Genotyping single nucleotide polymorphisms by mass spectrometry

Mass Spectrometry Reviews

Volumn 21, Issue 6, 2002, Pages 388-418

  Tost, Jörg ^a   Gut, Ivo G ^a  

^a CENTRE NATIONAL DE GÉNOTYPAGE   (France)

Author keywords

Automation; Electrospray ionization; ESI; Genotyping; Haplotyping; High throughput; MALDI; Mass spectrometry; Matrix assisted laser desorption ionization; Quantitation; Single nucleotide polymorphism; SNP

Indexed keywords

DESORPTION; DNA SEQUENCES; GENETIC ENGINEERING; HISTORY; IONIZATION; LASER APPLICATIONS;

GENOMICS; GENOTYPING; MATRIX ASSISTED LASER DESORPTION IONIZATION MASS SPECTROMETRY; SINGLE NUCLEOTIDE POLYMORPHISMS;

MASS SPECTROMETRY;

ALLELE; GENETICS; GENOTYPE; HUMAN; MASS SPECTROMETRY; METHODOLOGY; NUCLEOTIDE SEQUENCE; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; BASE SEQUENCE; DNA MUTATIONAL ANALYSIS; GENOTYPE; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 0038243876     PISSN: 02777037     EISSN: None     Source Type: Journal    
DOI: 10.1002/mas.1009     Document Type: Article

References (200)

1. Abdi F, Bradbury EM, Doggett N, Chen X. 2001. Rapid characterization of DNA oligomers and genotyping of single nucleotide polymorphism using nucleotide-specific mass tags. Nucleic Acids Res 29:E61.
2. Abdi FA, Mundt M, Doggett N, Bradbury EM, Chen X. 2002. Validation of DNA sequences using mass spectrometry coupled with nucleoside mass tagging. Genome Res 12:1135-1141.
3. Altshuler D, Pollara VJ, Cowles CR, Van Etten WJ, Baldwin J, Linton L, Lander ES. 2000. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407:513-516.
4. Amexis G, Oeth P, Abel K, Ivshina A, Pelloquin F, Cantor CR, Braun A, Chumakov K. 2001. Quantitative mutant analysis of viral quasispecies by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc Natl Acad Sci USA 98:12097-12102.
5. Babinger P, Kobl I, Mages W, Schmitt R. 2001. A link between DNA methylation and epigenetic silencing in transgenic Volvox carteri. Nucleic Acids Res 29:1261-1271.
6. Bartlet-Jones M, Jeffery WA, Hansen HF, Pappin DJC. 1994. Peptide ladder sequencing by mass spectrometry using a novel, volatile degradation reagent. Rapid Commun Mass Spectrom 8:737-742.
7. Bentzley CM, Johnston MV, Larsen BS, Gutteridge S. 1996. Oligonucleotide sequence and composition determined by matrix-assisted laser desorption/ionization. Anal Chem 68:2141-2146.
8. Berkenkamp S, Kirpekar F, Hillenkamp F. 1998. Infrared MALDI mass spectrometry of large nucleic acids. Science 281:260-262.
9. Berlin K, Gut IG. 1999. Analysis of negatively "charge tagged" DNA by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 13:1739-1743.
10. Bird A. 2002. DNA methylation patterns and epigenetic memory. Genes Dev 16:6-21.
11. Braun A, Little DP, Köster H. 1997. Detecting CFTR gene mutations by using primer oligo base extension and mass spectrometry. Clin Chem 43:1151-1158.
12. Bray MS, Boerwinkle E, Doris PA. 2001. High-throughput multiplex SNP genotyping with MALDI-TOF mass spectrometry: Practice, problems and promise. Hum Mutat 17:296-304.
13. Brookes AJ. 1999. The essence of SNPs. Gene 234:177-186.
14. Bruenner BA, Yip TT, Hutchens TW. 1996. Quantitative analysis of oligonucleotides by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 10:1797-1801.
15. Buetow KH, Edmonson M, MacDonald R, Clifford R, Yip P, Kelley J, Little DP, Strausberg R, Köster H, Cantor CR, Braun A. 2001. High-throughput development and characterization of a genomewide collection of gene-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc Natl Acad Sci USA 98:581-584.
16. Butler JM, Jiang-Baucom P, Huang M, Belgrader P, Girard J. 1996. Peptide nucleic acid characterization by MALDI-TOF mass spectrometry. Anal Chem 68:3283-3287.
17. Cardon LR, Bell JI. 2001. Association study designs for complex diseases. Nat Rev Genet 2:91-99.
18. Cashman JR, Zhang J, Leushner J, Braun A. 2001. Population distribution of human flavin-containing monooxygenase form 3 gene polymorphisms. Drug Metab Dispos 29:1629-1637.
19. Ch'ang LY, Tang K, Schell M, Ringelberg C, Matteson KJ, Allman SL, Chen CH. 1995. Detection of delta F508 mutation of the cystic fibrosis gene by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 9:772-774.
20. Chen X, Fei Z, Smith LM, Bradbury EM, Majidi V. 1999. Stable-isotope-assisted MALDI-TOF mass spectrometry for accurate determination of nucleotide compositions of PCR products. Anal Chem 71:3118-3125.
