High-throughput sequencing in mitochondrial DNA research

Mitochondrion

Volumn 17, Issue , 2014, Pages 157-163

  Ye, Fei ^a   Samuels, David C ^a   Clark, Travis ^a   Guo, Yan ^b  

^a VANDERBILT UNIVERSITY   (United States)

^b VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Copy number; Heteroplasmy; High throughput sequencing; Mutation; Next generation sequencing; SNP

Indexed keywords

MITOCHONDRIAL DNA;

ANALYTIC METHOD; DISEASE ASSOCIATION; DNA DETERMINATION; DNA SEQUENCE; EXOME; GENE DOSAGE; GENETIC VARIABILITY; HETEROPLASMY; HIGH THROUGHPUT SEQUENCING; HUMAN; MALIGNANT NEOPLASTIC DISEASE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUALITY CONTROL; REVIEW; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; CHEMISTRY; COPY NUMBER VARIATION; GENETICS; MITOCHONDRIAL DISEASES; PROCEDURES; UTILIZATION;

DNA COPY NUMBER VARIATIONS; DNA, MITOCHONDRIAL; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MITOCHONDRIAL DISEASES; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84907598441     PISSN: 15677249     EISSN: 18728278     Source Type: Journal    
DOI: 10.1016/j.mito.2014.05.004     Document Type: Review

References (104)

1. Albers C.A., Lunter G., MacArthur D.G., McVean G., Ouwehand W.H., Durbin R. Dindel: accurate indel calls from short-read data. Genome Res. 2011, 21:961-973.
2. Ameur A., Stewart J.B., Freyer C., Hagstrom E., Ingman M., Larsson N.G., Gyllensten U. Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins. PLoS Genet. 2011, 7:e1002028.
3. Andrews R.M., Kubacka I., Chinnery P.F., Lightowlers R.N., Turnbull D.M., Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 1999, 23:147.
4. Annon. Comprehensive molecular portraits of human breast tumours. Nature 2012, 490:61-70.
5. Bai R.K., Wong L.J. Detection and quantification of heteroplasmic mutant mitochondrial DNA by real-time amplification refractory mutation system quantitative PCR analysis: a single-step approach. Clin. Chem. 2004, 50:996-1001.
6. Bai R.K., Leal S.M., Covarrubias D., Liu A., Wong L.J. Mitochondrial genetic background modifies breast cancer risk. Cancer Res. 2007, 67:4687-4694.
7. Bai R.K., Chang J., Yeh K.T., Lou M.A., Lu J.F., Tan D.J., Liu H., Wong L.J. Mitochondrial DNA content varies with pathological characteristics of breast cancer. J. Oncol. 2011, 2011:496189.
8. Bainbridge M.N., Wang M., Wu Y., Newsham I., Muzny D.M., Jefferies J.L., Albert T.J., Burgess D.L., Gibbs R.A. Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol. 2011, 12:R68.
9. Baysal B.E., Ferrell R.E., Willett-Brozick J.E., Lawrence E.C., Myssiorek D., Bosch A., van der Mey A., Taschner P.E., Rubinstein W.S., Myers E.N., Richard C.W., Cornelisse C.J., Devilee P., Devlin B. Mutations in SDHD, a mitochondrial complex II gene, in hereditary paraganglioma. Science 2000, 287:848-851.
10. Bhat H.K., Epelboym I. Quantitative analysis of total mitochondrial DNA: competitive polymerase chain reaction versus real-time polymerase chain reaction. J. Biochem. Mol. Toxicol. 2004, 18:180-186.
11. Bogenhagen D., Clayton D.A. The number of mitochondrial deoxyribonucleic acid genomes in mouse L and human HeLa cells. Quantitative isolation of mitochondrial deoxyribonucleic acid. J. Biol. Chem. 1974, 249:7991-7995.
