Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: A novel tool for the identification and differentiation of humans

Analytical Biochemistry

Volumn 344, Issue 1, 2005, Pages 53-69

  Hall, Thomas A ^a   Budowle, Bruce ^b   Jiang, Yun ^a   Blyn, Lawrence ^a   Eshoo, Mark ^a   Sannes Lowery, Kristin A ^a   Sampath, Rangarajan ^a   Drader, Jared J ^a   Hannis, James C ^a   Harrell, Patina ^a   Samant, Vivek ^a   White, Neill ^a   Ecker, David J ^a   Hofstadler, Steven A ^a  

^a ISIS PHARMACEUTICALS   (United States)

^b FBI LABORATORY   (United States)

Author keywords

Human forensics; Mass spectrometry; Mitochondrial DNA

Indexed keywords

DNA; FORENSIC ENGINEERING; GENE ENCODING; MASS SPECTROMETRY; MITOCHONDRIA; MIXTURES; NUCLEOTIDES; POLYMERASE CHAIN REACTION;

ELECTROSPRAY IONIZATION MASS SPECTROMETRY; HUMAN FORENSICS; HYBRIDIZATION PROBE; MITOCHONDRIAL DNA; MITOCHONDRIAL DNA (MTDNA); NUMBER OF SAMPLES; SINGLE-NUCLEOTIDE POLYMORPHISMS; TRADITIONAL APPROACHES;

ELECTROSPRAY IONIZATION;

MITOCHONDRIAL DNA; NUCLEOTIDE;

AMPLICON; ARTICLE; DNA BASE COMPOSITION; DNA SEQUENCE; ELECTROSPRAY MASS SPECTROMETRY; GENETIC VARIABILITY; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 27644509687     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2005.05.028     Document Type: Article

References (54)