21. Chicurel M. 2001. Faster, better, cheaper genotyping. Nature 412:580-582.
22. Chou C-W, Bingham SE, Williams P. 1996. Affinity methods for purification of DNA sequencing reaction products for mass spectrometric analysis. Rapid Commun Mass Spectrom 10:1410-1414.
23. Davidson S. 2000. Research suggests importance of haplotypes over SNPs. Nat Biotechnol 18:1134-1135.
24. Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E, Lathrop M, Gyapay G, Morissette J, Weissenbach J. 1996. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380:152-154.
25. Edwards JR, Itagaki Y, Ju J. 2001. DNA sequencing using biotinylated dideoxynucleotides and mass spectrometry. Nucleic Acids Res 29:E104.
26. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, Berg RH, Kim SK, Norden B, Nielsen PE. 1993. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 365:566-568.
27. Fei Z, Ono T, Smith LM. 1998. MALDI-TOF mass spectrometric typing of single nucleotide polymorphisms with mass-tagged ddNTPs. Nucleic Acids Res 26:2827-2828.
28. Fei Z, Smith LM. 2000. Analysis of single nucleotide polymorphisms by primer extension and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 14:950-959.
29. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. 1989. Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64-71.
30. Fitzgerald MC, Parr GR, Smith LM. 1993. Basic matrices for the matrix-assisted laser desorption/ionization mass spectrometry of proteins and oligonucleotides. Anal Chem 65:3204-3211.
31. Fitzgerald MC, Zhu L, Smith LM. 1993. The analysis of a mock DNA sequencing reactions using matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 7:895-897.
32. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89:1827-1831.
33. Fu DJ, Tang K, Braun A, Reuter D, Darnhofer-Demar B, Little DP, O'Donnell MJ, Cantor CR, Köster H. 1998. Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry. Nat Biotechnol 16:381-384.
34. Garvin AM, Parker KC, Haff L. 2000. MALDI-TOF based mutation detection using tagged in vitro synthesized peptides. Nat Biotechnol 18:95-97.
35. Giesen U, Kleider W, Berding C, Gieger A, Orum H, Nielsen PE. 1998. A formula for thermal stability (Tm) prediction of PNA/DNA duplexes. Nucleic Acids Res 26:5004-5006.
36. Gilar M, Belenky A, Wang BH. 2001. High-throughput biopolymer desalting by solid-phase extraction prior to mass spectrometric analysis. J Chromatogr A 921:3-13.
37. Griffin TJ, Tang W, Smith LM. 1997. Genetic analysis by peptide nucleic acid affinity MALDI-TOF mass spectrometry. Nat Biotechnol 15:1368-1372.
38. Griffin TJ, Smith LM. 1998. An approach to predicting the stabilities of peptide nucleic acid: DNA duplexes. Anal Biochem 260:56-63.
39. Griffin TJ, Smith LM. 2000a. Genetic identification by mass spectrometric analysis of single-nucleotide polymorphisms: Ternary encoding of genotypes. Anal Chem 72:3298-3302.
40. Griffin TJ, Smith LM. 2000b. Single-nucleotide polymorphism analysis by MALDI-TOF mass spectrometry. Trends Biotechnol 18:77-84.
41. Griffin TJ, Hall JG, Prudent JR, Smith LM. 1999. Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry. Proc Natl Acad Sci USA 96:6301-6306.
42. Guo B. 1999. Mass Spectrometry in DNA analysis. Anal Chem 71:333R-337R.
43. Guo Z, Liu Q, Smith LM. 1997. Enhanced discrimination of single nucleotide polymorphisms by artificial mismatch hybridization. Nat Biotechnol 15:331-335.
44. Gut IG. 2001. Automation in genotyping of single nucleotide polymorphisms. Hum Mutat 17:475-492.
45. Gut IG, Beck S. 1995. A procedure for selective DNA alkylation and detection by mass spectrometry. Nucleic Acids Res 23:1367-1373.
46. Gut IG, Jeffery WA, Pappin DJC, Beck S. 1997. Analysis of DNA by "Charge Tagging" and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 11:43-50.
47. Gyapay G, Morissette J, Vignal A, Dib C, Fizames C, Millasseau P, Marc S, Bernardi G, Lathrop M, Weissenbach J. 1994. The 1993-94 Genethon human genetic linkage map. Nat Genet 7:246-339.
48. Haff LA, Smirnov IP. 1997a. Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res 7:378-388.
49. Haff LA, Smirnov IP. 1997b. Multiplex genotyping of PCR products with MassTag-labeled primers. Nucleic Acids Res 25:3749-3750.
50. Haff LA, Belden AC, Hall LR, Ross PL, Smirnov IP. 2001. SNP genotyping by MALDI-TOF mass spectrometry. In: Housby JN, editor. Mass Spectrometry and Genomic Analysis. Dordrecht: Kluwer Academic Publishers, p 16-32.
51. Hahner S, Lüdemann HC, Kirpekar F, Nordhoff E, Roepstorff P, Galla HJ, Hillenkamp F. 1997. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) of endonuclease digests of RNA. Nucleic Acids Res 25:1957-1964.
