References

1. Southern EM. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 1975; 98:503-517.

2. Southern E. Tools for genomics. Nat Med 2005; 11(10):1029-1034.

3. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74(12):5463-5467.

4. Alwine JC, Kemp DJ, Stark GR. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci USA 1977; 74(12):5350-5354.

5. Wyman AR, White R. A highly polymorphic locus in human DNA. Proc Natl Acad Sci USA 1980; 77:6754-6758.

6. Waterman MS. Genomic sequence databases. Genomics 1990; 6(4):700-701.

7. Smith TF. The history of the genetic sequence databases. Genomics 1990; 6(4):701-707.

8. Jeffreys AJ, Wilson V, Thein SL. Individual-specific fingerprints of human DNA. Nature 1985; 316:76-79.

9. Polsky-Cynkin R, Parsons GH, Allerdt L, Landes G, Davis G, Rashtchian A. Use of DNA immobilized on plastic and agarose supports to detect DNA by sandwich hybridization. Clin Chem 1985; 31(9):1438-1443.

10. Lipman DJ, Pearson WR. Rapid and sensitive protein similarity searches. Science 1985; 227(4693):1435-1441.

11. Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, Connell CR, et al. Fluorescence detection in automated DNA sequence analysis. Nature 1986; 321(6071): 674-679.

12. Mullis KB, Faloona FA. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 1987; 155:335-350.

13. Rosenthal N. Tools of the trade—recombinant DNA. N Engl J Med 1994; 331(5): 315-317.

14. Hillenkamp F, Karas M, Beavis RC, Chait BT. Matrix-assisted laser desorption/ ionization mass spectrometry of biopolymers. Anal Chem 1991; 63(24):1193A-1203A.

15. Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000; 28(1):10-14.

16. Ristaldi MS, Piratsu M, Rositelli C, Monni G, Erlich H, Saiki R, et al. Prenatal daignosis of beta-thalaessemia in Mediterranean populations by dot blot analysis with DNA amplification and allele specific oligonucleotide probes. Prenat Diagn 2003; 9:629-638.

17. Wu DY, Nozari G, Schold M, Cooner BJ, Wallace RB. Direct analysis of single nucleotide variation in human DNA and RNA using in situ dot blot hybridization. DNA 1989; 8:135-142.

18. Fields S, Song O. A novel genetic system to detect protein-protein interactions. Nature 1989; 340(6230):245-246.

19. Kawasaki E, Saiki R, Erlich H. Genetic analysis using polymerase chain reaction-amplified DNA and immobilized oligonucleotide probes: Reverse dot-blot typing. Methods Enzymol 1993; 218:369-381.

20. Southern EM, Maskos U. Parallel synthesis and analysis of large numbers of related chemical compounds: Applications to oligonucleotides. J Biotechnol 1994; 35(2-3): 217-227.

21. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SP. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA 1994; 91(11):5022-5026.

22. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of the gene expression patterns with a comprehensive DNA microarray. Science 1995; 270: 467-470.

23. DeRisi J, Penland L, Brown PO, Bittner ML, Melzer PS, Ray M, et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996; 14:457-460.

24. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8(3):175-185.

25. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8(3):186-194.

26. Kirpekar F, Nordhoff E, Larsen LK, Kristiansen K, Roepstorff P, Hillenkamp F. DNA sequence analysis by MALDI mass spectrometry. Nucleic Acids Res 1998; 26(11):2554-2559.

27. von Wintzingerode F, Bocker S, Schlotelburg C, Chiu NH, Storm N, Jurinke C, et al. Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spec-trometry: A tool for rapid bacterial identification. Proc Natl Acad Sci USA 2002; 99(10):7039-7044.

28. Mohlke KL, Erdos MR, Scott LJ, Fingerlin TE, Jackson AU, Silander K, et al. High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools. Proc Natl Acad Sci USA 2002; 99(26):16928-16933.

29. Hartmer R, Storm N, Boecker S, Rodi CP, Hillenkamp F, Jurinke C, et al. RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis. Nucleic Acids Res 2003; 31(9):e47.

30. Vidal M. A biological atlas of functional maps. Cell 2001; 104(3):333-339.

31. Stanssens P, Zabeau M, Meersseman G, Remes G, Gansemans Y, Storm N, et al. High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res 2004; 14(1):126-133.

