Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same

Chee, Mark; Gingeras, Thomas R; Fodor, Stephen P. A.; Hubble, Earl A; Morris, MacDonald S

Title: Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same

Abstract

The invention provides an array of oligonucleotide probes immobilized on a solid support for analysis of a target sequence from a human immunodeficiency virus. The array comprises at least four sets of oligonucleotide probes 9 to 21 nucleotides in length. A first probe set has a probe corresponding to each nucleotide in a reference sequence from a human immunodeficiency virus. A probe is related to its corresponding nucleotide by being exactly complementary to a subsequence of the reference sequence that includes the corresponding nucleotide. Thus, each probe has a position, designated an interrogation position, that is occupied by a complementary nucleotide to the corresponding nucleotide. The three additional probe sets each have a corresponding probe for each probe in the first probe set. Thus, for each nucleotide in the reference sequence, there are four corresponding probes, one from each of the probe sets. The three corresponding probes in the three additional probe sets are identical to the corresponding probe from the first probe or a subsequence thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes.

Inventors:

Chee, Mark ^[1]; Gingeras, Thomas R ^[2]; Fodor, Stephen P. A. ^[1]; Hubble, Earl A ^[3]; Morris, MacDonald S ^[4]

Palo Alto, CA
Santa Clara, CA
Mountain View, CA
San Jose, CA

Issue Date:: 1999-01-19

Research Org.:: Affymetrix, Inc. (Santa Clara, CA)

OSTI Identifier:: 872103

Patent Number(s):: 5861242

Application Number:: 08/781,550

Assignee:: Affymetrix, Inc. (Santa Clara, CA)

Patent Classifications (CPCs):: Y - NEW / CROSS SECTIONAL TECHNOLOGIES Y10 - TECHNICAL SUBJECTS COVERED BY FORMER USPC Y10S - TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS

B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY

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Y - NEW / CROSS SECTIONAL TECHNOLOGIES Y10 - TECHNICAL SUBJECTS COVERED BY FORMER USPC Y10S - TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
Y10S435/81 - Packaged device or kit

B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY
B01J2219/00722 - Nucleotides
B01J2219/00626 - Covalent

C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07H - SUGARS
C07H21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids

B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY
B01J2219/00432 - Photolithographic masks

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
C12Q1/703 - {Viruses associated with AIDS}

B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY
B01J2219/00689 - using computers

B - PERFORMING OPERATIONS B82 - NANOTECHNOLOGY B82Y - SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES
B82Y30/00 - Nanotechnology for materials or surface science, e.g. nanocomposites

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
C12Q2565/513 - characterised by the pattern of the arrayed oligonucleotides

C - CHEMISTRY C40 - COMBINATORIAL TECHNOLOGY C40B - COMBINATORIAL CHEMISTRY
C40B60/14 - for creating libraries

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
C12Q1/6837 - using probe arrays or probe chips

C - CHEMISTRY C40 - COMBINATORIAL TECHNOLOGY C40B - COMBINATORIAL CHEMISTRY
C40B40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof

C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07B - GENERAL METHODS OF ORGANIC CHEMISTRY
C07B2200/11 - Compounds covalently bound to a solid support

B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY
B01J2219/00659 - Two-dimensional arrays
B01J2219/00608 - DNA chips
B01J2219/00529 - DNA chips
B01J2219/00711 - Light-directed synthesis
B01J19/0046 - {Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides
B01J2219/00596 - Solid-phase processes

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DOE Contract Number:: FG03-92ER81275; 1R01HG00813-01

Resource Type:: Patent

Country of Publication:: United States

Language:: English

Subject:: array; nucleic; acid; probes; biological; chips; diagnosis; hiv; methods; provides; oligonucleotide; immobilized; solid; support; analysis; target; sequence; human; immunodeficiency; virus; comprises; sets; 21; nucleotides; length; probe; set; corresponding; nucleotide; reference; related; exactly; complementary; subsequence; position; designated; interrogation; occupied; additional; identical; oligonucleotide probes; reference sequence; solid support; acid probes; nucleic acid; target sequence; acid probe; array comprises; complementary nucleotide; oligonucleotide probe; biological chips; /435/422/436/999/

Citation Formats


                    Chee, Mark, Gingeras, Thomas R, Fodor, Stephen P. A., Hubble, Earl A, and Morris, MacDonald S. Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same.  United States: N. p., 1999. 
        Web.

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                    Chee, Mark, Gingeras, Thomas R, Fodor, Stephen P. A., Hubble, Earl A, & Morris, MacDonald S. Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same.  United States.

