Mitochondrial DNA variant discovery and evaluation in human cardiomyopathies through next generation sequencing

PLoS ONE

Volumn 5, Issue 8, 2010, Pages

  Zaragoza, Michael V ^a   Fass, Joseph ^b   Diegoli, Marta ^c   Lin, Dawei ^b   Arbustini, Eloisa ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c FONDAZIONE IRCCS POLICLINICO SAN MATTEO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA; SERINE; TRANSFER RNA;

ARTICLE; CARDIOMYOPATHY; CLINICAL ARTICLE; CONGESTIVE CARDIOMYOPATHY; CONTROLLED STUDY; DNA DETERMINATION; GENE AMPLIFICATION; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENOTYPE; HEART FAILURE; HETEROPLASMY; HOMOPLASY; HUMAN; HYPERTROPHIC CARDIOMYOPATHY; MITOCHONDRIAL DNA DISORDER; MITOCHONDRION; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PYROSEQUENCING; SUDDEN DEATH; BIOLOGY; DISORDERS OF MITOCHONDRIAL FUNCTIONS; DNA SEQUENCE; EVALUATION; FEMALE; GENETIC VARIABILITY; GENETICS; MALE; METHODOLOGY; MUTATION;

BASE SEQUENCE; CARDIOMYOPATHIES; COMPUTATIONAL BIOLOGY; DNA, MITOCHONDRIAL; FEMALE; GENETIC VARIATION; HUMANS; MALE; MITOCHONDRIAL DISEASES; MUTATION; SEQUENCE ANALYSIS, DNA;

EID: 77957925524     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012295     Document Type: Article

References (35)

1. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, et al. (1981) Sequence and organization of the human mitochondrial genome. Nature 290: 457-465.
2. Wallace DC (2007) Why do we still have a maternally inherited mitochondrial DNA? Insights from evolutionary medicine. Annu Rev Biochem 76: 781-821.
3. Giles RE, Blanc H, Cann HM, Wallace DC (1980) Maternal inheritance of human mitochondrial DNA. Proc Natl Acad Sci U S A 77: 6715-6719.
4. Cree LM, Samuels DC, Chinnery PF (2009) The inheritance of pathogenic mitochondrial DNA mutations. Biochim Biophys Acta 1792: 1097-1102.
5. Cao L, Shitara H, Horii T, Nagao Y, Imai H, et al. (2007) The mitochondrial bottleneck occurs without reduction of mtDNA content in female mouse germ cells. Nat Genet 39: 386-390.
6. Cree LM, Samuels DC, de Sousa Lopes SC, Rajasimha HK, Wonnapinij P, et al. (2008) A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes. Nat Genet 40: 249-254.
7. Fan W, Waymire KG, Narula N, Li P, Rocher C, et al. (2008) A mouse model of mitochondrial disease reveals germline selection against severe mtDNA mutations. Science 319: 958-962.
8. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chainterminating inhibitors. Proc Natl Acad Sci U S A 74: 5463-5467.
9. Schrijver I, Pique LM, Traynis I, Scharfe C, Sehnert AJ (2009) Mitochondrial DNA analysis by multiplex denaturing high-performance liquid chromatography and selective sequencing in pediatric patients with cardiomyopathy. Genet Med 11: 118-126.
10. Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55: 641-658.
11. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10: R32.
12. Meyer M, Stenzel U, Myles S, Prüfer K, Hofreiter M (2007) Targeted highthroughput sequencing of tagged nucleic acid samples. Nucleic Acids Res 35: e97.
13. Meyer M, Stenzel U, Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protoc 3: 267-278.
14. He Y, Wu J, Dressman DC, Iacobuzio-Donahue C, Markowitz SD, et al. (2010) Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. Nature 464: 610-614.
15. Tang S, Huang T (2010) Characterization of mitochondrial DNA heteroplasmy using a parallel sequencing system. BioTechniques 48: 287-296.
16. Vasta V, Ng SB, Turner EH, Shendure J, Hahn SH (2009) Next generation sequence analysis for mitochondrial disorders. Genome Med 1: 100.
17. Arbustini E, Fasani R, Morbini P, Diegoli M, Grasso M, et al. (1998) Coexistence of mitochondrial DNA and beta myosin heavy chain mutations in hypertrophic cardiomyopathy with late congestive heart failure. Heart 80: 548-558.
18. Jex AR, Hall RS, Littlewood DT, Gasser RB (2010) An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Nucleic Acids Res 38: 522-533.
19. Hu M, Jex AR, Campbell BE, Gasser RB (2007) Long PCR amplification of the entire mitochondrial genome from individual helminths for direct sequencing. Nat Protoc 2: 2339-2344.
20. Clarke LA, Rebelo CS, Gonc ̧alves J, Boavida MG, Jordan P (2001) PCR amplification introduces errors into mononucleotide and dinucleotide repeat sequences. Mol Pathol 54: 351-353.
21. Bordoni R, Bonnal R, Rizzi E, Carrera P, Benedetti S, et al. (2008) Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer. BMC Genomics 9: 464-471.
22. McCaughan F, Dear PH (2010) Single-molecule genomics. J Pathol 220: 297-306.
23. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
24. Moore MJ, Dhingra A, Soltis PS, Shaw R, Farmerie WG, et al. (2006) Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol 6: 17.
25. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
26. Hancock DK, Tully LA, Levin BC (2005) A Standard Reference Material to determine the sensitivity of techniques for detecting low-frequency mutations, SNPs, and heteroplasmies in mitochondrial DNA. Genomics 86: 446-61.
27. Zifa E, Giannouli S, Theotokis P, Stamatis C, Mamuris Z, et al. (2007) Mitochondrial tRNA mutations: clinical and functional perturbations. RNA Biol 4: 38-66.
28. Brandon MC, Ruiz-Pesini E, Mishmar D, Procaccio V, Lott MT, et al. (2009) MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences. Hum Mutat 30: 1-6.
29. Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, et al. (2009) The diversity present in 5140 human mitochondrial genomes. Am J Hum Genet 84: 628.
30. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
31. Thomas RK, Nickerson E, Simons JF, Janne PA, Tengs T, et al. (2006) Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med 12: 852-855.
32. 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.
33. Ruiz-Pesini E, Lott MT, Procaccio V, Poole J, Brandon MC, et al. (2007) An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Research 35 (Database issue):D823-D828. URL: http://www.mitomap.org.
34. van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:E386-E394. http://www.phylotree.org.
35. Szibor R, Plate I, Heinrich M, Michael M, Schöning R, et al. (2007) Mitochondrial D-loop (CA)n repeat length heteroplasmy: frequency in a German population sample and inheritance studies in two pedigrees. Int J Legal Med 121: 207-213.