32. Syvanen AC. Toward genome-wide SNP genotyping. Nat Genet 2005; 37 Suppl: S5-10.

33. Jurinke C, Denissenko MF, Oeth P, Ehrich M, van den BD, Cantor CR. A single nucleotide polymorphism based approach for the identification and characterization of gene expression modulation using MassARRAY. Mutat Res 2005; 573(1-2): 83-95.

34. Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G, et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci USA 2005; 102(44):15785-15790.

35. Jeffreys AJ. Genetic fingerprinting. Nat Med 2005; 11(10):1035-1039.

36. Sutcharichan P, Saiki R, Huisman TH, Kutlar A, McKie V, Erlich H, et al. Reverse dot blot detection of the African-American beta-thalessaemia mutations. Blood 1995; 86:1580-1585.

37. Erlich H, Bugawan T, Begovich AB, Scharf S, Griffith R, Saiki R, et al. HLA-DR, DQ and DP typing using PCR amplification and immobilized probes. Eur J Im-munogenet 1991; 18(1-2):33-55.

38. Grant DM, Phillips MS. Technologies for the analysis of single-nucleotide polymorphisms. In: Kalow W, Meyer UA, Tyndale RF, editors. Pharmacogenomics. New York: Marcel Dekker, 2001: 183-189.

39. Mir KU, Southern EM. Sequence variation in genes and genomic DNA: Methods for large-scale analysis. Annu Rev Genomics Hum Genet 2000; 1(2000):329-360.

40. Stockley TL, Ray PN. Molecular diagnostics and development of biotechnology-based diagnostics. In: Kalow W, Meyer UA, Tyndale RF, editors. Pharmacogeno-mics. New York: Marcel Dekker, 2001: 169-181.

41. Dovichi NJ. DNA sequencing by capillary electrophoresis. Electrophoresis 1997; 18(12-13):2393-2399.

42. O'Donovan MC, Oefner PJ, Roberts SC, Austin J, Hoogendoorn B, Guy C, et al. Blind analysis of denaturing high-performance liquid chromatography as a tool for mutation detection. Genomics 1998; 52(1):44-49.

43. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 1999; 22(3):231-238.

44. Bray MS, Boerwinkle E, Doris PA. High-throughput multiplex SNP genotyping with MALDI-TOF mass spectrophotometry: Practice, problems and promise. Human Mut 2001; 17:296-304.

45. Koster H, Tang K, Fu DJ, Braun A, van den BD, Smith CL, et al. A strategy for rapid and efficient DNA sequencing by mass spectrometry. Nat Biotechnol 1996; 14(9):1123-1128.

46. Little DP, Braun A, O'Donnell MJ, Koster H. Mass spectrometry from miniaturized arrays for full comparative DNA analysis. Nat Med 1997; 3(12):1413-1416.

47. Ross PL, Hall L, Haff L, Gravin A. Multiplex genotyping by specialized mass spectrometry. In: Kalow W, Meyer UA, Tyndale RF, editors. Pharmacogenomics. New York: Marcel Dekker, 2001: 201-221.

48. Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays. Nature 2000; 405(6788):827-836.

49. Chen J, Iannone MA, Li MS, Taylor JD, Rivers P, Nelsen AJ, et al. A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res 2000; 10(4):549-557.

50. Stevens PW, Hall JG, Lyamichev V, Neri BP, Lu M, Wang L, et al. Analysis of single nucleotide polymorphisms with solid phase invasive cleavage reactions. Nucleic Acids Res 2001; 29(Online).

51. Grompe M. The rapid detection of unknown mutations in nucleic acids. Nature Genet 1993; 5:111-117.

52. Nollau P, Wagener C. Methods for detection of point mutations: Performance and quality assessment. IFCC Scientific Division, Committee on Molecular Biology Techniques. Clin Chem 1997; 43(7):1114-1128.

53. Schafer AJ, Hawkins JR. DNA variation and the future of human genetics. Nature Biotechnol 1998; 16(1):33-39.

54. Cotton RG. Mutation detection and mutation databases. Clin Chem Lab Med 1998; 36(8):519-522.

55. Sanger F. Sequences, sequences, and sequences. Annu Rev Biochem 1988; 57:1-28.

56. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74(12):5463-5467.

