Modica-Napolitano JS, Kulawiec M, Singh KK. Mitochondria and human cancer. Curr Mol Med. 2007;7(1):121–31.
Article
CAS
PubMed
Google Scholar
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(2):147.
Article
CAS
PubMed
Google Scholar
Verma M, Kumar D. Application of mitochondrial genome information in cancer epidemiology. Clin Chim Acta. 2007;383(1-2):41–50.
Article
CAS
PubMed
Google Scholar
Bogenhagen DF. Repair of mtDNA in vertebrates. Am J Hum Genet. 1999;64(5):1276–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Macmillan C, Lach B, Shoubridge EA. Variable distribution of mutant mitochondrial DNAs (tRNA(Leu[3243])) in tissues of symptomatic relatives with MELAS: the role of mitotic segregation. Neurology. 1993;43(8):1586–90.
Article
CAS
PubMed
Google Scholar
Chinnery PF. Mitochondrial disorders overview. 2014.
Google Scholar
Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, Nekrutenko A. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biol. 2011;12(6):R59.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lott MT, Leipzig JN, Derbeneva O, Xie HM, Chalkia D, Sarmady M, Procaccio V, Wallace DC. mtDNA variation and analysis using MITOMAP and MITOMASTER. Curr Protoc Bioinformatics. 2013;1(123):1–23. 21-21 23 26.
PubMed Central
Google Scholar
Ramos A, Santos C, Mateiu L, Gonzalez Mdel M, Alvarez L, Azevedo L, Amorim A, Aluja MP. Frequency and pattern of heteroplasmy in the complete human mitochondrial genome. PLoS ONE. 2013;8(10):e74636.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wallace DC. Mitochondrial DNA mutations in disease and aging. Environ Mol Mutagen. 2010;51(5):440–50.
CAS
PubMed
Google Scholar
Wallace DC. A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a dawn for evolutionary medicine. Annu Rev Genet. 2005;39:359–407.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robin ED, Wong R. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J Cell Physiol. 1988;136(3):507–13.
Article
CAS
PubMed
Google Scholar
He Y, Wu J, Dressman DC, Iacobuzio-Donahue C, Markowitz SD, Velculescu VE, Diaz Jr LA, Kinzler KW, Vogelstein B, Papadopoulos N. Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. Nature. 2010;464(7288):610–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smigrodzki RM, Khan SM. Mitochondrial microheteroplasmy and a theory of aging and age-related disease. Rejuvenation Res. 2005;8(3):172–98.
Article
CAS
PubMed
Google Scholar
Yu J, Sadakari Y, Shindo K, Suenaga M, Brant A, Almario JA, Borges M, Barkley T, Fesharakizadeh S, Ford M et al. Digital next-generation sequencing identifies low-abundance mutations in pancreatic juice samples collected from the duodenum of patients with pancreatic cancer and intraductal papillary mucinous neoplasms. Gut. 2016. doi:10.1136/gutjnl-2015-311166.
Lin MT, Simon DK, Ahn CH, Kim LM, Beal MF. High aggregate burden of somatic mtDNA point mutations in aging and Alzheimer’s disease brain. Hum Mol Genet. 2002;11(2):133–45.
Article
CAS
PubMed
Google Scholar
Parker Jr WD, Parks JK. Mitochondrial ND5 mutations in idiopathic Parkinson’s disease. Biochem Biophys Res Commun. 2005;326(3):667–9.
Article
CAS
PubMed
Google Scholar
Irwin JA, Saunier JL, Niederstatter H, Strouss KM, Sturk KA, Diegoli TM, Brandstatter A, Parson W, Parsons TJ. Investigation of heteroplasmy in the human mitochondrial DNA control region: a synthesis of observations from more than 5000 global population samples. J Mol Evol. 2009;68(5):516–27.
Article
CAS
PubMed
Google Scholar
Meierhofer D, Mayr JA, Ebner S, Sperl W, Kofler B. Rapid screening of the entire mitochondrial DNA for low-level heteroplasmic mutations. Mitochondrion. 2005;5(4):282–96.
Article
CAS
PubMed
Google Scholar
Cassandrini D, Calevo MG, Tessa A, Manfredi G, Fattori F, Meschini MC, Carrozzo R, Tonoli E, Pedemonte M, Minetti C, et al. A new method for analysis of mitochondrial DNA point mutations and assess levels of heteroplasmy. Biochem Biophys Res Commun. 2006;342(2):387–93.
Article
CAS
PubMed
Google Scholar
Dobrowolski SF, Hendrickx AT, van den Bosch BJ, Smeets HJ, Gray J, Miller T, Sears M. Identifying sequence variants in the human mitochondrial genome using high-resolution melt (HRM) profiling. Hum Mutat. 2009;30(6):891–8.
Article
CAS
PubMed
Google Scholar
Wong LJ, Chen TJ, Tan DJ. Detection of mitochondrial DNA mutations using temporal temperature gradient gel electrophoresis. Electrophoresis. 2004;25(15):2602–10.
Article
CAS
PubMed
Google Scholar
Mashima Y, Nagano M, Funayama T, Zhang Q, Egashira T, Kudho J, Shimizu N, Oguchi Y. Rapid quantification of the heteroplasmy of mutant mitochondrial DNAs in Leber’s hereditary optic neuropathy using the Invader technology. Clin Biochem. 2004;37(4):268–76.