1. M. Allen, A.A. Engstrom, S. Myers, O. Handt, T. Saldeen, A. von Haeseler, S. Paabo, U. Gyllenstein, Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities, J. Forensic Sci. 43 (1998) 453-464.
2. B. Budowle, M.W. Allard, M.R. Wilson, R. Chakraborty, Forensics and mitochondrial DNA: applications, debates, and foundations, Annu. Rev. Genom. Hum. Genet. 4 (2003) 119-141.
3. C. Ginther, L. Issel-Tarver, M.C. King, Identifying individuals by sequencing mitochondrial DNA from teeth, Nat. Genet. 2 (1992) 135-138.
4. K.M. Sullivan, R. Hopgood, B. Lang, P. Gill, Automated amplification and sequencing of human mitochondrial DNA, Electrophoresis 12 (1991) 17-21.
5. K.M. Sullivan, R. Hopgood, P. Gill, Identification of human remains by amplification and automated sequencing of mitochondrial DNA, Int. J. Leg. Med. 105 (1992) 83-86.
6. M.R. Wilson, J.A. DiZinno, D. Polanskey, J. Replogle, B. Budowle, Validation of mitochondrial DNA sequencing for forensic casework analysis, Int. J. Leg. Med. 108 (1995) 68-74.
7. D. Bogenhagen, D.A. Clayton, The number of mitochondrial deoxyribonucleic acid genomes in mouse L and human HeLa cells, J. Biol. Chem. 249 (1974) 7791-7795.
8. J.T. Case, D.C. Wallace, Maternal inheritance of mitochondrial DNA polymorphisms in cultured human fibroblasts, Somatic Cell Genet. 7 (1981) 103-108.
9. R.E. Giles, H. Blanc, H.M. Cann, D.C. Wallace, Maternal inheritance of human mitochondrial DNA, Proc. Natl. Acad. Sci. USA 77 (1980) 6715-6719.
10. C.A. Hutchinson, J.E. Newbold, S.S. Potter, M.H. Edgell, Maternal influence of mammalian mitochondrial DNA, Nature 251 (1974) 536-538.
11. S. Kumar, P. Hedrick, T. Dowling, M. Stoneking, Questioning evidence for recombination in human mitochondrial DNA, Science 288 (2000) 1931a.
12. F.S. Sanger, S. Nicklen, A.R. Coulson, DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. USA 74 (1977) 5463-5467.
13. B. Budowle, M.R. Wilson, J.A. DiZinno, C. Stauffer, M.A. Fasano, M.M. Holland, K.L. Monson, Mitochondrial DNA regions HVI and HVII population data, Forensic Sci. Int. 103 (1999) 23-35.
14. B.D. Greenberg, J.E. Newbold, A. Sugino, Intraspecific nucleotide sequence variability surrounding the origin of replication in human mitochondrial DNA, Gene 21 (1983) 33-49.
15. L.M. Vigilant, M. Stoneking, H. Harpending, K. Hawkes, A.C. Wilson, African populations and the evolution of human mitochondrial DNA, Science 253 (1991) 1503-1507.
16. R. Reynolds, K. Walker, J. Varlaro, M. Allen, E. Clark, M. Alavaren, H. Erlich, Detection of sequence variation in the HVII region of human mitochondrial genome of 689 individuals using immobilized sequence-specific oligonucleotide probes, J. Forensic Sci. 45 (2000) 1210.
17. R.K. Saiki, P.S. Walsh, C.H. Levenson, H.A. Erlich, Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes, Proc. Natl. Acad. Sci. USA 86 (1989) 6230-6234.
18. A.C. Syvanen, From gels to chips: minisequencing primer extension for analysis of point mutation and single nucleotide polymorphisms, Hum. Mutat. 13 (1999) 1-10.
19. A.C. Syvanen, K. Aalto-Setala, L. Harju, K. Kontula, H.A. Soderlund, Primer-guide nucleotide incorporation assay in genotyping of apolipoprotein E, Genomics 8 (1990) 684-692.
20. A. Ahmadian, B. Gharizadeh, A.C. Gustafsson, F. Sterky, P. Nyren, M. Uhlen, J. Lundeberg, Single-nucleotide polymorphism analysis by pyrosequencing, Anal. Biochem. 280 (2000) 103-110.
21. H. Andreasson, A. Asp, A. Alderborn, Y. Gyllensten, M. Allen, Mitochondrial sequence analysis for forensic identification using pyrosequencing technology, Biotechniques 32 (2002) 124-133.
22. M. Ronaghi, S. Karamohamed, B. Petterson, M. Uhlen, P. Nyren, Real-time DNA sequencing using detection of pyrophosphate release, Anal. Biochem. 242 (1996) 84-89.