57. Meldrum D. Automation for genomics, Part One: Preparation for sequencing. Part two: Sequencers, microarrays, and future trends. Genome Res 2000; 10:1081, 12881092, 1303.

58. Orita M, Suzuki Y, Sekiya T, Hatashi K. Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics 1989; 5:874-879.

Sheffield VC, Beckm JS, Kwitek AE, Sandstrom DW, Stone EM. The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions. Genomics 1993; 16:325-332.

Larsen LA, Christiansen M, Vuust J, Andersen PS. High-throughput single-strand conformation polymorphism analysis by automated capillary electrophoresis: Robust multiplex analysis and pattern-based identification of allelic variants. Hum Mut 1999; 13(4):318-327.

Larsen LA, Christiansen M, Vuust J, Andersen PS. High throughput mutation screening by automated capillary electrophoresis. Comb Chem High Throughput Screen 2000; 3(5):393-409.

Fischer SG, Lerman LS. DNA fragments differing by single base pair substitutions are separated in denaturing gradient gels: Correspondence with melting theory. Proc Natl Acad Sci USA 1983; 80:1579-1583.

Myers RM, Maniatis T, Lerman LS. Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol 1987; 155:501-527.

Riesner D, Steger G, Zimmat R, Owens RA, Wagenhofer M, Hillen W, et al. Temperature-gradient gel electrophoresis of nucleic acids: Analysis of conforma-tional transtions, sequence variations, and protein-nucleic acid interactions. Electrophoresis 2002; 10(5):377-389.

White MB, Carvalho M, Derse D, O'Brien SJ, Dean M. Detecting single base substitutions as heteroduplex polymorphisms. Genomics 1992; 12(2):301-306. Rozycka M, Collins N, Stratton MR, Wooster R. Rapid detection of DNA sequence variants by conformation-sensitive capillary electrophoresis. Genomics 2000; 70(1):34-40.

Bolla MK, Wood N, Humphries SE. Rapid determination of apolipoprotein E genotype using a heteroduplex generator. J Lipid Res 1999; 40:2340-2345. Myers RM, Larin Z, Maniatis T. Detection of single base substitutions by ribonu-clease cleavage at mismatches in RNA:DNA duplexes. Science 1985; 230:12421246.

Myers RM, Sheffield SG, Cox DR. Detection of single base changes in DNA: Ribonuclease cleavage and denaturing gradient gel electrophoresis In: Davies KE, editor. Genome Analysis. A Practical Approach. New York: Oxford University Press, 1988: 95-139.

Zheng H, Hasty P, Brennaman MA, Grompe M, Gibbs RA, Wilson JH, et al. Fidelity of targeted recombination in human fibroblasts and murine embryonic stem cells. Proc Natl Acad Sci USA 1991; 88(Sep):8067-8071.

Mashal RD, Koontz J, Sklar J. Detection of mutations by cleavage of DNA het-eroduplexes with bacteriophage resolvases. Nat Genet 1995; 9(Feb):177-183. Youil R, Kemper BW, Cotton RGH. Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Proc Natl Acad Sci USA 1995; 92( Jan):87-91. Del TB Jr, Poff HE III, Novotny MA, Cartledge DM, Walker RI, Earl CD, et al. Automated fluorescent analysis procedure for enzymatic mutation detection. Clin Chem 1998; 44(4):731-739.

Multiauthored. The chipping forecast I (1999) and II (2002). Nat Genet 1999; 21 Suppl(1):1-60.

Multiauthored. The chipping forecast II. Nature 2002; 32 Suppl(Dec):461-552. Multiauthored. Functional genomics. Nature 2000; 405(15 June):819-865. Hacia JG. Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet 1999; 21(1 Suppl):42-47.

78. Hacia JG, Brody LC, Chee MS, Fodor SP, Collins FS. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nat Genet 1996; 14(4):441-447.

79. Southern E, Mir K, Shchepinov M. Molecular interactions on microarrays. Nat Genet Suppl 1999; 21(Jan):5-9.

80. Pastinen T, Syvanen A-C. Minisequencing: A specific tool for DNA analysis and diagnosis on oligonucleotide arrays. Genome Res 1997; 7:606-614.

