-
1
-
-
10244219858
-
Accessing genetic information with high-density DNA arrays
-
of outstanding interest. Simultaneous analysis of the entire human mitochondrial genome (16.6 kilobase) was performed on DNA arrays of up to 135,000 different probe oligonucleotides. A two-color scheme allows differential measurement of hybridization on a single chip. This paper is of outstanding interest because it is the most complete measurement to date utilizing several of the principles we outlined at the start of the review: parallelization, automation, and miniaturization. Although it may not be the ideal mesurement scheme, it is the current standard that must be improved upon for future work
-
Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, Winkler J, Lockhart DJ, Morris MS, Fodor SPA. Accessing genetic information with high-density DNA arrays. of outstanding interest Science. 274:1996;610-614 Simultaneous analysis of the entire human mitochondrial genome (16.6 kilobase) was performed on DNA arrays of up to 135,000 different probe oligonucleotides. A two-color scheme allows differential measurement of hybridization on a single chip. This paper is of outstanding interest because it is the most complete measurement to date utilizing several of the principles we outlined at the start of the review: parallelization, automation, and miniaturization. Although it may not be the ideal mesurement scheme, it is the current standard that must be improved upon for future work.
-
(1996)
Science
, vol.274
, pp. 610-614
-
-
Chee, M.1
Yang, R.2
Hubbell, E.3
Berno, A.4
Huang, X.C.5
Stern, D.6
Winkler, J.7
Lockhart, D.J.8
Morris, M.S.9
Fodor, S.P.A.10
-
2
-
-
0030890466
-
Sequence analysis by hybridization with oligonucleotide microchip: Identification of β-thalassemia mutations
-
Drobyshev A, Nologina N, Shik V, Pobedimskaya D, Yershov G, Mirzabekov A. Sequence analysis by hybridization with oligonucleotide microchip: identification of β-thalassemia mutations. Gene. 188:1997;45-52.
-
(1997)
Gene
, vol.188
, pp. 45-52
-
-
Drobyshev, A.1
Nologina, N.2
Shik, V.3
Pobedimskaya, D.4
Yershov, G.5
Mirzabekov, A.6
-
3
-
-
0030872685
-
Fractionation, phosphorylation and ligation on oligonucleotide microchips to enhance sequencing by hybridization
-
of special interest. Arrays of oligonucleotides are anchored in miniature polyacrilimide gel pads, rather than on a flat chip surface. The primary advantage is a higher density of target oligomers. In addition, typical reactions (e.g. hybridization or ligation) occur with solution phase characteristics as opposed to the solid phase behavior of standard DNA arrays.
-
Dubiley S, Kirillov E, Lysov Y, Mirzabekov A. Fractionation, phosphorylation and ligation on oligonucleotide microchips to enhance sequencing by hybridization. of special interest Nucleic Acids Res. 25:1997;2259-2265 Arrays of oligonucleotides are anchored in miniature polyacrilimide gel pads, rather than on a flat chip surface. The primary advantage is a higher density of target oligomers. In addition, typical reactions (e.g. hybridization or ligation) occur with solution phase characteristics as opposed to the solid phase behavior of standard DNA arrays.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 2259-2265
-
-
Dubiley, S.1
Kirillov, E.2
Lysov, Y.3
Mirzabekov, A.4
-
4
-
-
0031213779
-
Manual manufacturing of oligonucleotide, DNA and protein microchips
-
Gruschin D, Yershov G, Zaslavsky A, Gemmell A, Shick V, Proudnikov D, Arenkov P, Mirzabekov A. Manual manufacturing of oligonucleotide, DNA and protein microchips. Anal Biochem. 250:1997;203-211.
-
(1997)
Anal Biochem
, vol.250
, pp. 203-211
-
-
Gruschin, D.1
Yershov, G.2
Zaslavsky, A.3
Gemmell, A.4
Shick, V.5
Proudnikov, D.6
Arenkov, P.7
Mirzabekov, A.8
-
5
-
-
0029910179
-
Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides
-
Livshits, Mirzabekov AD. Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides. Biophys J. 71:1996;2795-2801.