52. Hall JG, Eis PS, Law SM, Reynaldo LP, Prudent JR, Marshall DJ, Allawi HT, Mast AL, Dahlberg JE, Kwiatkowski RW, de Arruda M, Neri BP, Lyamichev VI. 2000. Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc Natl Acad Sci USA 97:8272-8277.
53. Harksen A, Ueland PM, Refsum H, Meyer K. 1999. Four common mutations of the cystathionine beta-synthase gene detected by multiplex PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin Chem 45:1157-1161.
54. Higgins GS, Little DP, Köster H. 1997. Competitive oligonucleotide single-base extension combined with mass spectrometric detection for mutation screening. Biotechniques 23:710-714.
55. Hosfield DJ, Frank G, Weng Y, Tainer JA, Shen B. 1998. Newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for DNA substrate binding and catalysis resembling human flap endonuclease-1. J Biol Chem 273:27154-27161.
56. Huber CG, Oberacher H. 2001. Analysis of nucleic acids by on-line liquid chromatography-mass spectrometry. Mass Spectrom Rev 20:310-343.
57. Hugot JP, Chamaillard M, Zouali H, Lesage S, Cezard JP, Belaiche J, Almer S, Tysk C, O'Morain CA, Gassull M, Binder V, Finkel Y, Cortot A, Modigliani R, Laurent-Puig P, Gower-Rousseau C, Macry J, Colombel JF, Sahbatou M, Thomas G. 2001. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 411:599-603.
58. Hung K, Sun X, Ding H, Kalafatis M, Simioni P, Guo B. 2002. A matrix-assisted laser desorption/ionization time-of-flight based method for screening the 1691G ← A mutation in the factor V gene. Blood Coagul Fibrinolysis 13:117-122.
59. Huth-Fehre T, Gosine JN, Wu KJ, Becker CH. 1992. Matrix-assisted laser desorption mass spectrometry of oligodeoxythymidylic acids. Rapid Commun Mass Spectrom 6:209-213.
60. Isola NR, Allman SL, Golovlov VV, Chen CH. 1999. Chemical cleavage sequencing of DNA using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Chem 71:2266-2269.
61. Jackson PE, Scholl PF, Groopman JD. 2000. Mass spectrometry for genotyping: An emerging tool for molecular medicine. Mol Med Today 6:271-276.
62. Jackson PE, Qian GS, Friesen MD, Zhu YR, Lu P, Wang JB, Wu Y, Kensler TW, Vogelstein B, Groopman JD. 2001. Specific p53 mutations detected in plasma and tumors of hepatocellular carcinoma patients by electrospray ionization mass spectrometry. Cancer Res 61:33-35.
63. Jiang-Baucom P, Girard JE, Butler J, Belgrader P. 1997. DNA typing of human leukocyte antigen sequence polymorphisms by peptide nucleic acid probes and MALDI-TOF mass spectrometry. Anal Chem 69:4894-4898.
64. Jones PA, Baylin SB. 2002. The fundamental role of epigenetic events in cancer. Nat Rev Genet 3:415-428.
65. Judson R, Stephens JC. 2001. Notes from the SNP vs. haplotype front. Pharmacogenomics 2:7-10.
66. Juhasz P, Roskey MT, Smirnov IP, Haff LA, Vestal ML, Martin SA. 1996. Applications of delayed extraction matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to oligonucleotide analysis. Anal Chem 68:941-946.
67. Jurinke C, van den Boom D, Jacob A, Tang K, Wörl R, Köster H, 1996. Analysis of ligase chain reaction products via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 273:174-181.
68. Jurinke C, van den Boom D, Collazo V, Lüchow A, Jacob A, Köster H. 1997. Recovery of nucleic acids from immobilized biotin-streptavidin complexes using ammonium hydroxide and applications in MALDI-TOF mass spectrometry. Anal Chem 69:904-910.
69. Kaiser MW, Lyamincheva N, Ma W, Miller C, Neri B, Fors L, Lyamichev VI. 1999. A comparison of eubacterial and archaeal structure-specific 5'-exonucleases. J Biol Chem 274:21387-21394.
70. Kallweit U, Börnsen KO, Kresbach GM, Widmer H. 1996. Matrix compatible buffers for analysis of proteins with matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 10:845-850.
71. Karas M, Hillenkamp F. 1988. Laser desorption ionization of proteins with molecular masses exceeding 10.000 daltons. Anal Chem 60:2299-2301.
72. Khrapko KR, Lysov Yu P, Khorlyn AA, Shick VV, Florentiev VL, Mirzabekov AD. 1989. An oligonucleotide hybridization approach to DNA sequencing. FEBS Lett 256:118-122.
73. Kim S, Edwards JR, Deng L, Chung W, Ju J. 2002. Solid phase capturable dideoxynucleotides for multiplex genotyping using mass spectrometry. Nucleic Acids Res 30:E85.
74. Kirpekar F, Nordhoff E, Kristiansen K, Roepstorff P, Lezius A, Hahner S, Karas M, Hillenkamp F. 1994. Matrix assisted laser desorption/ionization mass spectrometry of enzymatically synthesized RNA up to 150 kDa. Nucleic Acids Res 22:3866-3870.
75. Kirpekar F, Nordhoff E, Kristiansen K, Roepstorff P, Hahner S, Hillenkamp F. 1995. 7-Deaza purine bases offer a higher ion stability in the analysis of DNA by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 9:525-531.