81. Nikiforov TT, Rendle RB, Goelet P, Rogers YH, Kotewicz ML, Anderson S, et al. Genetic bit analysis: A solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res 1994; 22(20):4167-4175.

82. Tsujikawa M, Tsujikawa K, Maeda N, Watanabe H, Inoue Y, Mashima Y, et al. Rapid detection of M1S1 mutations by the protein truncation test. Invest Ophthalmol Visual Sci 2000; 41(9):2466-2468.

83. Traverso G, Shuber A, Levin B, Johnson C, Oleson L, Schoetz DJ, et al. Detection of APC mutations in fecal DNA from patients with colorectal tumors. N Engl J Med 2002; 346(5):311-320.

84. Cooper DN, Youssoufian H. The CpG dinucleotide and human genetic disease. Hum Genet 1988; 78(2):151-155.

85. Blomeke B, Bennett WP, Harris CC, Shields PG. Serum, plasma, and paraffin-embedded tissues as sources of DNA for studying cancer susceptibility genes. Carcinogenesis 1997; 18(6):1271-1275.

86. Nowell S, Sweeney C, Winters M, Stone A, Lang NP, Hutchins LF, et al. Association between sulfotransferase 1A1 genotype and survival of breast cancer patients receiving tamoxifen therapy. J Natl Cancer Inst 2002; 94(21):1635-1640.

87. Rae JM, Cordero KE, Scheys JO, Lippman ME, Flockhart DA, Johnson MD. Genotyping for polymorphic drug metabolizing enzymes from paraffin-embedded and immunohistochemically stained tumor samples. Pharmacogenetics 2003; 13: 501-507.

88. Day INM, Humphries SE. Electrophoresis for genotyping: Microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose. Anal Biochem 1994; 222:389-395.

89. Nauck M, Hoffmann MM, Wieland H, Marz W. Evaluation of the apo E genotyping kit on the Light-Cycler. Clin Chem 2000; 46(5):722-724.

90. Dahlen P, Carlso J, Liukkonen L, Lilja H, Siitari H, Hurskainen P, et al. Europiumlabeled oligonucleotides to detect point mutations: Application to PIZ alpha 1-antitrypsin deficiency. Clin Chem 1993; 39:1626-1631.

91. Newton CR, Graham A, Heptinstall LE, Powell SJ, Summers C, Kalsheker N, et al. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 1989; 17:2503-2515.

92. Gibbs RA, Nguyen PN, Caskey CT. Detection of single DNA base differences by competitive oligonucleotide priming. Nucleic Acids Res 1989; 17(7):2437-2448.

93. Gibson NJ, Gillard HL, Whitcombe D, Ferrie RM, Newton CR, Little S. A homogeneous method for genotyping with fluorescence polarization. Clin Chem 1997; 43(8 Pt 1):1336-1341.

94. Zhou G, Kamahori M, Okano K, Chuan G, Harada K, Kambara H. Quantitative detection of single nucleotide polymorphisms for a pooled sample by a biolumi-nometric assay coupled with modified primer extension reactions (BAMPER). Nucleic Acids Res 2001; 29(19):E93.

95. Landegren U, Kaiser R, Sanders J, Hood L. A ligase-mediated gene detection technique. Science 1988; 241(26 Aug):1077-1080.

96. Nickerson DA, Kaiser R, Lappin S, Stewart J, Hood L, Landegren U. Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay. Proc Natl Acad Sci USA 1990; 87(Nov):8923-8927.

97. ALves AM, Carr FJ. Dot blot detection of point mutations with adjacently hybridising synthetic oligonucleotide probes. Nucleic Acids Res 1988; 16(17):8723.

98. Baron H, Fung S, Aydin A, Bahring S, Luft FC, Schuster H. Oligonucleotide ligation assay (OLA) for the diagnosis of familial hypercholesterolemia. Nat Bio-technol 1996; 14(10):1279.

99. Hansen TS, Petersen NE, Iitia A, Blaabjerg O, Hyloft-Petersn P, Horder M. Robust nonradioactive oligonucleotide ligation assay to detect a common point mutation in the CYP2D6 gene causing abnormal drug metabolism. Clin Chem 1995; 41:413418.

100. Foy CA, Parks HC. Emerging homogeneous DNA-based technologies in the clinical laboratory. Clin Chem 2001; 47(6):990-1000.