-
(1996)
Biophys J
, vol.71
, pp. 2795-2801
-
-
Livshits1
Mirzabekov, A.D.2
-
6
-
-
0030758618
-
Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays
-
Weiler J, Gausepohy H, Hauser N, Jensen ON, Hoheisel JD. Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays. Nucleic Acids Res. 25:1997;2792-2799.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 2792-2799
-
-
Weiler, J.1
Gausepohy, H.2
Hauser, N.3
Jensen, O.N.4
Hoheisel, J.D.5
-
7
-
-
0030810721
-
Minisequencing: A specific tool for DNA analysis and diagnostics on oligonucleotide arrays
-
Pastinen T, Kurg A, Metspalu A, Peltonen L, Syvänen A. Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 7:1997;606-614.
-
(1997)
Genome Res
, vol.7
, pp. 606-614
-
-
Pastinen, T.1
Kurg, A.2
Metspalu, A.3
Peltonen, L.4
Syvänen, A.5
-
8
-
-
0030852959
-
Detecting CFTR gene mutations by using primer oligo base extension and mass spectrometry
-
of special interest. The primer oligo base extension (PROBE) technique involves an isothermal extension of a primer oligomer, which is first annealed to a region of interest in the genome. Careful selection of the mixture of dNTPs and ddNTPs present during the extension reaction allows accurate characterization of several bases downstream from the 3′ end of the primer.
-
Braun A, Little DP, Köster H. Detecting CFTR gene mutations by using primer oligo base extension and mass spectrometry. of special interest Clin Chem. 43:1997;1151-1158 The primer oligo base extension (PROBE) technique involves an isothermal extension of a primer oligomer, which is first annealed to a region of interest in the genome. Careful selection of the mixture of dNTPs and ddNTPs present during the extension reaction allows accurate characterization of several bases downstream from the 3′ end of the primer.
-
(1997)
Clin Chem
, vol.43
, pp. 1151-1158
-
-
Braun, A.1
Little, D.P.2
Köster, H.3
-
9
-
-
0030821797
-
Detection of RET proto-oncogene codon 634 mutations using mass spectrometry
-
Little DP, Braun A, Darnhofer-Demar B, Frilling A, Li Y, McIver RT, Köster H. Detection of RET proto-oncogene codon 634 mutations using mass spectrometry. J Mol Med. 75:1997;745-750.
-
(1997)
J Mol Med
, vol.75
, pp. 745-750
-
-
Little, D.P.1
Braun, A.2
Darnhofer-Demar, B.3
Frilling, A.4
Li, Y.5
McIver, R.T.6
Köster, H.7
-
10
-
-
0031573414
-
Improved analysis of microsatellites using mass spectrometry
-
of special interest. The authors use MALDI-TOF mass spectrometry and the PROBE technique (see Braun et al. 1997 [8]) to accurately characterize the size of tandem repeat microsatellites. Limiting the dNTPs in the mixture to those nucleotides which occur in tandem repeat regions allows the extension reaction to proceed up to the end of the repeat region. The mass differences between varying length microsatellites correspond to entire repeat units, which vary between ~600 daltons for dinucleotide repeats and ~1200 daltons for tetranucleotide repeats. These mass differences are easily within the resolving power of current MALDI-TOF instruments.
-
Braun A, Little DP, Reuter D, Müller-Mysok B, Köster H. Improved analysis of microsatellites using mass spectrometry. of special interest Genomics. 46:1997;18-23 The authors use MALDI-TOF mass spectrometry and the PROBE technique (see Braun et al. 1997 [8]) to accurately characterize the size of tandem repeat microsatellites. Limiting the dNTPs in the mixture to those nucleotides which occur in tandem repeat regions allows the extension reaction to proceed up to the end of the repeat region. The mass differences between varying length microsatellites correspond to entire repeat units, which vary between ~600 daltons for dinucleotide repeats and ~1200 daltons for tetranucleotide repeats. These mass differences are easily within the resolving power of current MALDI-TOF instruments.