76. Kirpekar F, Nordhoff E, Larsen LK, Kristiansen K, Roepstorff P, Hillenkamp F. 1998. DNA sequence analysis by MALDI mass spectrometry. Nucleic Acids Res 26:2554-2559.
77. Kokoris M, Dix K, Moynihan K, Mathis J, Erwin B, Grass P, Hines B, Duesterhoeft A. 2000. High-throughput SNP genotyping with the Masscode system. Mol Diagn 5:329-340.
78. Kolchinsky A, Mirzabekov A. 2002. Analysis of SNPs and other genomic variations using gel-based chips. Hum Mutat 19:343-360.
79. Krahmer MT, Johnson YA, Walters JJ, Fox KF, Fox A, Nagpal M. 1999. 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 71:2893-2900.
80. Krahmer MT, Walters JJ, Fox KF, Fox A, Creek KE, Pirisi L, Wunschel DS, Smith RD, Tabb DL, Yates JR, IIIrd. 2000. MS for identification of single nucleotide polymorphisms and MS/MS for discrimination of isomeric PCR products. Anal Chem 72:4033-4040.
81. Kruglyak L. 1999. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139-144.
82. Kwok PY. 2000. High-throughput genotyping assay approaches. Pharmacogenomics 1:95-100.
83. Kwok PY. 2001. Methods for genotyping single nucleotide polymorphisms. Annu Rev Genomics Hum Genet 2:235-258.
84. Kwok S, Kellogg DE, McKinney N, Spasic D, Goda L, Levenson C, Sninsky JJ. 1990. Effects of primer-template mismatches on the polymerase chain reaction: Human immunodeficiency virus type 1 model studies. Nucleic Acids Res 18:999-1005.
85. Kwon Y, Tang K, Cantor C, Köster H, Kang C. 2001. DNA sequencing and genotyping by transcriptional synthesis of chain-terminated RNA ladders and MALDI-TOF mass spectrometry. Nucleic Acids Res 29:E11.
86. Köster H, Tang K, Fu DJ, Braun A, van den Boom D, Smith CL, Cotter RJ, Cantor CR. 1996. A strategy for rapid and efficient DNA sequencing by mass spectrometry. Nat Biotechnol 14:1123-1128.
87. Laken SJ, Jackson PE, Kinzler KW, Vogelstein B, Strickland PT, Groopman JD, Friesen MD. 1998. Genotyping by mass spectrometric analysis of short DNA fragments. Nat Biotechnol 16:1352-1356.
88. Landegren U, Nilsson M, Kwok PY. 1998. Reading bits of genetic information: Methods for single-nucleotide polymorphism analysis. Genome Res 8:769-776.
89. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L. Lehoczky J, Le Vine R, McEwan P, McKernan K, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
90. Le Hellard S, Ballereau SJ, Visscher PM, Torrance HS, Pinson J, Morris SW, Thomson ML, Semple CA, Muir WJ, Blackwood DH, Porteous DJ, Evans KL. 2002. SNP genotyping on pooled DNAs: Comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res 30:E74.
91. Lechner D, Lathrop GM, Gut IG. 2002. Large-scale genotyping by mass spectrometry: Experience, advances and obstacles. Curr Opin Chem Biol 6:31-38.
92. Leushner J, Chiu NH. 2000. Automated mass spectrometry: A revolutionary technology for clinical diagnostics. Mol Diagn 5:341-348.
93. Li J, Butler JM, Tan Y, Lin H, Royer S, Ohler L, Shaler TA, Hunter JM, Pollart DJ, Monforte JA, Becker CH, 1999. Single nucleotide polymorphism determination using primer extension and time-of-flight mass spectrometry. Electrophoresis 20:1258-1265.
94. Lin H, Hunter JM, Becker CH. 1999. Laser desorption of DNA oligomers larger than one kilobase from cooled 4-nitrophenol. Rapid Commun Mass Spectrom 13:2335-2340.
95. Little DP, Braun A, Darnhofer-Demar B, Köster H. 1997a. Identification of apolipoprotein E polymorphisms using temperature cycled primer oligo base extension and mass spectrometry. Eur J Clin Chem Clin Biochem 35:545-548.
96. Little DP, Cornish TJ, O'Donnell MJ, Braun A, Cotter RJ, Köster H. 1997b. MALDI on a chip: Analysis of arrays of low-femtomole to subfemtomole quantities of synthetic oligo-nucleotides and DNA diagnostic products dispensed by a piezoelectric pipet. Anal Chem 69:4540-4546.
97. Liu Y-H, Bai J, Zhu Y, Liang X, Siemieniak D, Venta PJ, Lubman DM. 1995. Rapid screening of genetic polymorphisms using buccal cell DNA with detection by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 9:735-743.
98. Lu M, Shortreed MR, Hall JG, Wang L, Berggren T, Stevens PW, Kelso DM, Lyamichev V, Neri B, Smith LM. 2002. A surface invasive cleavage assay for highly parallel SNP analysis. Hum Mutat 19:416-422.
99. Lyamichev V, Mast AL, Hall JG, Prudent JR, Kaiser MW, Takova T, Kwiatkowski RW, Sander TJ, de Arruda M, Arco DA, Neri BP, Brow MA. 1999. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat Biotechnol 17:292-296.