23. M.J. Doktycz, G.B. Hurst, S. Habibi-Goudarzi, S.A. McLuckey, K. Tang, C.H. Chen, M. Uziel, K.B. Jacobson, R.P. Woychik, M.V. Buchanan, Analysis of polymerase chain reaction-amplified DNA products by mass spectrometry using matrix-assisted laser desorption and electrospray: current status, Anal. Biochem. 230 (1995) 205-214.
24. G.B. Hurst, M.J. Doktycz, A.A. Vass, M.V. Buchanan, Detection of bacterial DNA polymerase chain reaction products by matrix-assisted laser desorption ionization mass spectrometry, Rapid Commun. Mass Spectrom. 10 (1996) 377-382.
25. M.T. Krahmer, Y.A. Johnson, J.J. Walters, K.F. Fox, A. Fox, M. Nagpal, Electrospray quadrupole mass spectrometry analysis of model oligonucleotides and polymerase chain reaction products: determination of base substitutions, nucleotide additions/deletions, and chemical modifications, Anal. Chem. 71 (1999) 2893-2900.
26. Y. Naito, K. Ishikawa, Y. Koga, T. Tsuneyoshi, H. Terunuma, Molecular mass measurement of polymerase chain reaction products amplified from human blood DNA by electrospray ionization mass spectrometry, Rapid Commun. Mass Spectrom. 9 (1995) 1484-1486.
27. Y. Naito, K. Ishikawa, Y. Koga, T. Tsuneyoshi, H. Terunuma, R. Arakawa, Genetic diagnosis by polymerase chain reaction and electrospray ionization mass spectrometry: detection of five base deletion from blood DNA of a familial adenomatous polyposis patient, J. Am. Soc. Mass Spectrom. 8 (1997) 737-742.
28. K.H. Buetow, M. Edmonson, R. MacDonald, R. Clifford, P. Yip, J. Kelley, D.P. Little, R. Strausberg, H. Koester, C.R. Cantor, A. Braun, High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Proc. Natl. Acad. Sci. USA 98 (2001) 581-584.
29. D.J. Aaserud, Z. Guan, D.P. Little, F.W. McLafferty, DNA sequencing with blackbody infrared radiative dissociation of electrosprayed ions, Int. J. Mass Spectrom. Ion Processes 167/168 (1997) 705-712.
30. D.C. Muddiman, G.A. Anderson, S.A. Hofstadler, R.D. Smith, Length and base composition of PCR-amplified nucleic acids using mass measurements from electrospray ionization mass spectrometry, Anal. Chem. 69 (1997) 1543-1549.
31. D.C. Muddiman, D.S. Wunschel, C.L. Liu, L. Pasatolic, K.F. Fox, A. Fox, G.A. Anderson, R.D. Smith, Characterization of PCR products from bacilli using electrospray ionization FTICR mass spectrometry, Anal. Chem. 68 (1996) 3705-3712.
32. S.A. Hofstadler, R. Sampath, L.B. Blyn, M.W. Eshoo, T.A. Hall, Y. Jiang, J.J. Drader, J.C. Hannis, K.A. Sannes-Lowery, L.L. Cummins, B. Libby, D.J. Walcott, A. Schink, C. Massire, R. Ranken, N. White, V. Samant, J.A. McNeil, D. Knize, D. Robbins, K. Rudnik, A. Desai, E. Moradi, D.J. Ecker, TIGER: the universal biosensor, Int. J. Mass Spectrom. 242 (2005) 23-41.
33. M. Van Ert, S.A. Hofstadler, Y. Jiang, J.D. Busch, D.M. Wagner, J.J. Drader, D.E. Ecker, J.C. Hannis, L.Y. Huynh, J.M. Schupp, T. Simonson, P. Keim, Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis, Biotechniques 37 (2004) 642-651.
34. K.L. Monson, K.W.P. Miller, M.R. Wilson, J.A. DiZinno, B. Budowle, The mtDNA population database: an integrated software and database resource for forensic comparison, Forensic Sci. Commun. 4 (2002).
35. S. Anderson, A.T. Bankier, B.G. Barrell, M.H.L. de Bruijn, A.R. Coulson, J. Drouin, I.C. Eperon, D.P. Nierlich, B.A. Roe, F. Sanger, P.H. Schreier, A.J.H. Smith, R. Staden, I.G. Young, Sequence and organization of the human mitochondrial genome, Nature 290 (1981) 457-465.
36. R.M. Andrews, I. Kubacka, P.F. Chinnery, R.N. Lightowlers, D.M. Turnbull, N. Howell, Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA, Nat. Genet. 23 (1999) 147.