12. Bogliolo M., Izzotti A., De Flora S., Carli C., Abbondandolo A., Degan P. Detection of the '4977bp' mitochondrial DNA deletion in human atherosclerotic lesions. Mutagenesis 1999, 14:77-82.
13. Calloway C.D., Reynolds R.L., Herrin G.L., Anderson W.W. The frequency of heteroplasmy in the HVII region of mtDNA differs across tissue types and increases with age. Am. J. Hum. Genet. 2000, 66:1384-1397.
14. Calvo S.E., Compton A.G., Hershman S.G., Lim S.C., Lieber D.S., Tucker E.J., Laskowski A., Garone C., Liu S., Jaffe D.B., Christodoulou J., Fletcher J.M., Bruno D.L., Goldblatt J., Dimauro S., Thorburn D.R., Mootha V.K. Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci. Transl. Med. 2012, 4:118ra110.
15. Canter J.A., Kallianpur A.R., Parl F.F., Millikan R.C. Mitochondrial DNA G10398A polymorphism and invasive breast cancer in African-American women. Cancer Res. 2005, 65:8028-8033.
16. Castle J.C., Biery M., Bouzek H., Xie T., Chen R., Misura K., Jackson S., Armour C.D., Johnson J.M., Rohl C.A., Raymond C.K. DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing. BMC Genomics 2010, 11:244.
17. Chen E.I. Mitochondrial dysfunction and cancer metastasis. J. Bioenerg. Biomembr. 2012, 44:619-622.
18. Craven L., Tuppen H.A., Greggains G.D., Harbottle S.J., Murphy J.L., Cree L.M., Murdoch A.P., Chinnery P.F., Taylor R.W., Lightowlers R.N., Herbert M., Turnbull D.M. Pronuclear transfer in human embryos to prevent transmission of mitochondrial DNA disease. Nature 2010, 465:82-85.
19. Cui H., Li F., Chen D., Wang G., Truong C.K., Enns G.M., Graham B., Milone M., Landsverk M.L., Wang J., Zhang W., Wong L.J. Comprehensive next-generation sequence analyses of the entire mitochondrial genome reveal new insights into the molecular diagnosis of mitochondrial DNA disorders. Genet. Med. 2013, 15:388-394.
20. Dames S., Chou L.S., Xiao Y., Wayman T., Stocks J., Singleton M., Eilbeck K., Mao R. The development of next-generation sequencing assays for the mitochondrial genome and 108 nuclear genes associated with mitochondrial disorders. J. Mol. Diagn. 2013, 15:526-534.
21. Dasgupta S., Hoque M.O., Upadhyay S., Sidransky D. Mitochondrial cytochrome B gene mutation promotes tumor growth in bladder cancer. Cancer Res. 2008, 68:700-706.
22. Degner J.F., Marioni J.C., Pai A.A., Pickrell J.K., Nkadori E., Gilad Y., Pritchard J.K. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 2009, 25:3207-3212.
23. DePristo M.A., Banks E., Poplin R., Garimella K.V., Maguire J.R., Hartl C., Philippakis A.A., del Angel G., Rivas M.A., Hanna M., McKenna A., Fennell T.J., Kernytsky A.M., Sivachenko A.Y., Cibulskis K., Gabriel S.B., Altshuler D., Daly M.J. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 2011, 43:491-498.
24. Dinwiddie D.L., Smith L.D., Miller N.A., Atherton A.M., Farrow E.G., Strenk M.E., Soden S.E., Saunders C.J., Kingsmore S.F. Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome. Genomics 2013, 102:148-156.