Article
CAS
PubMed
Google Scholar
Bannwarth S, Procaccio V, Paquis-Flucklinger V. Surveyor Nuclease: a new strategy for a rapid identification of heteroplasmic mitochondrial DNA mutations in patients with respiratory chain defects. Hum Mutat. 2005;25(6):575–82.
Article
CAS
PubMed
Google Scholar
Bai R, Higgs J, Suchy S, Arjona D, Smaoui N, Richard G, Compton J, Bale S, Parikh S, Tarnopolsky M, et al. Whole mitochondrial genome amplification and next generation sequencing for the diagnosis of mitochondrial disorders: yield of 613 cases. Mitochondrion. 2013;13(6):935–6.
Article
Google Scholar
Huang T. Next generation sequencing to characterize mitochondrial genomic DNA heteroplasmy. Curr Protoc Hum Genet. 2011;Chapter 19:Unit19.18.
Google Scholar
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(2):237–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li M, Schroeder R, Ko A, Stoneking M. Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs. Nucleic Acids Res. 2012;40(18):e137.
Article
CAS
PubMed
PubMed Central
Google Scholar
Giannoulatou E, Park SH, Humphreys DT, Ho JW. Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie. BMC Bioinform. 2014;15 Suppl 16:S15.
Article
Google Scholar
Hatem A, Bozdag D, Toland AE, Catalyurek UV. Benchmarking short sequence mapping tools. BMC Bioinform. 2013;14:184.
Article
Google Scholar
Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform. 2010;11(5):473–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ruffalo M, LaFramboise T, Koyuturk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics. 2011;27(20):2790–6.
Article
CAS
PubMed
Google Scholar
Ye F, Samuels DC, Clark T, Guo Y. High-throughput sequencing in mitochondrial DNA research. Mitochondrion. 2014;17:157–63.
Article
CAS
PubMed
Google Scholar
Guo Y, Li J, Li CI, Shyr Y, Samuels DC. MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. Bioinformatics. 2013;29(9):1210–1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y. Finding the lost treasures in exome sequencing data. Trends Genet. 2013;29(10):593–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics. 2008;9:267.
Article
PubMed
PubMed Central
Google Scholar
Ramos A, Barbena E, Mateiu L, del Mar GM, Mairal Q, Lima M, Montiel R, Aluja MP, Santos C. Nuclear insertions of mitochondrial origin: database updating and usefulness in cancer studies. Mitochondrion. 2011;11(6):946–53.
Article
CAS
PubMed
Google Scholar
Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics. 2011;12:517.
Article
PubMed
PubMed Central
Google Scholar
Calabrese FM, Simone D, Attimonelli M. Primates and mouse NumtS in the UCSC Genome Browser. BMC Bioinform. 2012;13 Suppl 4:S15.
Article
Google Scholar
Leinonen R, Sugawara H, Shumway M. The sequence read archive. Nucleic Acids Res. 2011;39:D19–21.
Article
CAS
PubMed
Google Scholar
Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, et al. The European nucleotide archive. Nucleic Acids Res. 2011;39:D28–31.
Article
CAS
PubMed
Google Scholar
Tomczak K, Czerwińska P, Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol (Pozn). 2015;19:A68–77.
Google Scholar
Zhang J, Baran J, Cros A, Guberman JM, Haider S, Hsu J, Liang Y, Rivkin E, Wang J, Whitty B, et al. International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data. Database (Oxford). 2011;2011:bar026.
Google Scholar
Tsuji J, Frith MC, Tomii K, Horton P. Mammalian NUMT insertion is non-random. Nucleic Acids Res. 2012;40(18):9073–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Meyer M, Stenzel U, Myles S, Prufer K, Hofreiter M. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res. 2007;35(15):e97.
Article
PubMed
PubMed Central
Google Scholar
Schonberg A, Theunert C, Li M, Stoneking M, Nasidze I. High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences. Eur J Hum Genet. 2011;19(9):988–94.
Article
PubMed
PubMed Central
Google Scholar
Qu W, Zhang C. Selecting specific PCR primers with MFEprimer. Methods Mol Biol. 2015;1275:201–13.
Article
CAS
PubMed
Google Scholar
Fortes GG, Paijmans JL. Analysis of whole mitogenomes from ancient samples. Methods Mol Biol. 2015;1347:179–95.
Article
PubMed
Google Scholar
Lippold S, Xu H, Ko A, Li M, Renaud G, Butthof A, Schroder R, Stoneking M. Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. Investig Genet. 2014;5:13.
Article
PubMed
PubMed Central
Google Scholar
de Sousa F, Bertrand YJ, Nylinder S, Oxelman B, Eriksson JS, Pfeil BE. Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing. PLoS ONE. 2014;9(10):e109704.
Article
PubMed
PubMed Central
Google Scholar
King TE, Fortes GG, Balaresque P, Thomas MG, Balding D, Maisano Delser P, Neumann R, Parson W, Knapp M, Walsh S, et al. Identification of the remains of King Richard III. Nat Commun. 2014;5:5631.
Article
CAS
PubMed
PubMed Central
Google Scholar