100. Maxam AM, Gilbert W. 1977. A new method for sequencing DNA. Proc Natl Acad Sci USA 74:560-564.
101. Monforte JA, Becker CH. 1997. High-throughput DNA analysis by time-of-flight mass spectrometry. Nat Med 3:360-362.
102. Mouradian S, Rank DR, Smith LM. 1996. Analyzing sequencing reactions from bacteriophage M13 by matrix assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 10:1475-1478.
103. Muddiman DC, Wunschel DS, Liu C, Pasa-Tolic L, Fox KF, Fox A, Anderson GA, Smith RD. 1996. Characterization of PCR products from bacilli using electrospray ionization FTICR mass spectrometry. Anal Chem 68:3705-3712.
104. Murray KK. 1996. DNA sequencing by mass spectrometry. J Mass Spectrom 31:1203-1215.
105. Müller S, van den Boom D, Zirkel D, Köster H, Berthold F, Schwab M, Westphal M, Zumkeller W. 2000. Retention of imprinting of the human apoptosis-related gene TSSC3 in human brain tumors. Hum Mol Genet 9:757-763.
106. Naito Y, Ishikawa K, Koga Y, Tsuneyoshi T, Terunuma H, Arakawa R. 1995. Molecular mass measurement of polymerase chain reaction products amplified from human blood DNA by electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom 9:1484-1486.
107. Naito Y, Ishikawa K, Koga Y, Tsuneyoshi T, Terunuma H, Arakawa R. 1997. 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 8:737-742.
108. Nakai K, Habano W, Fujita T, Schnackenberg J, Kawazoe K, Suwabe A, Itoh C. 2002. Highly multiplexed genotyping of coronary artery disease-associated SNPs using MALDI-TOF mass spectrometry. Hum Mutat 20:133-138.
109. Nielsen PE. 2001. Peptide nucleic acid: A versatile tool in genetic diagnostics and molecular biology. Curr Opin Biotechnol 12:16-20.
110. Nielsen PE, Egholm M, Berg RH, Buchardt O. 1991. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254:1497-1500.
111. Nordhoff E, Kirpekar F, Roepstorff P. 1996. Mass spectrometry of nucleic acids. Mass Spectrom Rev 15:67-138.
112. Nordhoff E, Ingendoh A, Cramer R, Overberg A, Stahl B, Karas M, Hillenkamp F, Crain PF. 1992. Matrix-assisted laser desorption/ionization mass spectrometry of nucleic acids with wavelengths in the ultraviolet and infrared. Rapid Commun Mass Spectrom 6:771-776.
113. Nordhoff E, Cramer R, Karas M, Hillenkamp F, Kirpekar F, Kristiansen K, Roepstorff P. 1993. Ion stability of nucleic acids in infrared matrix-assisted laser desorption/ionization mass spectrometry. Nucl Acids Res 21:3347-3357.
114. Nordhoff E, Kirpekar F, Karas M, Cramer R, Hahner S, Hillenkamp F, Kristiansen K, Roepstroff P, Lezius A, 1994. Comparison of IR- and UV-matrix-assisted laser desorption/ionization mass spectrometry of oligodeoxynucleotides. Nucleic Acids Res 22:2460-2465.
115. Nordhoff E, Karas M, Cramer R, Hahner S, Hillenkamp F, Kirpkar F, Lezius A, Muth J, Meier C, Engels JW. 1995. Direct mass spectrometric sequencing of low-picomole amounts of oligonucleotides up to 21 based by matrix-assisted laser desorption/ionization mass spectrometry. J Mass Spectrom 30:99-112.
116. Nordhoff E, Luebbert C, Thiele G, Heiser V, Lehrach H. 2000. Rapid determination of short DNA sequences by the use of MALDI-MS. Nucleic Acids Res 28:E86.
117. Oakeley EJ. 1999. DNA methylation analysis: A review of current methodologies. Pharmacol Ther 84:389-400.
118. Oberacher H, Wellenzohn B, Huber CG. 2002. Comparative sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry. Anal Chem 74:211-218.
119. Oberacher H, Oefner PJ, Parson W, Huber CG. 2001. On-line liquid chromatography mass spectrometry: A useful tool for the detection of DNA sequence variation. Angew Chem Int Ed Engl 40:3828-3830.
120. Oberacher H, Oefner PJ, Holzl G, Premstaller A, Davis K, Huber CG. 2002. Re-sequencing of multiple single nucleotide polymorphisms by liquid chromatography-electrospray ionization mass spectrometry. Nucleic Acids Res 30:E67.
121. Oefner PJ. 2000. Allelic discrimination by denaturing high-performance liquid chromatography. J Chromatogr B Biomed Sci Appl 739:345-355.
122. Ogura Y, Bonen DK, Inohara N, Nicolae DL, Chen FF, Ramos R, Britton H, Moran T, Karaliuskas R, Duerr RH, Achkar JP, Brant SR, Bayless TM, Kirschner BS, Hanauer SB, Nunez G, Cho JH. 2001. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 411:603-606.