25. Durbin R.M., Altshuler D.L., Abecasis G.R., Bentley D.R., Chakravarti A., Clark A.G., Collins F.S., De la Vega F.M., Donnelly P., Egholm M., Flicek P., Gabriel S.B., Gibbs R.A., Knoppers B.M., Lander E.S., Lehrach H., Mardis E.R., McVean G.A., Nickerson D., Peltonen L., Schafer A.J., Sherry S.T., Wang J., Wilson R.K., Gibbs R.A., Deiros D., Metzker M., Muzny D., Reid J., Wheeler D., Wang J., Li J.X., Jian M., Li G., Li R.Q., Liang H.Q., Tian G., Wang B., Wang J., Wang W., Yang H.M., Zhang X.Q., Zheng H.S., Lander E.S., Altshuler D.L., Ambrogio L., Bloom T., Cibulskis K., Fennell T.J., Gabriel S.B., Jaffe D.B., Shefler E., Sougnez C.L., Bentley D.R., Gormley N., Humphray S., Kingsbury Z., Koko-Gonzales P., Stone J., McKernan K.J., Costa G.L., Ichikawa J.K., Lee C.C., Sudbrak R., Lehrach H., Borodina T.A., Dahl A., Davydov A.N., Marquardt P., Mertes F., Nietfeld W., Rosenstiel P., Schreiber S., Soldatov A.V., Timmermann B., Tolzmann M., Egholm M., Affourtit J., Ashworth D., Attiya S., Bachorski M., Buglione E., Burke A., Caprio A., Celone C., Clark S., Conners D., Desany B., Gu L., Guccione L., Kao K., Kebbel A., Knowlton J., Labrecque M., McDade L., Mealmaker C., Minderman M., Nawrocki A., Niazi F., et al. A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
26. Ericson N.G., Kulawiec M., Vermulst M., Sheahan K., O'Sullivan J., Salk J.J., Bielas J.H. Decreased mitochondrial DNA mutagenesis in human colorectal cancer. PLoS Genet. 2012, 8:e1002689.
27. Ewing B., Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8:186-194.
28. Ewing B., Hillier L., Wendl M.C., Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998, 8:175-185.
29. Fernandez-Vizarra E., Bugiani M., Goffrini P., Carrara F., Farina L., Procopio E., Donati A., Uziel G., Ferrero I., Zeviani M. Impaired complex III assembly associated with BCS1L gene mutations in isolated mitochondrial encephalopathy. Hum. Mol. Genet. 2007, 16:1241-1252.
30. Fischer C.P., Bode B.P., Souba W.W. Adaptive alterations in cellular metabolism with malignant transformation. Ann. Surg. 1998, 227:627-634. (discussion 634-626).
31. Fliss M.S., Usadel H., Caballero O.L., Wu L., Buta M.R., Eleff S.M., Jen J., Sidransky D. Facile detection of mitochondrial DNA mutations in tumors and bodily fluids. Science 2000, 287:2017-2019.
32. Fridjonsson O., Olafsson K., Tompsett S., Bjornsdottir S., Consuegra S., Knox D., de Leaniz C.G., Magnusdottir S., Olafsdottir G., Verspoor E., Hjorleifsdottir S. Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing. BMC Genomics 2011, 12:179.
33. Goto H., Dickins B., Afgan E., Paul I.M., Taylor J., Makova K.D., Nekrutenko A. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biol. 2011, 12:R59.
34. Grzybowski T., Malyarchuk B.A., Czarny J., Miscicka-Sliwica D., Kotzbach R. High levels of mitochondrial DNA heteroplasmy in single hair roots: reanalysis and revision. Electrophoresis 2003, 24:1159-1165.
35. Guo W., Jiang L., Bhasin S., Khan S.M., Swerdlow R.H. DNA extraction procedures meaningfully influence qPCR-based mtDNA copy number determination. Mitochondrion 2009, 9:261-265.
36. Guo Y., Cai Q., Samuels D.C., Ye F., Long J., Li C.I., Winther J.F., Tawn E.J., Stovall M., Lahteenmaki P., Malila N., Levy S., Shaffer C., Shyr Y., Shu X.O., Boice J.D. The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation. Mutat. Res. 2012, 744:154-160.