37. M.R. Wilson, M.W. Allard, K.L. Monson, K.W.P. Miller, B. Budowle, Recommendations for consistent treatment of length variants in the human mitochondrial DNA control region, Forensic Sci. Int. 129 (2002) 35-42.
38. K.E. Bendall, B.C. Sykes, Length heteroplasmy in the first hypervariable segment of the human mtDNA control region, Am. J. Hum. Genet. 57 (1995) 248-256.
39. D. Comas, S. Paabo, J. Bertranpetit, Heteroplasmy in the control region of human mitochondrial DNA, Genet. Res. 5 (1995) 89-90.
40. P. Gill, P.L. Ivanov, C. Kimpton, R. Piercy, N. Benson, G. Tull, I. Evett, E. Hagelberg, K. Sullivan, Identification of the remains of the Romanov family by DNA analysis, Nat. Genet. 6 (1994) 130-135.
41. M.R. Wilson, D. Polanskey, J. Replogle, J.A. DiZinno, B. Budowle, A family exhibiting heteroplasmy in the human mitochondrial DNA control region reveals both somatic mosaicism and pronounced segregation of mitotypes, Hum. Genet. 100 (1997) 167-171.
42. Y. Jiang, S.A. Hofstadler, A highly efficient and automated method of purifying and desalting PCR products for analysis by electrospray ionization mass spectrometry, Anal. Biochem. 316 (2003) 50-57.
43. G.A. Anderson, J.E. Bruce, Pacific Northwest National Laboratory, 1995.
44. D.M. Horn, R.A. Zubarev, F.W. McLafferty, Automated reduction and interpretation of high resolution electrospray mass spectra of large molecule, J. Am. Soc. Mass Spectrom. 11 (2000) 320-332.
45. M.R. Wilson, D. Polanskey, J. Butler, J.A. DiZinno, J. Replogle, B. Budowle, Extraction, PCR amplification, and sequencing of mitochondrial DNA from human hair shafts, Biotechniques 18 (1995) 662-669.
46. B. Budowle, J.A. DiZinno, M.R. Wilson, Interpretation guidelines for mitochondrial DNA sequencing, in Tenth International Symposium on Human Identification, 1999, www.promega.com/geneticidproc/ussymp10proc/default.htm.
47. W. Bar, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, M. Holland, P.J. Lincoln, W. Mayr, N. Morling, B. Olaisen, P.M. Schneider, G. Tully, M. Wilson, Guidelines for mitochondrial DNA typing: DNA Commission of the international society for forensic genetics, Vox Sang. 79 (2000) 121-125.
48. J.E. Stewart, C.L. Fisher, P.J. Aagaard, M.R. Wilson, A.R. Isenberg, D. Polanskey, E. Pokorak, J.A. DiZinno, B. Budowle, Length variation in HV2 of the human mitochondrial DNA control region, J. Forensic Sci. 46 (2001) 862-870.
49. H. Pfeiffer, S. Lutz-Bonengel, S. Pollak, R. Fimmers, M.P. Baur, B. Brinkmann, Mitochondrial DNA control region diversity in hairs and body fluids of monozygotic triplets, Int. J. Leg. Med. 118 (2004) 71-74.
50. B. Ewing, L. Hillier, M.C. Wendl, P. Green, Base-calling of automated sequencer traces using phred: I. accuracy assessment, Genome Res. 8 (1998) 175-185.
51. B. Ewing, P. Green, Base-calling of automated sequencer traces using phred: II. error probabilities, Genome Res. 8 (1998) 186-194.
52. M.N. Gabriel, C.D. Calloway, R.L. Reynolds, S. Andelinovic, D. Primorac, Population variation of human mitochondrial DNA hypervariable regions I and II in 105 Croatian individuals demonstrated by immobilized sequence-specific oligonucleotide probe analysis, Croat. Med. J. 42 (2001) 328.
53. K.A. Sannes-Lowery, J.J. Drader, R.H. Griffey, S.A. Hofstadler, Fourier transform ion cyclotron resonance mass spectrometry as a high throughput affinity screen to identify RNA binding ligands, Trends Anal. Chem. 19 (2000) 481-491.
54. W. Bar, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, M. Holland, P.J. Lincoln, W. Mayr, N. Morling, B. Olaisen, P.M. Schneider, G. Tully, M. Wilson, DNA commission of the international society for forensic genetics: guidelines for mitochondrial dna typing, Int. J. Leg. Med. 113 (2000) 193-196.