101. Shi MM. Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. Clin Chem 2001; 47(2):164-172.

102. Little MC, Andrews J, Moore R, Bustos S, Jones L, Embres C, et al. Strand displacement amplification and homogeneous real-time detection incorporated in a second-generation DNA probe system, BDProbeTecET. Clin Chem 1999; 45(6): 777-784.

103. Ausina V, Gamboa F, Gazapo E, Manterola JM, Lonca J, Matas L, et al. Evaluation of the semiautomated Abbott LCx Mycobacterium tuberculosis assay for direct detection of Mycobacterium tuberculosis in respiratory specimens. J Clin Microbiol 1997; 35(8):1996-2002.

104. Clegg RM. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol 1992; 211:353-388.

105. Chen X, Levine L, Kwok PY. Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res 1999; 9(5):492-498.

106. Syvanen AC. From gels to chips: ''Minisequencing'' primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum Mutat 1999; 13(1): 1-10.

107. Sitbon G, Syvanen AC. Multiplex fluorescent minisequencing applied to the typing of genes encoding drug-metabolizing enzymes. In: Kalow W, Meyer UA, Tyndale RF, editors. Pharmacogenomics. New York: Marcel Dekker, 2001: 191-200.

108. Chen X, Zehnbauer B, Gnirke A, Kwok PY. Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. Proc Natl Acad Sci USA 1997; 94(20):10756-10761.

109. Lovmar L, Syvanen AC. Genotyping single-nucleotide polymorphisms by minisequencing using tag arrays. Methods Mol Med 2005; 114:79-92.

110. Livak KJ. Allelic discrimination using fluorogenic probes and the 5' nuclease assay. Genet Anal 199; 14:143-149.

111. Shi MM, Bleavins MR, de la Iglesia FA. Technologies for detecting genetic polymorphisms in pharmacogenomics. Mol Diagn 1999; 4(4):343-351.

112. Shi MM, Myrand SP, Bleavins MR, de la Iglesia FA. High-throughput genotyping method for glutathione S-transferase T1 and M1 gene deletions using TaqMan probes. Res Commun Mol Pathol Pharmacol 1999; 103(1):3-15.

113. Hiratsuka M, Agatsuma Y, Omori F, Narahara K, Inoue T, Kishikawa Y, et al. High throughput detection of drug-metabolizing enzyme polymorphisms by allele-specific fluorogenic 5' nuclease chain reaction assay. Biol Pharm Bull 2000; 23(10): 1131-1135.

114. Smit ML, Giesendorf BA, Vet JA, Trijbels FJ, Blom HJ. Semiautomated DNA mutation analysis using a robotic workstation and molecular beacons. Clin Chem 2001; 47(4):739-744.

115. Whitcombe D, Theaker J, Guy SP, Brown T, Little S. Detection of PCR products using self-probing amplicons and fluorescence. Nat Biotechnol 1999; 17(Aug): 804-807.

116. Thelwell N, Millington S, Solinas A, Booth J, Brown T. Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res 2000; 28(19):3752-3761.

117. Lyamichev V, Mast AL, Hall JG, Prudent JR, Kaiser MW, Takova T, et al. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat Biotechnol 1999; 17(3):292-296.

118. Kwiatkowski RW, Lyamichev V, de Arruda M, Neri B. Clinical, genetic and pharmacogenetic applications of the invader assay. Mol Diagn 1999; 4(4):353-364.

119. Ohnishi Y. [A high-throughput SNP typing system for genome-wide association studies]. Gan To Kagaku Ryoho 2002; 29(11):2031-2036.

120. Staden R. Sequence data handling by computer. Nucleic Acids Res 1977; 4(11): 4037-4051.

121. Schena M. Charting the microarray revolution. Scientist 2004; 18(19 Oct 11): 30-31.

122. Alper J. Weighing DNA for fast genetic diagnosis. Science 2001; 279(27 Mar): 2044-2045.

123. Uetz P. A comprehensive analysis of protein-protein interactions in Saccharamyces cerevisiae. Nature 2003; 403(10 Feb):623-627.

124. Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, et al. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 1977; 265(5596): 687-695.

125. Sutcliffe JG. Nucleotide sequence of the ampicillin resistance gene of Escherichia coli plasmid pBR322. Proc Natl Acad Sci USA 1978; 75(8):3737-3741.