37. Guo Y., C.Q., Samuels D.C., Ye F., Long J., Li C.I., Winther J.F., Tawn E.J., Stovall M., Lähteenmäki P., Malila N., Levy S., Shaffer C., Shyr Y., Shu X.O., Boice J.D. The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation. Mutat. Res. Genet. Toxicol. Environ. Mutagen. 2012, 744:154-160.
38. Guo Y., Li J., Li C.I., Long J., Samuels D.C., Shyr Y. The effect of strand bias in Illumina short-read sequencing data. BMC Genomics 2012, 13:666.
39. Guo Y., Long J., He J., Li C.I., Cai Q., Shu X.O., Zheng W., Li C. Exome sequencing generates high quality data in non-target regions. BMC Genomics 2012, 13:194.
40. Guo Y., Li C.I., Sheng Q., Winther J.F., Cai Q., Boice J.D., Shyr Y. Very low-level heteroplasmy mtDNA variations are inherited in humans. J. Genet. Genomics 2013, 40:607-615.
41. Guo Y., Li J., Li C.I., Shyr Y., Samuels D.C. MitoSeek: extracting mitochondria information and performing high throughput mitochondria sequencing analysis. Bioinformatics 2013, 29:1210-1211.
42. Guo Y., Samuels D.C., Li J., Clark T., Li C.I., Shyr Y. Evaluation of allele frequency estimation using pooled sequencing data simulation. ScientificWorldJournal 2013, 2013:895496.
43. Guo Y., Ye F., Sheng Q., Clark T., Samuels D.C. Three-stage quality control strategies for DNA re-sequencing data. Brief. Bioinform. 2013.
44. Hazkani-Covo E., Zeller R.M., Martin W. Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet. 2010, 6:e1000834.
45. He Y., Wu J., Dressman D.C., Iacobuzio-Donahue C., Markowitz S.D., Velculescu V.E., Diaz L.A., Kinzler K.W., Vogelstein B., Papadopoulos N. Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. Nature 2010, 464:610-614.
46. Herrmann P.C., Gillespie J.W., Charboneau L., Bichsel V.E., Paweletz C.P., Calvert V.S., Kohn E.C., Emmert-Buck M.R., Liotta L.A., Petricoin E.F. Mitochondrial proteome: altered cytochrome c oxidase subunit levels in prostate cancer. Proteomics 2003, 3:1801-1810.
47. Holt I.J., Harding A.E., Petty R.K., Morgan-Hughes J.A. A new mitochondrial disease associated with mitochondrial DNA heteroplasmy. Am. J. Hum. Genet. 1990, 46:428-433.
48. Kaiser-Wilhelm-Institut fu\r Biologie B.-D., Warburg O.H. The metabolism of tumours: investigations from the Kaiser Wilhelm Institute for Biology, Berlin-Dahlem 1930, Constable and Co., London.
49. Kann L.M., Rosenblum E.B., Rand D.M. Aging, mating, and the evolution of mtDNA heteroplasmy in Drosophila melanogaster. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:2372-2377.
50. Katada S., Mito T., Ogasawara E., Hayashi J., Nakada K. Mitochondrial DNA with a large-scale deletion causes two distinct mitochondrial disease phenotypes in mice. Genes, Genomes, Genet (Bethesda) 2013, 3:1545-1552.
51. Kroemer G. Mitochondria in cancer. Oncogene 2006, 25:4630-4632.
52. Lam E.T., Bracci P.M., Holly E.A., Chu C., Poon A., Wan E., White K., Kwok P.Y., Pawlikowska L., Tranah G.J. Mitochondrial DNA sequence variation and risk of pancreatic cancer. Cancer Res. 2012, 72:686-695.
53. Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9:357-359.
54. Larman T.C., Depalma S.R., Hadjipanayis A.G., Protopopov A., Zhang J., Gabriel S.B., Chin L., Seidman C.E., Kucherlapati R., Seidman J.G. Spectrum of somatic mitochondrial mutations in five cancers. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:14087-14091.