-
(1997)
Genomics
, vol.46
, pp. 18-23
-
-
Braun, A.1
Little, D.P.2
Reuter, D.3
Müller-Mysok, B.4
Köster, H.5
-
11
-
-
0030890116
-
Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry
-
Haff LA, Smirnov IP. Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res. 7:1997;378-388.
-
(1997)
Genome Res
, vol.7
, pp. 378-388
-
-
Haff, L.A.1
Smirnov, I.P.2
-
12
-
-
0031058319
-
High-throughput DNA analysis by time-of-flight mass spectrometry
-
Monforte JA, Becker CH. High-throughput DNA analysis by time-of-flight mass spectrometry. Nat Med. 3:1997;360-362.
-
(1997)
Nat Med
, vol.3
, pp. 360-362
-
-
Monforte, J.A.1
Becker, C.H.2
-
13
-
-
0000184162
-
MALDI on a chip: Analysis of low- To sub-femtomole quantities of synthetic oligonucleotides and DNA diagnostic products dispensed by a piezoelectric pipette
-
of special interest. of outstanding interest The authors have developed and tested a chip based 10 × 10 array of oligonucleotides, utilizing nanoliter volume pits in the chip. The array of oligonucleotides can be completely automatically scanned, which eliminates the usual search for the MALDI 'sweet spot', which has previously limited the attainable throughput. Combination of this array technology with other diagnostic techniques, such as PROBE (see Braun et al. 1997 [8, 10]), present a very promising avenue to high throughput, high sensitivity, diagnostic DNA measurements
-
Little DP, Cornish TJ, O'Donnell MJ, Braun A, Cotter RJ, Köster H. MALDI on a chip: analysis of low- to sub-femtomole quantities of synthetic oligonucleotides and DNA diagnostic products dispensed by a piezoelectric pipette. of special interest of outstanding interest Anal Chem. 1997; The authors have developed and tested a chip based 10 × 10 array of oligonucleotides, utilizing nanoliter volume pits in the chip. The array of oligonucleotides can be completely automatically scanned, which eliminates the usual search for the MALDI 'sweet spot', which has previously limited the attainable throughput. Combination of this array technology with other diagnostic techniques, such as PROBE (see Braun et al. 1997 [8, 10]), present a very promising avenue to high throughput, high sensitivity, diagnostic DNA measurements.
-
(1997)
Anal Chem
-
-
Little, D.P.1
Cornish, T.J.2
O'Donnell, M.J.3
Braun, A.4
Cotter, R.J.5
Köster, H.6
-
14
-
-
0029997988
-
Sequencing oligonucleotides by exonuclease digestion and delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry
-
Smirnov IP, Roskey MT, Juhasz P, Takach EJ, Martin SA, Haff LA. Sequencing oligonucleotides by exonuclease digestion and delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Anal Biochem. 238:1996;19-25.
-
(1996)
Anal Biochem
, vol.238
, pp. 19-25
-
-
Smirnov, I.P.1
Roskey, M.T.2
Juhasz, P.3
Takach, E.J.4
Martin, S.A.5
Haff, L.A.6
-
15
-
-
0029927530
-
Applications of delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry to oligonucleotide analysis
-
of outstanding interest. Delayed extraction MALDI is performed by delaying the onset of the accelerating voltage for several hundred nanonseconds after the desorption/ionization event. This delay has been shown to greatly increase the mass resolution attainable in continuous field MALDI, by up to an order of magnitude for RNA fragments. Increased mass resolution allows for diagnostic measurements of larger fragments, which in turn will allow for increased throughput in measurements.
-
Juhasz P, Roskey MT, Smirnov IP, Haff LA, Vestal ML, Martin SA. Applications of delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry to oligonucleotide analysis. of outstanding interest Anal Chem. 68:1996;941-946 Delayed extraction MALDI is performed by delaying the onset of the accelerating voltage for several hundred nanonseconds after the desorption/ionization event. This delay has been shown to greatly increase the mass resolution attainable in continuous field MALDI, by up to an order of magnitude for RNA fragments. Increased mass resolution allows for diagnostic measurements of larger fragments, which in turn will allow for increased throughput in measurements.
