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

• US 5,861,242 A
• Filed: 01/09/1997
• Issued: 01/19/1999
• Est. Priority Date: 06/25/1993
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Hubble, Earl A., Gingeras, Thomas R., Chee, Mark, Fodor, Stephen P. A., Morris, MacDonald S.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/781,550
• Time in Patent Office: 740 Days
• Field of Search: 435/5, 435/6, 435/283.1, 435/810, 436/501, 536/23.1, 536/24.1, 536/24.3-24.33, 935/77, 935/78, 422/50, 422/68.1
• US Class Current: 506/3
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/703 Viruses associated with AIDS
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: Y10S 435/81 Packaged device or kit

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.

Claims

1. An array of oligonucleotide probes immobilized on a solid support, the array having at least four sets of oligonucleotide probes at least 9 nucleotides in length,

(1) a first probe set having a probe corresponding to each nucleotide in a reference sequence from a human immunodeficiency virus, each probe being exactly complementary to a subsequence of the reference sequence that includes the corresponding nucleotide and each probe having an interrogation position occupied by a complementary nucleotide to the corresponding nucleotide,

(2) three additional probe sets, each of which has a corresponding probe for each probe in the first probe set, the three corresponding probes in the three additional probe sets being identical to the corresponding probe from the first probe set 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;

provided the array lacks a complete set of oligonucleotide probes of a given length.

2. The array of claim 1, wherein the reference sequence is from a reverse transcriptase gene of the human immunodeficiency virus.

3. The array of claim 2, wherein the reference sequence is a full-length reverse transcriptase gene.

4. The array of claim 2 having at least 3200 oligonucleotide probes.

5. The array of claim 4, wherein the array has at least 10,000 oligonucleotide probes.

6. The array of claim 5, wherein the HIV gene is from the BRU HIV strain.

7. The array of claim 5, wherein the HIV gene is from the SF2 HIV strain.

8. The array of claim 1, wherein the array further comprises fifth, sixth, seventh and eighth probe sets,

(1) the fifth probe set having a probe corresponding to each nucleotide in a second reference sequence, each probe being exactly complementary to a subsequence of the second reference sequence that includes the corresponding nucleotide from the second reference sequence, and each probe having an interrogation position occupied by a complementary nucleotide to the corresponding nucleotide in the second reference sequence, and

(2) the sixth, seventh, and eight probe sets, each having a corresponding probe for each probe in the fifth probe set, the three corresponding probes in the sixth, seventh, and eighth probe sets being identical to the corresponding probe from the fifth probe set 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 from the fifth, sixth, seventh and eighth probe sets.

9. The array of claim 8, wherein the reference sequence is from the coding strand of the reverse transcriptase gene and the second reference sequence is from the noncoding strand of the reverse transcriptase gene.

10. The array of claim 8, wherein the first, second, third and fourth probe sets have probes of a first length and the fifth, sixth, seventh and eight probe sets have probes of a second length different from the first length.

11. The array of claim 8, wherein the second reference sequence comprises a subsequence of the first reference sequence with a substitution of at least one nucleotide.

12. The array of claim 11, wherein the substitution confers drug resistance to a human immunodeficiency virus comprising the second reference sequence.

13. The array of claim 8, wherein the second reference sequence is from a reverse transcriptase gene of a second strain of a human immunodeficiency virus.

14. The array of claim 8, wherein the second reference sequence is from a 16S RNA, or DNA encoding the 16S RNA, from a pathogenic microorganism.

22. The array of claim 1, having up to 100,000 probes.

23. The array of claim 1, wherein the reference sequence is at least 50 nucleotides long.

24. The array of claim 1, wherein the first probe set comprises a series of overlapping probes spanning the reference sequence.

25. The array of claim 1, wherein the probes are 9 to 21 nucleotides in length.

15. A method of comparing a target nucleic acid from a human immunodeficiency virus with a reference sequence from a second human immunodeficiency virus having a predetermined sequence of nucleotides, the method comprising:

(a) hybridizing the target nucleic acid to an array of oligonucleotide probes immobilized on a solid support, the array comprising oligonucleotide probes at least 9 nucleotides in length, the oligonucleotide probes comprising at least four sets of probes,

(1) the first probe set having a probe corresponding to each nucleotide in a reference sequence, each probe being exactly complementary to a subsequence of the reference sequence that includes the corresponding nucleotide, and each probe having an interrogation position occupied by a complementary nucleotide to the corresponding nucleotide in the reference sequence, and

(2) three additional probe sets, each of which has a corresponding probe for each probe in the first probe set, the three corresponding probes in the three additional probe sets being identical to the corresponding probe from the first probe set 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

(b) comparing the relative specific binding of four corresponding probes from the first, second, third and fourth probe sets to determine the identity of the corresponding nucleotide in the target sequence,

(c) repeating (b) by comparing the relative specific binding of a further four corresponding probes until the identity of each nucleotide of interest in the target sequence has been determined thereby indicating whether the target sequence is the same or different from the reference sequence.

16. The method of claim 15, wherein the target sequence is from the reverse transcriptase gene of the human immunodeficiency virus and the reference sequence is from the reverse transcriptase gene of second immunodeficiency virus.

17. The method of claim 16, wherein the target sequence has a substituted nucleotide relative to the reference sequence in at least one undetermined position, and the comparing step indicates the identity of the nucleotide occupying the position in the target sequence.

18. The method of claim 16, wherein the target sequence has a substituted nucleotide relative to the reference sequence in at least one position, the substitution conferring drug resistance to the human immunodeficiency virus, and the comparing step indicates the identity of the substituted nucleotide.

19. The method of claim 16, wherein:

the hybridizing step comprises hybridizing the target nucleic acid and a second target nucleic acid, the second target sequence being from a reverse transcriptase gene of a third human immunodeficiency virus to the array; and

the relative specific binding of four corresponding probes from the first, second, third and fourth probe sets further determines the identity of a corresponding nucleotide in the second target sequence.

20. The method of claim 19, wherein the first target sequence has a first label and the second target sequence has a second label different from the first label.

21. The method of claim 20, wherein undetermined first and second proportions of the first and second target sequences are hybridized to the array and the relative specific binding of the four corresponding probes from the first, second, third and fourth probe sets further indicates the proportions.

26. The method of claim 15, wherein the probes are 9 to 21 nucleotides length.