Nucleic acids arrays and methods of use therefor

• US 7,439,346 B2
• Filed: 05/17/2004
• Issued: 10/21/2008
• Est. Priority Date: 10/12/2001
• Status: Expired due to Fees

• Current Assignee: PerkinElmer LAS, Inc. (Perkinelmer Incorporated)
• Original Assignee: PerkinElmer LAS, Inc. (Perkinelmer Incorporated)
• Inventors: Johnson, Robert C., Mohammed, Mansoor, Kim, Jae Weon, Lu, Xan-Yan
• Primary Examiner(s): Martinell; James
• Application Number:
  US10/847,149
• Publication Number:
  US 20050059041A1
• Time in Patent Office: 1,618 Days
• Field of Search: None
• US Class Current: 536/23.1
• 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: C40B 20/04 Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• CPC Class Codes: C40B 60/10 for identifying library members

Abstract

Compilations of nucleic acids, articles of manufacture which are surfaces comprising multiple blocks of arrays comprising such compilations, methods of use of the compilations and arrays for detection of chromosomal disorders, such as a chromosomal aneuploidies, deletions, amplifications, and diagnosis and prognosis of syndromes associated with a contiguous gene abnormality and kits are provided.

Claims

1. A surface for detecting a genetic syndrome of a subject, the surface comprising a plurality of non-contiguous microarrays, wherein each microarray comprises a plurality of cloned genomic nucleic acids immobilized on the surface at discrete and known spots, and each microarray comprises a first set of spots having nucleic acids selected to detect a genetic syndrome and a second set of spots having control nucleic acids for at least part of a chromosome of the subject.

2. A combination comprising the surface according to claim 1, and a cover for at least one of the plurality of microarrays.

3. The combination according to claim 2, wherein the cover separates fluid of the at least one microarray from other microarrays in the plurality of microarrays.

4. The combination according to claim 3, wherein the surface is planar, and the cover is planar or arcuate in cross section.

5. The surface according to claim 1, wherein the surface is selected from the group consisting of a metal, silicon, a polymer plastic, paper, ceramic, quartz, gallium arsenide, a metalloid, cellulose, cellulose acetate, nitrocellulose, and a glass.

6. The surface according to claim 5, wherein the plastic is selected from the group consisting of nylon, polycarbonate, polyethylene, polystyrene, polytetrafluoroethylene, polypropylene, poly(4-methylbutene), polystyrene, latex, polymethacrylate, poly(ethylene terephthalate), rayon, polyvinylbutyrate, polyvinylidene difluoride, and combinations thereof.

7. The surface according to claim 1, wherein the cloned genomic nucleic acids of the microarray comprise nucleic acids of a plurality of chromosomes.

8. The surface according to claim 7, wherein the plurality of chromosomes comprises the genome of the subject.

9. The surface according to claim 7, wherein the plurality of chromosomes comprises autosomes.

10. The surface according to claim 7, wherein the plurality of chromosomes comprises at least one sex chromosome.

11. The surface according to claim 1, wherein the cloned genomic nucleic acids of the microarray comprise nucleic acids of a single chromosome.

12. The surface according to claim 1, wherein the microarray comprises a plurality of cloned genomic nucleic acids selected to detect a genetic syndrome and a plurality of cloned control genomic nucleic acids.

13. The surface according to claim 12, wherein the plurality of cloned nucleic acids selected to detect a genetic syndrome are located on a single chromosome.

14. The surface according to claim 12, wherein the plurality of cloned nucleic acids selected to detect a genetic syndrome are located on a plurality of chromosomes.

15. The surface according to claim 12, wherein the plurality of cloned genomic nucleic acids selected to detect a genetic syndrome and the plurality of cloned control genomic nucleic acids are distributed among a plurality of chromosomes of the subject.

16. The surface according to claim 1, wherein the microarray further contains a plurality of cloned nucleic acids selected to detect a plurality of genetic syndromes.

17. The surface according to claim 16, wherein the plurality is at least 5 genetic syndromes.

18. The surface according to claim 16, wherein the plurality is at least 40 genetic syndromes.

19. The surface according to claim 16, wherein the plurality is less than 1,000 genetic syndromes.

20. The surface according to claim 1, wherein the microarray further comprises at least one calibration spot.

21. The surface according to claim 20, wherein the calibration spot comprises a mixture of the plurality of cloned genomic control nucleic acids.

22. The surface according to claim 20, wherein the calibration spot comprises cloned genomic nucleic acids selected to detect a genetic syndrome and located on the chromosome closely linked to centromere.

23. The surface according to claim 1, wherein the surface further comprises at least one fluid barrier located between at least two of the microarrays, wherein the barrier separates a fluid above at least one of the microarrays from fluid above at least another microarray of the plurality.

24. The surface according to claim 23, wherein the barrier is selected from an elevated structure of hydrophobic composition contiguous with the surface and a hydrophobic strip printed on the surface.

25. The surface according to claim 23, wherein the elevated structure is a glass barrier.

26. The surface according to claim 21, wherein the elevated structure comprises a hydrophobic polymer.

27. The surface according to claim 21, wherein the hydrophobic strip is selected from the group of polyethylene, silicone, paraffin, and polytetrafluoroethylene.

28. A kit comprising the surface of any of claims 1-27, a container, and instructions for use.

29. The kit according to claim 28, further comprising nucleic acid of a reference subject.

30. The kit according to claim 29, further comprising a first detectable label and a second detectable label.