-
(1996)
Anal Chem
, vol.68
, pp. 941-946
-
-
Juhasz, P.1
Roskey, M.T.2
Smirnov, I.P.3
Haff, L.A.4
Vestal, M.L.5
Martin, S.A.6
-
16
-
-
0031081531
-
Controlling DNA fragmentation in MALDI-MS by chemical modification
-
of special interest. Fragmentation is one of the most severe limitations on both resolution and maximum size of DNA fragments analyzed by MALDI-TOF mass spectrometry. This group is analyzing effects of chemical modification of the individual bases on the fragmentation rate, and has, in fact, shown that modifications of the 2′ carbon of an individual base can significantly reduce fragmentation.
-
Tang W, Zhu L, Smith LM. Controlling DNA fragmentation in MALDI-MS by chemical modification. of special interest Anal Chem. 69:1997;302-312 Fragmentation is one of the most severe limitations on both resolution and maximum size of DNA fragments analyzed by MALDI-TOF mass spectrometry. This group is analyzing effects of chemical modification of the individual bases on the fragmentation rate, and has, in fact, shown that modifications of the 2′ carbon of an individual base can significantly reduce fragmentation.
-
(1997)
Anal Chem
, vol.69
, pp. 302-312
-
-
Tang, W.1
Zhu, L.2
Smith, L.M.3
-
17
-
-
4244166752
-
High-speed DNA genotyping using microfabricated capillary array electrophoresis chips
-
Woolley AT, Sensabaugh GF, Mathies RA. High-speed DNA genotyping using microfabricated capillary array electrophoresis chips. Anal Chem. 69:1997;2181-2186.
-
(1997)
Anal Chem
, vol.69
, pp. 2181-2186
-
-
Woolley, A.T.1
Sensabaugh, G.F.2
Mathies, R.A.3
-
18
-
-
0030473161
-
Multiple capillary DNA sequencer that uses fiber-optic illumination and detection
-
Quesada MA, Zhang S. Multiple capillary DNA sequencer that uses fiber-optic illumination and detection. Electrophoresis. 17:1996;1841-1851.
-
(1996)
Electrophoresis
, vol.17
, pp. 1841-1851
-
-
Quesada, M.A.1
Zhang, S.2
-
19
-
-
0029988234
-
Rapid diagnosis of germline p53 mutation using the enzyme mismatch cleavage method
-
Giunta C, Youil R, Venter D, Chow CW, Somers G, Lafferty A, Kemper B, Cotton RGH. Rapid diagnosis of germline p53 mutation using the enzyme mismatch cleavage method. Diagn Mol Path. 5:1996;265-270.
-
(1996)
Diagn Mol Path
, vol.5
, pp. 265-270
-
-
Giunta, C.1
Youil, R.2
Venter, D.3
Chow, C.W.4
Somers, G.5
Lafferty, A.6
Kemper, B.7
Cotton, R.G.H.8
-
20
-
-
0030791118
-
Potassium permanganate and tetraethylammonium chloride are a safe and effective substitute for osmium tetroxide in solid-phase fluorescent chemical cleavage of mismatch
-
Roberts E, Deeble VJ, Woods CG, Taylor GR. Potassium permanganate and tetraethylammonium chloride are a safe and effective substitute for osmium tetroxide in solid-phase fluorescent chemical cleavage of mismatch. Nucleic Acids Res. 25:1997;3377-3378.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3377-3378
-
-
Roberts, E.1
Deeble, V.J.2
Woods, C.G.3
Taylor, G.R.4
-
21
-
-
0029657862
-
NIRCAÖ: A rapid robust method for screening for unknown point mutations
-
Goldrick MM, Kimball GR, Liu Q, Martin LA, Sommer SS, Tseng JY-H. NIRCAÖ: a rapid robust method for screening for unknown point mutations. Biotechniques. 21:1996;106-112.