123. Ohnishi Y, Tanaka T, Ozaki K, Yamada R, Suzuki H, Nakamura Y. 2001. A high-throughput SNP typing system for genome-wide association studies. J Hum Genet 46:471-477.
124. Ordoukhanian P, Taylor J-S. 1995. Design and synthesis of a versatile photocleavable DNA building block. Application to phototriggered hybridization. J Am Chem Soc 117:9570-9571.
125. Orum H, Nielsen PE, Egholm M, Berg RH, Buchardt O, Stanley C. 1993. Single base pair mutation analysis by PNA directed PCR clamping. Nucleic Acids Res 21: 5332-5336.
126. Paracchini S, Arredi B, Chalk R, Tyler-Smith C. 2002. Hierarchical high-throughput SNP genotyping of the human Y chromosome using MALDI-TOF mass spectrometry. Nucleic Acids Res 30:E27.
127. Parinov S, Barsky V, Yershov G, Kirillov E, Timofeev E, Belgovskiy A, Mirzabekov A. 1996. DNA sequencing by hybridization to microchip octa- and decanucleotides extended by stacked pentanucleotides. Nucleic Acids Res 24:2998-3004.
128. Parr GR, Fitzgerald MC, Smith LM. 1992. Matrix-assisted laser desorption/ionization mass spectrometry of synthetic oligodeoxyribonucleotides. Rapid Commun Mass Spectrom 6:369-372.
129. Pastinen T, Kurg A, Metspalu A, Peltonen L, Syvänen AC. 1997. Minisequencing: A specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res 7:606-614.
130. Pieles U, Zürcher W, Schär M, Moser HE. 1993. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: A powerful tool for the mass and sequence analysis of natural and modified oligonucleotides. Nucleic Acids Res 21:3191-3196.
131. Pluskal MG. 2000. Microscale sample preparation. Nat Biotechnol 18:104-105.
132. Puapaiboon U, Jai-nhuknan J, Cowan JA. 2000. Rapid and direct sequencing of double-stranded DNA using exonuclease III and MALDI-TOF MS. Anal Chem 72:3338-3341.
133. Pusch W, Kraeuter KO, Froehlich T, Stalgies Y, Kostrzewa M. 2001. Genotools SNP manager: A new software for automated high-throughput MALDI-TOF mass spectrometry SNP genotyping. Biotechniques 30:210-215.
134. Pusch W, Wurmbach JH, Thiele H, Kostrzewa M. 2002. MALDI-TOF mass spectrometry-based SNP genotyping. Pharmacogenomics 3:537-548.
135. Reik W, Walter J. 2001. Genomic imprinting: Parental influence on the genome. Nat Rev Genet 2:21-32.
136. Risch NJ. 2000. Searching for genetic determinants in the new millennium. Nature 405:847-856.
137. Risch N, Merikangas K. 1996. The future of genetic studies of complex human diseases. Science 273:1516-1517.
138. Rodi CP, Darnhofer-Patel B, Stanssens P, Zabeau M, van den Boom D. 2002. A strategy for the rapid discovery of disease markers using the MassARRAY system. Biotechniques Suppl 62-66:68-69.
139. Roskey MT, Juhasz P, Smirnov IP, Takach EJ, Martin SA, Haff LA. 1996. DNA sequencing by delayed extraction-matrix-assisted laser desorption/ionization time of flight mass spectrometry. Proc Natl Acad Sci USA 93:4724-4729.
140. Ross PL, Davis PA, Belgrader P. 1998. Analysis of DNA fragments from conventional and microfabricated PCR devices using delayed extraction MALDI-TOF mass spectrometry. Anal Chem 70:2067-2073.
141. Ross P, Hall L, Haff LA. 2000. Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. Biotechniques 29:620-626, 628-629.
142. Ross PL, Lee K, Belgrader P. 1997. Discrimination of single-nucleotide polymorphisms in human DNA using peptide nucleic acid probes detected by MALDI-TOF mass spectrometry. Anal Chem 69:4197-4202.
143. Ross PL, Belgrader P. 1997. Analysis of short tandem repeat polymorphisms in human DNA by matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem 69:3966-3972.
144. Ross P, Hall L, Smirnov I, Haff L. 1998. High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat Biotechnol 16:1347-1351.
145. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z., Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, et al. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933.
146. Sanger F, Nicklen S, Coulson AR, 1977. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467.
147. Sarracino D, Richert C. 1996. Quantitative MALDI-TOF MS of oligonucleotides and a nuclease assay. Bioorg Med Chem Lett 6:2543-2548.
148. Sauer S, Lechner D, Gut IG. 2001. The GOOD assay. In: Housby N, editor. Mass spectrometry and genomic analysis. Dordrecht: Kluwer Academic Publishers. p 50-65.
149. Sauer S, Lechner D, Berlin K, Lehrach H, Escary JL, Fox N, Gut IG. 2000a. A novel procedure for efficient genotyping of single nucleotide polymorphisms. Nucleic Acids Res 28:E13.
150. Sauer S, Lechner D, Berlin K, Plancon C, Heuermann A, Lehrach H, Gut IG. 2000b. Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay. Nucleic Acids Res 28:E100.
151. Sauer S, Gelfand DH, Boussicault F, Bauer K, Reichert F, Gut IG. 2002. Facile method for automated genotyping of single nucleotide polymorphisms by mass spectrometry. Nucleic Acids Res 30:E22.