55. Lee H.C., Lu C.Y., Fahn H.J., Wei Y.H. Aging- and smoking-associated alteration in the relative content of mitochondrial DNA in human lung. FEBS Lett. 1998, 441:292-296.
56. Lemasters J.J., Qian T., Bradham C.A., Brenner D.A., Cascio W.E., Trost L.C., Nishimura Y., Nieminen A.L., Herman B. Mitochondrial dysfunction in the pathogenesis of necrotic and apoptotic cell death. J. Bioenerg. Biomembr. 1999, 31:305-319.
57. Lewis P.D., Baxter P., Paul Griffiths A., Parry J.M., Skibinski D.O. Detection of damage to the mitochondrial genome in the oncocytic cells of Warthin's tumour. J. Pathol. 2000, 191:274-281.
58. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
59. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
60. Li M., Schonberg A., Schaefer M., Schroeder R., Nasidze I., Stoneking M. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am. J. Hum. Genet. 2010, 87:237-249.
61. Li M., Schroeder R., Ko A., Stoneking M. Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs. Nucleic Acids Res. 2012, 40:e137.
62. Liang M.H., Johnson D.R., Wong L.J. Preparation and validation of PCR-generated positive controls for diagnostic dot blotting. Clin. Chem. 1998, 44:1578-1579.
63. Lundholm K., Edstrom S., Karlberg I., Ekman L., Schersten T. Glucose turnover, gluconeogenesis from glycerol, and estimation of net glucose cycling in cancer patients. Cancer 1982, 50:1142-1150.
64. Maximo V., Soares P., Seruca R., Sobrinho-Simoes M. Comments on: mutations in mitochondrial control region DNA in gastric tumours of Japanese patients, Tamura, et al. Eur J Cancer 1999, 35, 316-319. Eur. J. Cancer 1999, 35:1407-1408.
65. Maximo V., Soares P., Seruca R., Rocha A.S., Castro P., Sobrinho-Simoes M. Microsatellite instability, mitochondrial DNA large deletions, and mitochondrial DNA mutations in gastric carcinoma. Genes Chromosomes Cancer 2001, 32:136-143.
66. Maximo V., Soares P., Lima J., Cameselle-Teijeiro J., Sobrinho-Simoes M. Mitochondrial DNA somatic mutations (point mutations and large deletions) and mitochondrial DNA variants in human thyroid pathology: a study with emphasis on Hürthle cell tumors. Am. J. Pathol. 2002, 160:1857-1865.
67. Mazurek S., Boschek C.B., Eigenbrodt E. The role of phosphometabolites in cell proliferation, energy metabolism, and tumor therapy. J. Bioenerg. Biomembr. 1997, 29:315-330.
68. Modica-Napolitano J.S., Singh K.K. Mitochondrial dysfunction in cancer. Mitochondrion 2004, 4:755-762.
69. Mourier T., Hansen A.J., Willerslev E., Arctander P. The human genome project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Mol. Biol. Evol. 2001, 18:1833-1837.
70. Ng S.B., Buckingham K.J., Lee C., Bigham A.W., Tabor H.K., Dent K.M., Huff C.D., Shannon P.T., Jabs E.W., Nickerson D.A., Shendure J., Bamshad M.J. Exome sequencing identifies the cause of a Mendelian disorder. Nat. Genet. 2010, 42:30-35.
71. Ockner R.K., Kaikaus R.M., Bass N.M. Fatty-acid metabolism and the pathogenesis of hepatocellular carcinoma: review and hypothesis. Hepatology 1993, 18:669-676.
72. Park J.S., Sharma L.K., Li H., Xiang R., Holstein D., Wu J., Lechleiter J., Naylor S.L., Deng J.J., Lu J., Bai Y. A heteroplasmic, not homoplasmic, mitochondrial DNA mutation promotes tumorigenesis via alteration in reactive oxygen species generation and apoptosis. Hum. Mol. Genet. 2009, 18:1578-1589.
