Targeted enrichment and high-resolution digital profiling of mitochondrial DNA deletions in human brain

Aging Cell

Volumn 13, Issue 1, 2014, Pages 29-38

  Taylor, Sean D ^a   Ericson, Nolan G ^a   Burton, Joshua N ^b   Prolla, Tomas A ^c   Silber, John R ^d   Shendure, Jay ^b   Bielas, Jason H ^a,d  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

^d UNIVERSITY OF WASHINGTON MEDICAL CENTER   (United States)

Author keywords

Aging; Genome instability; Mitochondrial disease; Mitochondrial DNA; Next generation sequencing; Rare deletion detection

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; BRAIN TISSUE; CONTROLLED STUDY; DNA FINGERPRINTING; DNA ISOLATION; GENE DELETION; GENE MUTATION; HUMAN; HUMAN TISSUE; MITOCHONDRIAL GENOME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; ADOLESCENT; ADULT; AGED; AGING; BRAIN; GENETIC HETEROGENEITY; GENETICS; METABOLISM; MIDDLE AGED; MITOSIS; NUCLEOTIDE SEQUENCE; PATHOLOGY; PROCEDURES; VERY ELDERLY; YOUNG ADULT;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; AGING; BRAIN; DNA MUTATIONAL ANALYSIS; DNA, MITOCHONDRIAL; GENETIC HETEROGENEITY; HUMANS; MIDDLE AGED; MITOSIS; SEQUENCE DELETION; YOUNG ADULT;

EID: 84892497789     PISSN: 14749718     EISSN: 14749726     Source Type: Journal    
DOI: 10.1111/acel.12146     Document Type: Article

References (43)