126. Sutcliffe JG. pBR322 and the advent of rapid DNA sequencing. Trends Biochem Sci 1995; 20(2):87-90.

127. Ambler RP, Scott GK. Partial amino acid sequence of penicillinase coded by Escherichia coli plasmid R6K. Proc Natl Acad Sci USA 1978; 75(8):3732-3736.

128. Wilbur WJ, Lipman DJ. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci USA 1983; 80(3):726-730.

129. Waterfield MD, Scrace GT, Whittle N, Stroobant P, Johnsson A, Wasteson A, et al. Platelet-derived growth factor is structurally related to the putative transforming protein p28sis of simian sarcoma virus. Nature 1983; 304(5921):35-39.

130. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988; 85(8):2444-2448.

131. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215(3):403-410.

132. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 1997; 25(17):3389-3402.

133. Gallagher R. Seven cheers for technology. Scientist 2005; 19(16):6-51.

134. Rogic S, Mackworth AK, Ouellette FB. Evaluation of gene-finding programs on mammalian sequences. Genome Res 2001; 11(5):817-832.

135. Fickett JW. Finding genes by computer: The state of the art. Trends Genet 1996; 12(8):316-320.

Gordon D, Abajian C, Green P. Consed: A graphical tool for sequence finishing. Genome Res 1998; 8(3):195-202.

Strausberg RL, Feingold EA, Klausner RD, Collins FS. The mammalian gene collection. Science 1999; 286(5439):455-457.

Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci USA 2002; 99(26):16899-16903. Lewis EK, Haaland WC, Nguyen F, Heller DA, Allen MJ, MacGregor RR, et al. Color-blind fluorescence detection for four-color DNA sequencing. Proc Natl Acad Sci USA 2005; 102(15):5346-5351.

Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437(7057):376-380.

Meinkoth J, Wahl G. Hybridization of nucleic acids immobilized on solid supports. Anal Biochem 1984; 138(2):267-284.

Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW. Mi-croarrays: Biotechnology's discovery platform for functional genomics. Trends Biotechnol 1998; 16(7):301-306.

Maskos U, Southern EM. A novel method for the analysis of multiple sequence variants by hybridisation to oligonucleotides. Nucleic Acids Res 1993; 21:22672268.

Maskos U, Southern EM. A novel method for the parallel analysis of multiple mutations in multiple samples. Nucleic Acids Res 1993; 21:2269-2270. Blanchard AP, Kaiser RJ, Hood LE. High-density oligonucleotide arrays. Biosens Bioelectron 1996; 11(6-7):687-690.

Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, et al. Multiple-laboratory comparison of microarray platforms. Nat Methods 2005; 2(5):345-350.

Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J. Independence and reproducibility across microarray platforms. Nat Methods 2005; 2(5):337-344. Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, et al. Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2005; 2(5):351-356.

Ekins R, Chu FW. Microarrays: Their origins and applications. Trends Biotechnol 1999; 17(6):217-218.

Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R, et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 1998; 280(5366):1077-1082.

Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996; 14(13):1675-1680.

Howbrook DN, van der Valk AM, O'Shaughnessy MC, Sraker DK, Baker SC, LLoyd AW. Development in microarray technologies. Drug Discov Today 2003; 8(14):642-651.

Fang Y, Lahiri J, Picard L. G protein-coupled receptor microarrays for drug discovery. Drug Discov Today 2003; 8(16):755-761.

Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, et al. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 1999; 286(5439):531-537.

Multiauthored. The chipping forecast III. Nat Genet Suppl 2005; 37( June):S1-S45.

156. Horning EC, Horning MG, Carroll DI, Dzidic I, Stillwell RN. Chemical ionization mass spectrometry. Adv Biochem Psychopharmacol 1973; 7:15-31.

157. Griffin TJ, Hall JG, Prudent JR, Smith LM. Direct genetic analysis by matrixassisted laser desorption/ionization mass spectrometry. Proc Natl Acad Sci USA 1999; 96(11):6301-6306.

158. Griffin TJ, Smith LM. Single-nucleotide polymorphism analysis by MALDI/TOF mass spectrometry. Trends Biotechnol 2000; 18(2):77-84.

