Nucleic acids arrays and methods of use therefor

• US 20050059041A1
• Filed: 05/17/2004
• Published: 03/17/2005
• Est. Priority Date: 10/12/2001
• Status: Active Grant

• 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
• Granted Patent: US 7,439,346 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 identifying a chromosomal disorder in a sample 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 associated with the chromosomal disorder and a second set of spots having control nucleic acids for the chromosome.

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.

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, metal, metalloid, cellulose, celluose 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, teflon, polypropylene, poly(4-methylbutene), polystyrene/latex, polymethacrylate, poly(ethylene terephthalate), rayon, polyvinylbutyrate, and polyvinylidene difluoride.

7. The surface according to claim 1, wherein the cloned genomic nucleic acids of the microarray comprise nucleic acids associated with 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 chromome.

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

12. The surface according to claim 1, wherein the microarray comprises a plurality of cloned genomic nucleic acids associated with the chromosomal disorder and a plurality of cloned genomic nucleic acids that are not associated with a known chromosomal disorder.

13. The surface according to claim 12, wherein the plurality of cloned nucleic acids associated with the chromosomal disorder are located on a single chromosome.

14. The surface according to claim 12, wherein the plurality of cloned nucleic acids associated with the chromosomal disorder are located on a plurality of chromosomes.

15. The surface according to claim 12, wherein the plurality of control portions and the plurality of disorder-associated portions 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 associated with a plurality of chromosomal disorders.

17. The surface according to claim 16, wherein the plurality is at least about 5 chromosomal disorders.

18. The surface according to claim 16, wherein the plurality is at least about 40 chromosomal disorders.

19. The surface according to claim 16, wherein the plurality is less than about 1,000 chromosomal disorders.

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 nucleic acid not associated with known disorders.

22. The surface according to claim 20, wherein the calibration spot comprises cloned genomic nucleic acid not associated with known disorders 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 Teflon®

.

65. A kit comprising the surface of any of claims 1-39, a container, and instructions for use.

66. The kit according to claim 65, further comprising nucleic acid of a reference subject.

67. The kit according to claim 66, further comprising a first detectable label and a second detectable label.

28. A set of cloned genomic nucleic acids comprising portions of nucleotide sequences of at least one chromosome of a subject, wherein the set includes a first subset of cloned nucleic acids associated with at least one chromosomal disorder, and a second subset of control cloned nucleic acids not associated with known chromosomal disorders.

29. The set according to claim 28, wherein the at least one chromosomal disorder is a plurality of chromosomal disorders.

30. The set according to claim 28, wherein the at least one chromosome is a plurality of chromosomes.

31. The set according to claim 30, wherein the plurality of chromosomes comprises autosomes.

32. The set according to claim 30, wherein the plurality of chromosomes comprises sex chromosomes.

33. The set according to claim 28, wherein the subject is a mammal.

34. The set according to claim 28, wherein the subject is a human.

35. The set according to claim 28, wherein the plurality of chromosomal disorders comprises chromosomal disorders each having a substantial frequency in a human population.

36. The set according to claim 28, wherein the second set further comprises a subset of control cloned nucleic acids not associated with known chromosomal disorders that are portions of the chromosome closely linked to the centromere.

37. The set according to claim 28, wherein the chromosomal disorder comprises:

1p36;

Adrenal Hypoplasia Congenita;

Alagille Syndrome;

Angelman Syndrome;

Azospermia Factor A;

Azospermia Factor B;

Azospermia Factor C;

Bruton Agammaglobulinemia Tyrosine Kinase;

Beckwith-Wiedemann Syndrome;

Charcot-Marie Tooth 1A;

Cri-du-chat Syndrome;

DiGeorge 1/VCF Syndrome;

DiGeorge 2 (10p13);

Down Syndrome;

Duchenne Muscular Dystrophy;

Fragile X syndrome;

Glycerol Kinase Deficiency;

Greig Syndrome (GLI3), Hereditary Neuropathy with Liability to Pressure Palsies;