73. Payne B.A., Wilson I.J., Yu-Wai-Man P., Coxhead J., Deehan D., Horvath R., Taylor R.W., Samuels D.C., Santibanez-Koref M., Chinnery P.F. Universal heteroplasmy of human mitochondrial DNA. Hum. Mol. Genet. 2013, 22:384-390.
74. Pereira L., Freitas F., Fernandes V., Pereira J.B., Costa M.D., Costa S., Maximo V., Macaulay V., Rocha R., Samuels D.C. The diversity present in 5140 human mitochondrial genomes. Am. J. Hum. Genet. 2009, 84:628-640.
75. Petrosillo G., Di Venosa N., Ruggiero F.M., Pistolese M., D'Agostino D., Tiravanti E., Fiore T., Paradies G. Mitochondrial dysfunction associated with cardiac ischemia/reperfusion can be attenuated by oxygen tension control. Role of oxygen-free radicals and cardiolipin. Biochim. Biophys. Acta 2005, 1710:78-86.
76. Picardi E., Pesole G. Mitochondrial genomes gleaned from human whole-exome sequencing. Nat. Methods 2012, 9:523-524.
77. Polyak K., Li Y., Zhu H., Lengauer C., Willson J.K., Markowitz S.D., Trush M.A., Kinzler K.W., Vogelstein B. Somatic mutations of the mitochondrial genome in human colorectal tumours. Nat. Genet. 1998, 20:291-293.
78. Putignani L., Raffa S., Pescosolido R., Rizza T., Del Chierico F., Leone L., Aimati L., Signore F., Carrozzo R., Callea F., Torrisi M.R., Grammatico P. Preliminary evidences on mitochondrial injury and impaired oxidative metabolism in breast cancer. Mitochondrion 2012, 12:363-369.
79. Quispe-Tintaya W., White R.R., Popov V.N., Vijg J., Maslov A.Y. Fast mitochondrial DNA isolation from mammalian cells for next-generation sequencing. Biotechniques 2013, 55:133-136.
80. Renis M., Cantatore P., Loguercio Polosa P., Fracasso F., Gadaleta M.N. Content of mitochondrial DNA and of three mitochondrial RNAs in developing and adult rat cerebellum. J. Neurochem. 1989, 52:750-754.
81. Robin E.D., Wong R. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J. Cell. Physiol. 1988, 136:507-513.
82. Samuels D.C., Han L., Li J., Quanghu S., Clark T.A., Shyr Y., Guo Y. Finding the lost treasures in exome sequencing data. Trends Genet. 2013, 29:593-599.
83. Schmitt M.W., Kennedy S.R., Salk J.J., Fox E.J., Hiatt J.B., Loeb L.A. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl. Acad. Sci. 2012, 109:14508-14513.
84. Shen J., Platek M., Mahasneh A., Ambrosone C.B., Zhao H. Mitochondrial copy number and risk of breast cancer: a pilot study. Mitochondrion 2010, 10:62-68.
85. Smigrodzki R.M., Khan S.M. Mitochondrial microheteroplasmy and a theory of aging and age-related disease. Rejuvenation Res. 2005, 8:172-198.
86. Sondheimer N., Glatz C.E., Tirone J.E., Deardorff M.A., Krieger A.M., Hakonarson H. Neutral mitochondrial heteroplasmy and the influence of aging. Hum. Mol. Genet. 2011, 20:1653-1659.
87. Sosa M.X., Sivakumar I.K., Maragh S., Veeramachaneni V., Hariharan R., Parulekar M., Fredrikson K.M., Harkins T.T., Lin J., Feldman A.B., Tata P., Ehret G.B., Chakravarti A. Next-generation sequencing of human mitochondrial reference genomes uncovers high heteroplasmy frequency. PLoS Comput. Biol. 2012, 8:e1002737.