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                    Chee, Mark, Gingeras, Thomas R, Fodor, Stephen P. A., Hubble, Earl A, and Morris, MacDonald S. Tue .  
        "Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same".  United States.  https://www.osti.gov/servlets/purl/872103.

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@article{osti_872103,

  title        = {Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same},

  author       = {Chee, Mark and Gingeras, Thomas R and Fodor, Stephen P. A. and Hubble, Earl A and Morris, MacDonald S},

  abstractNote = {The invention provides an array of oligonucleotide probes immobilized on a solid support for analysis of a target sequence from a human immunodeficiency virus. The array comprises at least four sets of oligonucleotide probes 9 to 21 nucleotides in length. A first probe set has a probe corresponding to each nucleotide in a reference sequence from a human immunodeficiency virus. A probe is related to its corresponding nucleotide by being exactly complementary to a subsequence of the reference sequence that includes the corresponding nucleotide. Thus, each probe has a position, designated an interrogation position, that is occupied by a complementary nucleotide to the corresponding nucleotide. The three additional probe sets each have a corresponding probe for each probe in the first probe set. Thus, for each nucleotide in the reference sequence, there are four corresponding probes, one from each of the probe sets. The three corresponding probes in the three additional probe sets are identical to the corresponding probe from the first probe or a subsequence thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {1999},

  month        = {1}

}

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Works referenced in this record:

Complete nucleotide sequence of the AIDS virus, HTLV-III
journal, January 1985

Ratner, Lee; Haseltine, William; Patarca, Roberto
Nature, Vol. 313, Issue 6000
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Likelihood DNA Sequencing By Hybridization
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Lipshutz, Robert J.
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Nucleotide sequence analysis of SA-OMVV, a visna-related ovine lentivirus: phylogenetic history of lentiviruses
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Querat, G.; Audoly, G.; Sonigo, P.
Virology, Vol. 175, Issue 2
https://doi.org/10.1016/0042-6822(90)90428-T

Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: Evaluation using experimental models
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Southern, E. M.; Maskos, U.; Elder, J. K.
Genomics, Vol. 13, Issue 4, p. 1008-1017
https://doi.org/10.1016/0888-7543(92)90014-J

DNA sequencing with chain-terminating inhibitors
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Sanger, F.; Nicklen, S.; Coulson, A. R.
Proceedings of the National Academy of Sciences, Vol. 74, Issue 12
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Nucleotide sequence of the AIDS virus, LAV
journal, January 1985

Wain-Hobson, Simon; Sonigo, Pierre; Danos, Olivier
Cell, Vol. 40, Issue 1
https://doi.org/10.1016/0092-8674(85)90303-4

Cellular protein modulates effects of human immunodeficiency virus type 1 Rev.
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Luo, Y.; Yu, H.; Peterlin, B. M.
Journal of Virology, Vol. 68, Issue 6
https://doi.org/10.1128/JVI.68.6.3850-3856.1994

A new method for sequencing DNA.
journal, February 1977

Maxam, A. M.; Gilbert, W.
Proceedings of the National Academy of Sciences, Vol. 74, Issue 2
https://doi.org/10.1073/pnas.74.2.560

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Title: Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same

Abstract

Citation Formats

Complete nucleotide sequence of the AIDS virus, HTLV-III journal, January 1985

Likelihood DNA Sequencing By Hybridization journal, December 1993

Nucleotide sequence analysis of SA-OMVV, a visna-related ovine lentivirus: phylogenetic history of lentiviruses journal, April 1990

Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: Evaluation using experimental models journal, August 1992

DNA sequencing with chain-terminating inhibitors journal, December 1977

Nucleotide sequence of the AIDS virus, LAV journal, January 1985

Cellular protein modulates effects of human immunodeficiency virus type 1 Rev. journal, January 1994

A new method for sequencing DNA. journal, February 1977

Complete nucleotide sequence of the AIDS virus, HTLV-III
journal, January 1985

Likelihood DNA Sequencing By Hybridization
journal, December 1993

Nucleotide sequence analysis of SA-OMVV, a visna-related ovine lentivirus: phylogenetic history of lentiviruses
journal, April 1990

Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: Evaluation using experimental models
journal, August 1992

DNA sequencing with chain-terminating inhibitors
journal, December 1977

Nucleotide sequence of the AIDS virus, LAV
journal, January 1985

Cellular protein modulates effects of human immunodeficiency virus type 1 Rev.
journal, January 1994

A new method for sequencing DNA.
journal, February 1977