159. Wu KJ, Steding A, Becker CH. Matrix-assisted laser desorption time-of-flight mass spectrometry of oligonucleotides using 3-hydroxypicolinic acid as an ultraviolet-sensitive matrix. Rapid Commun Mass Spectrom 1993; 7(2):142-146.

160. Hunter JM, Lin H, Becker CH. Cryogenic frozen solution matrixes for analysis of DNA by time-of-flight mass spectrometry. Anal Chem 1997; 69(17):3608-3612.

161. Ding C, Cantor CR. A high-throughput gene expression analysis technique using competitive PCR and matrix-assisted laser desorption ionization time-of-flight MS. Proc Natl Acad Sci USA 2003; 100(6):3059-3064.

162. Rubakhin SS, Jurchen JC, Monroe EB, Sweedler JV. Imaging mass spectrometry: Fundamentals and applications to drug discovery. Drug Discov Today 2005; 10(12): 823-837.

163. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, et al. Life with 6000 genes. Science 1996; 274(5287):546, 563-567.

164. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, et al. Toward a proteinprotein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci USA 2000; 97(3):1143-1147.

165. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 2001; 98(8):4569- 4574.

166. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, et al. A protein interaction map of Drosophila melanogaster. Science 2003; 302(5651):1727-1736.

167. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, et al. A map of the interactome network of the metazoan C. elegans. Science 2004; 303(5657):540-543.

168. Colland F, Jacq X, Trouplin V, Mougin C, Groizeleau C, Hamburger A, et al. Functional proteomics mapping of a human signaling pathway. Genome Res 2004; 14(7):1324-1332.

169. McGlennen RC. Miniaturization technologies for molecular diagnostics. Clin Chem 2001; 47(3):393-402.

170. Burns MA, Johnson BN, Brahmasandra SN, Handique K, Webster JR, Krishnan M, et al. An integrated nanoliter DNA analysis device. Science 1998; 282(5388): 484-487.

171. Zhou G, Kamahori M, Okano K, Harada K, Kambara H. Miniaturized pyr-osequencer for DNA analysis with capillaries to deliver deoxynucleotides. Elec-trophoresis 2001; 22(16):3497-3504.

172. Khandurina J, Guttman A. Bioanalysis in microfluidic devices. J Chromatogr A 2002; 943:159-183.

173. Vilkner T, Janasek D, Manz A. Micro total analysis systems. Recent developments. Anal Chem 2004; 76(12):3373-3385.

174. Anderson RC, Su X, Bogdan GJ, Fenton J. A miniature integrated device for automated multistep genetic assays. Nucleic Acids Res 2000; 28(12):E60.

Fiorini GS, Chiu DT. Disposable microfluidic devices: Fabrication, function, and application. BioTechniques 2005; 38(3):429-446.

Hanash S. Operomics: Molecular analysis of tissues from DNA to RNA to protein. Clin Chem Lab Med 2000; 38(9):805-813.

Velculescu V, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science 1995; 270:484-487.

Velculescu VE, Vogelstein B, Kinzler KW. Analysing uncharted transcriptomes with SAGE. Trends Genet 2000; 16(10):423-425.

Madden SL, Wang C, Landes G. Serial analysis of gene expression. Transcriptional insights into functional biology. In: Kalow W, Meyer UA, Tyndale RF, editors.

Pharmacogenomics. New York: Marcel Dekker, 2001: 223-251.

Datson NA, der Perdojong J, van den Berg MP, de Kloet ER, Vreugdenhil E.

MicroSAGE: A modified procedure for serial analysis of gene expression in limited amounts of tissue. Nucleic Acids Res 1999; 27(5):1300-1307.

Dixon AK, Richardson PJ, Pinnock RD, Lee K. Gene-expression analysis at the single-cell level. Trends Pharmacol Sci 2000; 21(2):65-70.

Schober MS, Min Y-N, Chen YQ. Serial analysis of gene expression in a single cell. BioTechniques 2001; 31(6):1240-1242.

Dear PH. One by one: Single molecule tools for genomics. Brief Funct Genomic Proteomic 2003; 1(4):397-416.

Woolley AT, Guillemette C, Li CC, Housman DE, Lieber CM. Direct haplotyping of kilobase-size DNA using carbon nanotube probes. Nat Biotechnol 2000; 18(7): 760-763.