Hypoparathyroidism, Sensorineural Deafness and Renal Dysplasia;

Kallman Syndrome;

Langer-Giedion Syndrome (Ext1 and TrpsI);

Miller-Dieker Syndrome;

Potocki-Shaffer Syndrome (with Multiple Exostoses

     2);

Neurofibromatosis 1;

Pelizaeus-Merzbacher Disorder;

Polycystic Kidney Disorder Type I;

Prader-Willi Syndrome;

Retinoblastoma 1;

Rubinstein-Taybi Syndrome;

Saethre-Chotzen Syndrome;

Sex determining region Y;

Smith-Magenis Syndrome;

Sotos Syndrome;

Steroid Sulfatase Deficiency;

Trichorhinophalangeal Syndrome;

Tuberous Sclerosis 1;

Williams-Beuren Syndrome;

Wilm'"'"'s Tumor;

Wilms Tumor-Aniridia-Genitourinary anomalies-Mental retardation (WAGR Syndrome); and

Wolf-Hirschhorn Syndrome.

39. The set of claim 28, wherein the chromosomal disorder is at least one selected from the group consisting of:

1p36;

Adrenal Hypoplasia Congenita;

Alagille Syndrome;

Angelman Syndrome;

Azospermia Factor A;

Azospermia Factor B;

Azospermia Factor C;

Bruton Agammaglobulinemia Tyrosine Kinase;

Beckwith-Wiedemann Syndrome;

Charcot-Marie Tooth 1A;

Cri-du-chat Syndrome;

DiGeorge 1/VCF Syndrome;

DiGeorge 2 (10p13);

Down Syndrome;

Duchenne Muscular Dystrophy;

Fragile X syndrome;

Glycerol Kinase Deficiency;

Greig Syndrome (GLI3), Hereditary Neuropathy with Liability to Pressure Palsies;

Hypoparathyroidism, Sensorineural Deafness and Renal Dysplasia;

Kallman Syndrome;

Langer-Giedion Syndrome (Ext1 and TrpsI);

Miller-Dieker Syndrome;

Potocki-Shaffer Syndrome (with Multiple Exostoses

     2);

Neurofibromatosis 1;

Pelizaeus-Merzbacher Disorder;

Polycystic Kidney Disorder Type I;

Prader-Willi Syndrome;

Retinoblastoma 1;

Rubinstein-Taybi Syndrome;

Saethre-Chotzen Syndrome;

Sex determining region Y;

Smith-Magenis Syndrome;

Sotos Syndrome;

Steroid Sulfatase Deficiency;

Trichorhinophalangeal Syndrome;

Tuberous Sclerosis 1;

Williams-Beuren Syndrome;

Wilm'"'"'s Tumor;

Wilms Tumor-Aniridia-Genitourinary anomalies-Mental retardation (WAGR Syndrome); and

Wolf-Hirschhorn Syndrome.

40. A method of detecting a chromosomal disorder in nucleic acid samples, the method comprising:

providing a substrate including a surface having a plurality of non-contiguous arrays, each array comprising a plurality of cloned genomic nucleic acids immobilized on the surface at discrete and known spots;

contacting a first array with a first solution comprising a detectably labeled first nucleic acid mixture under conditions allowing hybridization between nucleic acids in the first array to nucleci acids in the first mixture, and contacting a second array with a second solution comprising a detectably labeled second nucleic acid mixture under the conditions allowing hybridization, such that the first and second solutions are not in contact; and

analyzing amounts of detectable label associated with each spot in the first and second arrays, thereby analyzing the samples to detect the chromosomal disorder in the nucleic acid samples.

41. The method according to claim 40, wherein the first and second nucleic acid mixtures include nucleic acid sequences from a test subject and a reference subject.

42. The method according to claim 41, wherein the first nucleic acid mixture comprises test subject nucleic acid detectably labeled with a first fluorescent dye and reference nucleic acid detectably labeled with a second fluorescent dye, and wherein the second nucleic acid mixture comprises test subject nucleic acid detectably labeled with the second fluorescent dye and reference nucleic acid detectably labeled with the first fluorescent dye.