1. Ameur A, Stewart JB, Freyer C, Hagström E, Ingman M, Larsson N-G, Gyllensten U (2011) Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins. PLoS Genet. 7, e1002028.
2. Berdanier CD, Everts HB (2001) Mitochondrial DNA in aging and degenerative disease. Mutat. Res. 475, 169-183.
3. Bielas JH, Loeb LA (2005) Quantification of random genomic mutations. Nat. Methods 2, 285-290.
4. Brierley EJ, Johnson MA, Lightowlers RN, James OF, Turnbull DM (1998) Role of mitochondrial DNA mutations in human aging: implications for the central nervous system and muscle. Ann Neurol. 43, 217-223.
5. Chabi B, Mousson de Camaret B, Duborjal H, Issartel J-P, Stepien G (2003) Quantification of mitochondrial DNA deletion, depletion, and over-replication: application to diagnosis. Clin. Chem. 49, 1309-1317.
6. Chinnery PF (1993) Mitochondrial disorders overview. In GeneReviews. (Pagon RA, Adam MP, Bird TD, Dolan CR, Fong CT, Stephens K, eds). Seattle, WA: University of Washington. URL http://www.ncbi.nlm.nih.gov/books/NBK1224/ [accessed on 20 July 2013].
7. Coller HA, Khrapko K, Bodyak ND, Nekhaeva E, Herrero-Jimenez P, Thilly WG (2001) High frequency of homoplasmic mitochondrial DNA mutations in human tumors can be explained without selection. Nat. Genet. 28, 147-150.
8. Cortopassi GA, Arnheim N (1990) Detection of a specific mitochondrial DNA deletion in tissues of older humans. Nucleic Acids Res. 18, 6927-6933.
9. DiMauro S, Hirano M(1993). Mitochondrial DNA deletion syndromes. In GeneReviews. (Pagon RA, Adam MP, Bird TD, Dolan CR, Fong CT, Stephens K, eds). Seattle, WA: University of Washington. URL http://www.ncbi.nlm.nih.gov/books/NBK1203/ [accessed on 20 July 2013].
10. Durham SE, Samuels DC, Chinnery PF (2006) Is selection required for the accumulation of somatic mitochondrial DNA mutations in post-mitotic cells? Neuromuscul. Disord. 16, 381-386.
11. Elson JL, Samuels DC, Turnbull DM, Chinnery PF (2001) Random intracellular drift explains the clonal expansion of mitochondrial DNA mutations with age. Am. J. Hum. Genet. 68, 802-806.
12. Foury F, Hu J, Vanderstraeten S (2004) Mitochondrial DNA mutators. Cell. Mol. Life Sci. 61, 2799-2811.
13. Freyer C, Cree LM, Mourier A, Stewart JB, Koolmeister C, Milenkovic D, Wai T, Floros VI, Hagstrom E, Chatzidaki EE, Wiesner RJ, Samuels DC, Larsson NG, Chinnery PF (2012) Variation in germline mtDNA heteroplasmy is determined prenatally but modified during subsequent transmission. Nat. Genet. 44, 1282-1285.
14. Fukui H, Moraes CT (2009) Mechanisms of formation and accumulation of mitochondrial DNA deletions in aging neurons. Hum. Mol. Genet. 18, 1028-1036.
15. Greaves LC, Reeve AK, Taylor RW, Turnbull DM (2012) Mitochondrial DNA and disease. J. Pathol. 226, 274-286.
16. de Grey AD (2009) How is mutant mitochondrial DNA clonally amplified? Much new evidence, still no answers. Rejuvenation Res. 12, 217-219.
17. Guo X, Kudryavtseva E, Bodyak N, Nicholas A, Dombrovsky I, Yang D, Kraytsberg Y, Simon DK, Khrapko K (2010) Mitochondrial DNA deletions in mice in men: substantia nigra is much less affected in the mouse. Biochim. Biophys. Acta 1797, 1159-1162.
18. He L, Chinnery PF, Durham SE, Blakely EL, Wardell TM, Borthwick GM, Taylor RW, Turnbull DM (2002) Detection and quantification of mitochondrial DNA deletions in individual cells by real-time PCR. Nucleic Acids Res. 30, e68.
19. Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, Kitano TK, Hodel MR, Petersen JF, Wyatt PW, Steenblock ER, Shah PH, Bousse LJ, Troup CB, Mellen JC, Wittmann DK, Erndt NG, Cauley TH, Koehler RT, So AP, Dube S, Rose KA, Montesclaros L, Wang S, Stumbo DP, Hodges SP, Romine S, Milanovich FP, White HE, Regan JF, Karlin-Neumann GA, Hindson CM, Saxonov S, Colston BW (2011) High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal. Chem. 83, 8604-8610.
20. Kato M, Nakamura M, Ichiba M, Tomiyasu A, Shimo H, Higuchi I, S-i U, Sano A (2011) Mitochondrial DNA deletion mutations in patients with neuropsychiatric symptoms. Neurosci. Res. 69, 331-336.
21. Khrapko K (2011) The timing of mitochondrial DNA mutations in aging. Nat. Genet. 43, 726-727.
22. Khrapko K, Vijg J (2009) Mitochondrial DNA mutations and aging: devils in the details? Trends Genet. 25, 91-98.
23. Khrapko K, Nekhaeva E, Kraytsberg Y, Kunz W (2003) Clonal expansions of mitochondrial genomes: implications for in vivo mutational spectra. Mutat. Res. 522, 13-19.
24. Khrapko K, Ebralidse K, Kraytsberg Y (2004) Where and when do somatic mtDNA mutations occur? Ann. N. Y. Acad. Sci. 1019, 240-244.
25. Kraytsberg Y, Khrapko K (2005) Single-molecule PCR: an artifact-free PCR approach for the analysis of somatic mutations. Expert. Rev. Mol. Diagn. 5, 809-815.
26. Kraytsberg Y, Nicholas A, Caro P, Khrapko K (2008) Single molecule PCR in mtDNA mutational analysis: genuine mutations vs. damage bypass-derived artifacts. Methods 46, 269-273.
27. Krishnan KJ, Reeve AK, Samuels DC, Chinnery PF, Blackwood JK, Taylor RW, Wanrooij S, Spelbrink JN, Lightowlers RN, Turnbull DM (2008) What causes mitochondrial DNA deletions in human cells? Nat. Genet. 40, 275-279.
28. Lee HC, Chang CM, Chi CW (2010) Somatic mutations of mitochondrial DNA in aging and cancer progression. Ageing Res Rev. 9(Suppl 1), S47-S58.
29. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012, 11.
30. Meissner C (2007) Mutations of mitochondrial DNA - cause or consequence of the ageing process? Z. Gerontol. Geriatr. 40, 325-333.
31. Meissner C, Bruse P, Mohamed SA, Schulz A, Warnk H, Storm T, Oehmichen M (2008) The 4977 bp deletion of mitochondrial DNA in human skeletal muscle, heart and different areas of the brain: a useful biomarker or more? Exp. Gerontol. 43, 645-652.
32. Nicholas A, Kraytsberg Y, Guo X, Khrapko K (2009) On the timing and the extent of clonal expansion of mtDNA deletions: evidence from single-molecule PCR. Exp. Neurol. 218, 316-319.
33. Payne BA, Wilson IJ, Hateley CA, Horvath R, Santibanez-Koref M, Samuels DC, Price DA, Chinnery PF (2011) Mitochondrial aging is accelerated by anti-retroviral therapy through the clonal expansion of mtDNA mutations. Nat. Genet. 43, 806-810.
34. Pinheiro LB, Coleman VA, Hindson CM, Herrmann J, Hindson BJ, Bhat S, Emslie KR (2012) Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification. Anal. Chem. 84, 1003-1011.
35. R Core Team (2013). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/ [accessed on 5 October 2012].
36. Scheffler IE (2008) Mitochondria. Hoboken, NJ: Wiley-Liss.
37. Sequeira A, Martin MV, Rollins B, Moon EA, Bunney WE, Macciardi F, Lupoli S, Smith EN, Kelsoe J, Magnan CN, van Oven M, Baldi P, Wallace DC, Vawter MP (2012) Mitochondrial mutations and polymorphisms in psychiatric disorders. Front. genet. 3, 103.
38. Song Z, Cao Y, Samuels DC (2011) Replication pauses of the wild-type and mutant mitochondrial DNA polymerase gamma: a simulation study. PLoS Comput. Biol. 7, e1002287.
39. Spelbrink JN, Toivonen JM, Hakkaart GA, Kurkela JM, Cooper HM, Lehtinen SK, Lecrenier N, Back JW, Speijer D, Foury F, Jacobs HT (2000) In vivo functional analysis of the human mitochondrial DNA polymerase POLG expressed in cultured human cells. J. Biol. Chem. 275, 24818-24828.
40. Vermulst M, Bielas JH, Loeb LA (2008a) Quantification of random mutations in the mitochondrial genome. Methods 46, 263-268.
41. Vermulst M, Wanagat J, Kujoth GC, Bielas JH, Rabinovitch PS, Prolla TA, Loeb LA (2008b) DNA deletions and clonal mutations drive premature aging in mitochondrial mutator mice. Nat. Genet. 40, 392-394.
42. Vermulst M, Khrapko K, Wanagat J (2012). Mitochondrial mutagenesis in aging and disease. In Mutagenesis. (R Mishra ed.) ISBN: 978-953-51-0707-1, URL http://www.intechopen.com/books/mutagenesis/mitochondrial-mutagenesis-in-aging-and-disease [accessed on 20 July 2013].
43. Wallace DC (1989) Mitochondrial DNA mutations and neuromuscular disease. Trends Genet. 5, 9-13.