152. Schneider K, Chait BT. 1993. Matrix-assisted laser desorption mass spectrometry of homopolymer oligodeoxyribonucleotides. Influence of base composition on the mass spectrometric response. Org Mass Spectrom 28:1353-1361.
153. Schneider K, Chait BT. 1995. Increased stability of nucleic acids containing 7-deaza-guanosine and 7-deaza-adenosine may enable rapid DNA sequencing by matrix-assisted laser desorption mass spectrometry. Nucleic Acids Res 23:1570-1575.
154. Schuette JM, Pieles U, Maleknia SD, Srivatsa GS, Cole DL, Moser HE, Afeyan NB. 1995. Sequence analysis of phosphorothioate oligonucleotides via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Pharm Biomed Anal 13: 1195-1203.
155. Shahgholi M, Garcia BA, Chiu NH, Heaney PJ, Tang K. 2001. Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved. Nucleic Acids Res 29:E91.
156. Shaler TA, Tan Y, Wickham JN, Wu KJ, Becker CH. 1995. Analysis of enzymatic DNA sequencing reactions by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 9:942-947.
157. Shchepinov MS, Denissenko MF, Smylie KJ, Worl RJ, Leppin AL, Cantor CR, Rodi CP. 2001. Matrix-induced fragmentation of P3′-N5′ phosphoramidate-containing DNA: High-throughput MALDI-TOF analysis of genomic sequence polymorphisms. Nucleic Acids Res 29:3864-3874.
158. Siegert CW, Jacob A, Köster H. 1996. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the detection of polymerase chain reaction products containing 7-deazapurine moieties. Anal Biochem 243:55-65.
159. Smirnov IP, Roskey MT, Juhasz P, Takach EJ, Martin SA, Haff LA. 1996. Sequencing oligonucleotides by exonuclease digestion and delayed extraction matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 238:19-25.
160. Smirnov IP, Hall LR, Ross PL, Haff LA. 2001. Application of DNA-binding polymers for preparation of DNA for analysis by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 15:1427-1432.
161. Smith LM. 1993. The future of DNA sequencing. Science 262:530-532.
162. Srinivasan JR, Liu YH, Venta PJ, Siemieniak D, Killeen AA, Zhu Y, Lubman DM. 1997. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry as a rapid screening method to detect mutations causing Tay-Sachs disease. Rapid Commun Mass Spectrom 11:1144-1150.
163. Stoerker J, Mayo JD, Tetzlaff CN, Sarracino DA, Schwope I, Richert C. 2000. Rapid genotyping by MALDI-monitored nuclease selection from probe libraries. Nat Biotechnol 18:1213-1216.
164. Stomakhin AA, Vasiliskov VA, Timofeev E, Schulga D, Cotter RJ, Mirzabekov AD. 2000. DNA sequence analysis by hybridization with oligonucleotide microchips: MALDI mass spectrometry identification of 5mers contiguously stacked to microchip oligonucleotides. Nucleic Acids Res 28:1193-1198.
165. Sun X, Ding H, Hung K, Guo B. 2000. A new MALDI-TOF based mini-sequencing assay for genotyping of SNPS. Nucleic Acids Res 28:E68.
166. Sun X, Hung K, Wu L, Sidransky D, Guo B. 2002. Detection of tumor mutations in the presence of excess amounts of normal DNA. Nat Biotechnol 20:186-189.
167. Syvänen AC. 1999. From gels to chips: "Minisequencing" primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum Mutat 13:1-10.
168. Syvänen AC. 2001. Accessing genetic variation: Genotyping single nucleotide polymorphisms. Nat Rev Genet 2:930-942.
169. Syvänen AC, Aalto-Setala K, Harju L, Kontula K, Soderlund H. 1990. A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics 8:684-692.
170. Tanaka K, Waki H, Ido Y, Akita S, Yoshida Y, Yoshida T. 1988. Protein and polymer analysis up to m/z 100.000 by laser desorption time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2:151-153.
171. Tang W, Zhu L, Smith LM. 1997. Controlling DNA fragmentation in MALDI-MS by chemical modification. Anal Chem 69:331-335.
172. Tang K, Allman SL, Jones RB, Chen CH. 1993. Quantitative analysis of biopolymers by matrix-assisted laser desorption. Anal Chem 65:2164-2166.
173. Tang K, Fu DJ, Julien D, Braun A, Cantor CR, Köster H. 1999. Chip-based genotyping by mass spectrometry. Proc Natl Acad Sci USA 96:10016-10020.
174. Taranenko NI, Matteson KJ, Chung CN, Zhu YF, Chang LY, Allaman SL, Haff L, Martin SA, Chen CH. 1996. Laser desorption mass spectrometry for point mutation detection. Genet Anal: Genet Eng 13:87-94.
175. Taranenko NI, Chung CN, Zhu YF, Allman SL, Golovlev VV, Isola NR, Martin SA, Haff LA, Chen CH. 1997. Matrix-assisted laser desorption/ionization for sequencing single-stranded and double-stranded DNA. Rapid Commun Mass Spectrom 11:386-392.