88. Sun W., Zhou S., Chang S.S., McFate T., Verma A., Califano J.A. Mitochondrial mutations contribute to HIF1alpha accumulation via increased reactive oxygen species and up-regulated pyruvate dehydrogenease kinase 2 in head and neck squamous cell carcinoma. Clin. Cancer Res. 2009, 15:476-484.
89. Tang S., Huang T. Characterization of mitochondrial DNA heteroplasmy using a parallel sequencing system. Biotechniques 2010, 48:287-296.
90. Timmis J.N., Ayliffe M.A., Huang C.Y., Martin W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 2004, 5:123-135.
91. Tseng L.M., Yin P.H., Chi C.W., Hsu C.Y., Wu C.W., Lee L.M., Wei Y.H., Lee H.C. Mitochondrial DNA mutations and mitochondrial DNA depletion in breast cancer. Genes Chromosomes Cancer 2006, 45:629-638.
92. van der Walt E.M., Smuts I., Taylor R.W., Elson J.L., Turnbull D.M., Louw R., van der Westhuizen F.H. Characterization of mtDNA variation in a cohort of South African paediatric patients with mitochondrial disease. Eur. J. Hum. Genet. 2012, 20:650-656.
93. Vanharanta S., Buchta M., McWhinney S.R., Virta S.K., Peczkowska M., Morrison C.D., Lehtonen R., Januszewicz A., Jarvinen H., Juhola M., Mecklin J.P., Pukkala E., Herva R., Kiuru M., Nupponen N.N., Aaltonen L.A., Neumann H.P., Eng C. Early-onset renal cell carcinoma as a novel extraparaganglial component of SDHB-associated heritable paraganglioma. Am. J. Hum. Genet. 2004, 74:153-159.
94. Vasta V., Ng S.B., Turner E.H., Shendure J., Hahn S.H. Next generation sequence analysis for mitochondrial disorders. Genome Med. 2009, 1.
95. Verma M., Naviaux R.K., Tanaka M., Kumar D., Franceschi C., Singh K.K. Meeting report: mitochondrial DNA and cancer epidemiology. Cancer Res. 2007, 67:437-439.
96. Wallace K.B., Starkov A.A. Mitochondrial targets of drug toxicity. Annu. Rev. Pharmacol. Toxicol. 2000, 40:353-388.
97. White H.E., Durston V.J., Seller A., Fratter C., Harvey J.F., Cross N.C. Accurate detection and quantitation of heteroplasmic mitochondrial point mutations by pyrosequencing. Genet. Test. 2005, 9:190-199.
98. Yang Ai S.S., Hsu K., Herbert C., Cheng Z., Hunt J., Lewis C.R., Thomas P.S. Mitochondrial DNA mutations in exhaled breath condensate of patients with lung cancer. Respir. Med. 2013, 107:911-918.
99. Yang Z., Nielsen R. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol. 1998, 46:409-418.
100. Ye K., Schulz M.H., Long Q., Apweiler R., Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009, 25:2865-2871.
101. Yu M., Zhou Y., Shi Y., Ning L., Yang Y., Wei X., Zhang N., Hao X., Niu R. Reduced mitochondrial DNA copy number is correlated with tumor progression and prognosis in Chinese breast cancer patients. IUBMB Life 2007, 59:450-457.
102. Zhang D.X., Hewitt G.M. Nuclear integrations: challenges for mitochondrial DNA markers. Trends Ecol. Evol. 1996, 11:247-251.
103. Zhang W., Cui H., Wong L.J. Comprehensive one-step molecular analyses of mitochondrial genome by massively parallel sequencing. Clin. Chem. 2012, 58:1322-1331.
104. Zhu W., Qin W., Sauter E.R. Large-scale mitochondrial DNA deletion mutations and nuclear genome instability in human breast cancer. Cancer Detect. Prev. 2004, 28:119-126.