. 2002. Multiple neonatal deaths due to a homoplasmic mitochondrial DNA mutation. Nat Genet 30:145-146.
27. McFarland R, Elson JL, Taylor RW, Howell N, Turnbull DM. 2004a. Assigning pathogenicity to mitochondrial tRNA mutations: when 'definitely maybe' is not good enough. Trends Genet 20:591-596.
28. McFarland R, Taylor RW, Elson JL, Lightowlers RN, Turnbull DM, Howell N. 2004b. Proving pathogenicity: when evolution is not enough. Am J Med Genet A 131:107-108; author reply 109-110.
29. McFarland R, Taylor RW, Turnbull DM. 2010. A neurological perspective on mitochondrial disease. Lancet Neurol 9:829-840.
30. Mitchell AL, Elson JL, Howell N, Taylor RW, Turnbull DM. 2006. Sequence variation in mitochondrial complex I genes: mutation or polymorphism? J Med Genet 43:175-179.
31. Monnat RJ, Loeb LA. 1985. Nucleotide-sequence preservation of human mitochondrial-dna. Proc Natl Acad Sci USA 82:2895-2899.
32. Ou J, Niessen RC, Vonk J, Westers H, Hofstra RM, Sijmons RH. 2008. A database to support the interpretation of human mismatch repair gene variants. Hum Mutat 29:1337-1341.
33. Peltomäki P, Vasen H. 2004. Mutations associated with HNPCC predisposition-update of ICG-HNPCC/INSiGHT mutation database. Dis Markers 20:269-276.
34. Perli E, Giordano C, Tuppen HA, Montopoli M, Montanari A, Orlandi M, Pisano A, Catanzaro D, Caparrotta L, Musumeci B, et al. 2012. Isoleucyl-tRNA synthetase levels modulate the penetrance of a homoplasmic m.4277T>C mitochondrial tRNAIle mutation causing hypertrophic cardiomyopathy. Hum Mol Genet 21:85-100.
35. Phoenix C, Schaefer AM, Elson JL, Morava E, Bugiani M, Uziel G, Smeitink JA, Turnbull DM, McFarland R. 2006. A scale to monitor progression and treatment of mitochondrial disease in children. Neuromusc Disorders 16:814-820.
36. Prezant TR, Agapian JV, Bohlman MC, Bu XD, Oztas S, Qiu WQ, Arnos KS, Cortopassi GA, Jaber L, Rotter JI, et al. 1993. Mitochondrial ribosomal-rna mutation associated with both antibiotic-induced and non-syndromic deafness. Nat Genet 4:289-294.
37. Ruiz-Pesini E, Lott MT, Procaccio V, Poole JC, Brandon MC, Mishmar D, Yi C, Kreuziger J, Baldi P, Wallace DC. 2007b. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res 35:D823-D828.
38. Samuels DC, Carothers AD, Horton R, Chinnery PF. 2006. The power to detect disease associations with mitochondrial DNA haplogroups. Am J Hum Genet 78:713-720.
39. Schaefer AM, McFarland R, Blakely EL, He L, Whittaker RG, Taylor RW, Chinnery PF, Turnbull DM. 2008. Prevalence of mitochondrial DNA disease in adults. Ann Neurol 63:35-39.
40. Schaefer AM, Phoenix C, Elson JL, McFarland R, Chinnery PF, Turnbull DM. 2006. Mitochondrial disease in adults: a scale to monitor progression and treatment. Neurology 66:1932-1934.
41. Smuts I, Louw R, du Toit H, Klopper B, Mienie L, van der Westhuizen F. 2010. An overview of a cohort of South African patients with mitochondrial disorders. doi: 10.1007/s10545-009-9031-8.
42. Torroni A, Huoponen K, Francalacci P, Petrozzi M, Morelli L, Scozzari R, Obinu D, Savontaus ML, Wallace DC. 1996. Classification of European mtDNAs from an analysis three European populations. Genetics 144:1835-1850.
43. Tuppen HA, Blakely EL, Turnbull DM, Taylor RW. 2009. Mitochondrial DNA mutations and human disease. Biochim Biophys Acta 1797:113-128.
44. Tuppen HA, Fattori F, Carrozzo R, Zeviani M, DiMauro S, Seneca S, Martindale JE, Olpin SE, Treacy EP, McFarland R, et al. 2008. Further pitfalls in the diagnosis of mtDNA mutations: homoplasmic mt-tRNA mutations. J Med Genet 45:55-61.
45. van der Walt EM, Smuts I, Taylor RW, Elson JL, Turnbull DM, Louw R, van der Westhuizen FH. 2012. Characterization of mtDNA variation in a cohort of South African paediatric patients with mitochondrial disease. Eur J Hum Genet. 20: 650-656.
46. van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:E386-E394.
47. Wallace DC. 1999. Mitochondrial diseases in man and mouse. Science 283:1482-1488.
48. Wallace DC, Singh G, Lott MT, Hodge JA, Schurr TG, Lezza AMS, Elsas LJ, Nikoskelainen EK. 1988. Mitochondrial-dna mutation associated with lebers hereditary optic neuropathy. Science 242:1427-1430.
49. Yao YG, Kong QP, Salas A, Bandelt HJ. 2008. Pseudomitochondrial genome haunts disease studies. J Med Genet 45:769-772.
50. Yarham JW, Al-Dosary M, Blakely EL, Alston CL, Taylor RW, Elson JL, McFarland R. 2011. A comparative analysis approach to determining the pathogenicity of mitochondrial tRNA mutations. Hum Mutat 32:1319-1325.
51. Zaragoza MV, Brandon MC, Diegoli M, Arbustini E, Wallace DC. 2011. Mitochondrial cardiomyopathies: how to identify candidate pathogenic mutations by mitochondrial DNA sequencing, MITOMASTER and phylogeny. Eur J Hum Genet 19:200-207.