Guillemette C, Ritter JK, Auyeung DJ, Kessler FK, Housman DE. Structural heterogeneity at the UDP-glucuronosyltransferase 1 locus: Functional consequences of three novel missense mutations in the human UGT1A7 gene. Pharmacogenetics 2000; 10(7):629-644.

Baner J, Nilsson M, Mendel-Hartvig M, Landgren U. Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res 1998; 26(22):5073-5078.

Lizardi PM, Huang X, Zhu Z, Bray-Ward P, Thomas DC, Ward DC. Mutation detection and using single-molecule counting using isothermal rolling-circle amplification. Nat Genet 1998; 19( Jul):225-232.

Zhong X-B, Lizardi PM, Huang X-H, Bray-Ward PL, Ward DC. Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification. Proc Natl Acad Sci USA 2001; 98(7):3940-3945.

Deamer DW, Akeson M. Nanopores and nucleic acids: Prospects for ultrarapid sequencing. Trends Biotechnol 2000; 18:147-151.

Kasianowicz JJ, Brandin E, Branton D, Deamer DW. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 1996; 93(24):13770-13773.

Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW. Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys J 1999; 77(6):3227-3233.

Liljedahl U, Karlsson J, Melhus H, Kurland L, Lindersson M, Kahan T, et al. A microarray minisequencing system for pharmacogenetic profiling of antihyperten-sive drug response. Pharmacogenetics 2003; 13(1):7-17.

193. ARmstrong SA, Staunton JE, Silverman LB, Pieters R, den Boer ML, Minden MD, et al. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet 2002; 30( Jan):41-47.

194. Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 2000; 406(6795):536-540.

195. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000; 403(6769):503-511.

196. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, et al. Geneexpression profiles in hereditary breast cancer. N Engl J Med 2001; 344(8):539-548.

197. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002; 415(6871):530-536.

198. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002; 347(25):1999-2009.

199. van Steensel B, Henikoff S. Epigenomic profiling using microarrays. BioTechniques 2003; 35(2):346-4, 356.

200. van Steensel B. Mapping of genetic and epigenetic regulatory networks using mi-croarrays. Nat Genet 2005; 37(6 Suppl):S18-S24.

201. Havlis J, Trbusek M. 5-Methylcytosine as a marker for the monitoring of DNA methylation. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 781(1-2):373-392.

202. Hong KM, Yang SH, Guo M, Herman JG, Jen J. Semiautomatic detection of DNA methylation at CpG islands. BioTechniques 2005; 38(3):354, 356, 358.

203. Shi H, Maier S, Nimmrich I, Yan PS, Caldwell CW, Olek A, et al. Oligonucleotide-based microarray for DNA methylation analysis: Principles and applications. J Cell Biochem 2003; 88(1):138-143.

204. Chen CM, Chen HL, Hsiau TH, Hsiau AH, Shi H, Brock GJ, et al. Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes. Am J Pathol 2003; 163(1):37-45.

205. Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, Leighton S, et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med 1998; 4(7):844-847.

206. Pfarr W, Webersinke G, Paar C, Wechselberger C. Immunodetection of 5'-methylcytosine on Giemsa-stained chromosomes. BioTechniques 2005; 38(4):527-528, 530.

207. Golub TR. Genome-wide views of cancer. N Engl J Med 2001; 344(8):601-602.

208. Camp RL, Dolled-Filhart M, King BL, Rimm DL. Quantitative analysis of breast cancer tissue microarrays shows that both high and normal levels of HER2 expression are associated with poor outcome. Cancer Res 2003; 63(7):1445-1448.

209. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, et al. Detection of large-scale variation in the human genome. Nat Genet 2004; 36(9):949-951.

210. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, et al. Large-scale copy number polymorphism in the human genome. Science 2004; 305(5683):525-528.

211. FeukL, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet 2006; 7(2):85-97.

212. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, et al. Copy number variation: New insights in genome diversity. Genome Res 2006; 16(8): 949-961.

213. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, et al. Global variation in copy number in the human genome. Nature 2006; 444(7118):444-454.

214. Fiegler H, Redon R, Andrews D, Scott C, Andrews R, Carder C, et al. Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res 2006.

215. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature 2001; 409(6822):860-921.

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