-
(1996)
Biotechniques
, vol.21
, pp. 106-112
-
-
Goldrick, M.M.1
Kimball, G.R.2
Liu, Q.3
Martin, L.A.4
Sommer, S.S.5
Tseng Jy-H6
-
22
-
-
0031442518
-
Characterization of the yeast transcriptome
-
of special interest. Serial analysis of gene expression (SAGE) is used to characterize which genes are active in yeast cells under three different conditions. As the entire yeast genome has now been sequenced, SAGE tags (14 nucleotides long) can be used to uniquely identify active genes and then locate them within the genome.
-
Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE, Hieter P, Vogelstein B, Kinzler KW. Characterization of the yeast transcriptome. of special interest Cell. 88:1997;243-251 Serial analysis of gene expression (SAGE) is used to characterize which genes are active in yeast cells under three different conditions. As the entire yeast genome has now been sequenced, SAGE tags (14 nucleotides long) can be used to uniquely identify active genes and then locate them within the genome.
-
(1997)
Cell
, vol.88
, pp. 243-251
-
-
Velculescu, V.E.1
Zhang, L.2
Zhou, W.3
Vogelstein, J.4
Basrai, M.A.5
Bassett, D.E.6
Hieter, P.7
Vogelstein, B.8
Kinzler, K.W.9
-
23
-
-
0030962307
-
Gene expression profiles in normal and cancer cells
-
of outstanding interest. Serial analysis of gene expression is used to characterize the differential activity of thousands of different mRNA transcripts in normal and cancer cells. Measurements have indicated that whereas most genes are relatively unchanged, up to several hundred are found which are either over- or under-expressed by up to 100-fold. Information of this nature will help further our understanding of the mechanisms involved in cancer cell growth, and how they differ from normal cells.
-
Zhang L, Zhou W, Velculescu VE, Kern SE, Hruban RH, Hamilton SR, Vogelstein B, Kinzler KW. Gene expression profiles in normal and cancer cells. of outstanding interest Science. 276:1997;1268-1272 Serial analysis of gene expression is used to characterize the differential activity of thousands of different mRNA transcripts in normal and cancer cells. Measurements have indicated that whereas most genes are relatively unchanged, up to several hundred are found which are either over- or under-expressed by up to 100-fold. Information of this nature will help further our understanding of the mechanisms involved in cancer cell growth, and how they differ from normal cells.
-
(1997)
Science
, vol.276
, pp. 1268-1272
-
-
Zhang, L.1
Zhou, W.2
Velculescu, V.E.3
Kern, S.E.4
Hruban, R.H.5
Hamilton, S.R.6
Vogelstein, B.7
Kinzler, K.W.8
-
24
-
-
0030738232
-
Ordered differential display: A simple method for systematic comparison of gene expression profiles
-
Matz M, Usman N, Shagin D, Bogdanova E, Lukyanov S. Ordered differential display: a simple method for systematic comparison of gene expression profiles. Nucleic Acids Res. 25:1997;2541-2542.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 2541-2542
-
-
Matz, M.1
Usman, N.2
Shagin, D.3
Bogdanova, E.4
Lukyanov, S.5
-
25
-
-
0030575911
-
Laser capture microdissection
-
of special interest. Laser capture microdissection is a technique which allows simultaneous inspection and capture of tissue samples for further analysis. Preliminary tests indicate that samples captured with this technique can be manipulated with such procedures as PCR, ligation, and so on. Sample capture sizes have been demonstrated in the 60-700 micron size range. This is very promising with regards to preferential capture of tumor cells for differential analysis with normal cells.
-
Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA. Laser capture microdissection. of special interest Science. 274:1996;998-1001 Laser capture microdissection is a technique which allows simultaneous inspection and capture of tissue samples for further analysis. Preliminary tests indicate that samples captured with this technique can be manipulated with such procedures as PCR, ligation, and so on. Sample capture sizes have been demonstrated in the 60-700 micron size range. This is very promising with regards to preferential capture of tumor cells for differential analysis with normal cells.
-
(1996)
Science
, vol.274
, pp. 998-1001
-
-
Emmert-Buck, M.R.1
Bonner, R.F.2
Smith, P.D.3
Chuaqui, R.F.4
Zhuang, Z.5
Goldstein, S.R.6
Weiss, R.A.7
Liotta, L.A.8
|