176. Taranenko NI, Allman SL, Golovlev VV, Taranenko NV, Isola NR, Chen CH. 1998. Sequencing DNA using mass spectrometry for ladder detection. Nucleic Acids Res 26:2488-2490.
177. Taranenko NI, Hurt R, Zhou JZ, Isola NR, Huang H, Lee SH, Chen CH. 2002. Laser desorption mass spectrometry for microbial DNA analysis. J Microbiol Methods 48:101-106.
178. Tillib SV, Mirzabekov AD. 2001. Advances in the analysis of DNA sequence variations using oligonucleotide microchip technology. Curr Opin Biotechnol 12:53-58.
179. Tolson DA, Nicholson NH. 1998. Sequencing RNA by a combination of exonuclease digestion and uridine specific chemical cleavage using MALDI-TOF. Nucleic Acids Res 26:446-451.
180. Tomac S, Sarkar M, Ratilainen T, Wittung P, Nielsen PE, Norden B, Gräslund A. 1996. Ionic effects on the stability and confirmation of peptide nucleic acid complexes. J Am Chem Soc 118:5544-5552.
181. Tost J, Brandt O, Boussicault F, Derbala D, Caloustian C, Lechner D, Gut IG. 2002. Molecular haplotyping at high throughput. Nucleic Acids Res 30:E96.
182. Tretyakova N, Matter B, Ogdie A, Wishnok JS, Tannenbaum SR. 2001. Locating nucleobase lesions within DNA sequences by MALDI-TOF mass spectral analysis of exonuclease ladders. Chem Res Toxicol 14:1058-1070.
183. Tsuneyoshi T, Ishikawa K, Koga Y, Naito Y, Baba S, Terunuma H, Arakawa R, Prockop DJ. 1997. Mass spectrometric gene diagnosis of one-base substitution from polymerase chain reaction amplified human DNA. Rapid Commun Mass Spectrom 11:719-722.
184. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, et al. 2001. The sequence of the human genome. Science 291:1304-1351.
185. Vestal ML, Juhasz P, Martin SA. 1995. Delayed extraction matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 9:1044-1050.
186. von Wintzingerode F, Bocker S, Schlotelburg C, Chiu NH, Storm N, Jurinke C, Cantor CR, Gobel UB, van den Boom D. 2002. Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: A tool for rapid bacterial identification. Proc Natl Acad Sci USA 99:7039-7044.
187. Wada Y. 1998. Separate analysis of complementary strands of restriction enzyme-digested DNA. An application of restriction fragment mass mapping by matrix-assisted laser desorption/ionization mass spectrometry. J Mass Spectrom 33:187-192.
188. Wada Y, Yamamoto M. 1997. Detection of single-nucleotide mutations including substitutions and deletions by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 11:1657-1660.
189. Walters JJ, Muhammad W, Fox KF, Fox A, Xie D, Creek KE, Pirisi L. 2001. Genotyping single nucleotide polymorphisms using intact polymerase chain reaction products by electro-spray quadrupole mass spectrometry. Rapid Commun Mass Spectrom 15:1752-1759.
190. Watson JD, Crick FHC. 1953. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171:737-738.
191. Watson JD, Jordan E. 1989. The Human genome program at the National Institutes of Health. Genomics 5:654-656.
192. Weber JL, Wong C. 1993. Mutation of human short tandem repeats. Hum Mol Genet 2:1123-1128.
193. Wenzel T, Fröhlich T, Strassburger K, Richter S, Bimmler J, Franke C, Thomas I, Kostrzewa M. 2001. Novel propargylamine-linked nucleosides for high throughput SNP genotyping by MALDI-TOF MS. Nucleosides Nucleotides Nucleic Acids 20:883-887.
194. Werner M, Sych M, Herbon N, Illig T, König IR, Wjst M. 2002. Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry. Hum Mutat 20:57-64.
195. Wolfe JL, Kawate T, Sarracino DA, Zillmann M, Olson J, Stanton VP, Jr. Verdine GL. 2002. A genotyping strategy based on incorporation and cleavage of chemically modified nucleotides. Proc Natl Acad Sci USA 99:11073-11078.
196. Worrall TA, Schmeckpeper BJ, Corvera JS, Cotter RJ. 2000. Allele-specific HLA-DR typing by mass spectrometry: An alternative to hybridization-based typing methods. Anal Chem 72:5233-5238.
197. Wu KJ, Shaler TA, Becker CH. 1994. Time-of-flight mass spectrometry of underivatized single-stranded DNA oligomers by matrix-assisted laser desorption. Anal Chem 66:1637-1645.
198. Wu KJ, Steding A, Becker CH. 1993. Matrix-assisted laser desorption time-of-flight mass spectrometry of oligonucleotides using 3-hydroxypicolinic acid as ultraviolet-sensitive matrix. Rapid Commun Mass Spectrom 7:142-146.
199. Wunschel DS, Muddiman DC, Fox KF, Fox A, Smith RD. 1998. Heterogeneity in Bacillus cereus PCR products detected by ESI-FTICR mass spectrometry. Anal Chem 70:1203-1207.
200. Zhang S, Van Pelt CK, Schultz GA. 2001. Electrospray ionization mass spectrometry-based genotyping: An approach for identification of single nucleotide polymorphisms. Anal Chem 73:2117-2125.