43. The method according to claim 41, wherein the reference subject is a member of the same species as the test subject and does not carry known chromosomal disorders.

44. The method according to claim 41, wherein the reference subject is a member of a different species as the test subject.

45. The method according to claim 41, wherein the the reference subject is a member of the same species as the test subject and carries a known chromosomal disorder.

46. The method according to claim 40, wherein the cloned nucleic acids comprise at least one cloned portion of a chromosome in a bacterial artificial chromosome (BAC).

47. The method according to claim 40, wherein the cloned nucleic acids comprise plurality of BAC clones.

48. The method according to claim 40, wherein the cloned genomic nucleic acids in each array comprise at least one cloned portion of the genome associated with a chromosomal disorder on a chromosome, and at least one cloned portion of the genome not associated with a chromosomal disorder on the chromosome.

49. The method according to any of claims 40-48, wherein the first and second solutions further comprise a viscosity increasing solute.

50. The method according to any of claim 40-49, further comprising after contacting the first array and the second array, disposing a cover on each of the first and second solutions.

51. A method of analyzing genomic nucleic acid of a subject for the presence of a chroosomal disorder, the method comprising:

contacting a surface comprising a surface having a first microarray and a second microarray with a first nucleic acid mixture and a second nucleic acid mixture, respectively, the microarrays being non-contiguous on the surface, wherein each microarray comprises a plurality of cloned nucleic acids immobilized on the surface at discrete and known spots;

wherein the first mixture comprises test subject nucleic acids linked to a first detectable label and reference nucleic acids linked to a second detectable label, and the first mixture is applied to the first microarray; and

the second mixture comprises reference nucleic acids linked to the first detectable label and test nucleic acids linked to the second detectable label, wherein the first mixture and the second mixture are separately contacted to the first and second microarrays, respectively;

hybridizing the solution nucleic acids to the microarray nucleic acids under suitable conditions; and

,

analyzing amounts of first and second labels bound to spots in each of the first and second microarrays, thereby analyzing the sample for the presence of the chromosomal disorders.

52. The method according to claim 51, further comprising after contacting the surface with each mixture, applying a cover to each of the first mixture and the second mixture.

53. The method according to claim 51, wherein the first and second mixtures further comprise a viscosity-increasing solute.

54. The method according to claim 53, wherein the viscosity-increasing solute is selected from glycerol, polyethylene glycol, polyacrylamide, agarose, albumin, gelatin, and dextran.

55. The method according to claim 51, wherein analyzing amounts further is measuring the first and second labels bound to spots in the microarrays using an automated scanner.

56. The method according to claim 51, wherein analyzing amounts further is measuring labels bound to spots in the microarrays using a laser scanner.

57. The method according to claim 56, wherein using the automated scanner is using a CCD.

58. The method according to claim 51, wherein the first and second microarrays comprise a plurality of cloned portions of the genome associated with a chromosomal disorder on a chromosome, and a plurality of cloned portions of the genome not associated with a chromosomal disorder on the chromosome.

59. The method according to claim 58, wherein the first and second microarrays further comprise at least one calibration spot.

60. The method according to claim 59, wherein the calibration spot comprises a mixture of the plurality of cloned genomic nucleic acid from portions of chromosomes not associated with known disorders.

61. The method according to claim 60, wherein the calibration spot comprises cloned genomic nucleic acid from the portion of chromosomes not associated with known disorders and further having locations on the chromosomes closely linked to a centromere.

62. The method according to any of claims 51-61, wherein analyzing the amounts is contrasting with dye bound to calibration spots.

63. The method according to any of claims 51-59, wherein the calibration spot comprises nucleic acids from a species different than the test subject, and wherein positive control samples comprise predetermined quantities of complementary nucleic acid sequences capable of hybridizing to the calibration spots.

64. The method according to claim 63, further comprising analyzing the positive control data to determine copy number of a gene in the test sample.