Identification of molecular sequence signatures and methods involving the same

• US 6,391,550 B1
• Filed: 05/27/1999
• Issued: 05/21/2002
• Est. Priority Date: 09/19/1996
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Langer-Safer, Pennina, Lockhart, David J., Wong, Gordon G.
• Primary Examiner(s): Whisenant, Ethan C.
• Application Number:
  US09/321,481
• Time in Patent Office: 1,090 Days
• Field of Search: 435/6, 536/23.1, 536/24.3, 935/76, 935/77, 935/78
• US Class Current: 435/6.13
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• 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: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2565/515 characterised by the interaction between or sequential use of two or more arrays
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature, whether the target encodes a member of a gene family, or whether the target is derived from one of any number of genes.

Claims

1. A method for determining whether a target molecule has a sequence from a member of a gene family comprising:

providing a polynucleotide array comprising, for each of at least two different members of the gene family, a set of polynucleotide probes that define a reference nucleotide sequence from the member of the gene family;

generating hybridization data by performing a hybridization reaction between the target nucleic acid molecule and the probes in the sets and detecting hybridization between the target nucleic acid molecule and each of the probes in the sets; and

processing the hybridization data to determine whether the target nucleic acid has the reference sequence from one of the members of the gene family.

2. The method of claim 1 wherein the step of processing is performed by a programmable digital computer.

3. The method of claim 1 wherein the polynucleotide array further comprises, for each of the members of the gene family, a probe set defining a highly conserved region of the gene and a probe set defining a highly variable region of the gene.

4. The method of claim 1 wherein the polynucleotide array further comprises, for each of the members of the gene family, probe sets defining at least two highly conserved regions of the gene and probe sets defining at least two highly variable regions of the gene.

5. The method of claim 1 wherein the reference nucleotide sequence codes for an amino acid sequence and the array further comprises probe se s defining the degenerate set of nucleotide sequences encoding the amino acid sequence.

6. The method of claim 1 further comprising the step of determining the nucleotide sequence of the target nucleic acid molecule if the target does not have the sequence of the reference nucleotide sequence of a member of the gene family.

15. The method of claim 1, wherein said target molecule is first selected to be a target molecule by identifying nucleic acid molecules that hybridize to a nucleic acid probe that hybridizes to a gene encoding at least one of the members of the gene family.

16. The method of claim 1 further comprising the step of identifying target nucleic acid molecules for further analysis if a target molecule hybridizes to a nucleic acid probe that hybridizes to a gene encoding at least one of the members of the gene family.

7. A method of determining whether a nucleic acid in a sample is a member of a gene family, comprising:

selecting a hierarchy of assay techniques comprising at least a first and second assay, said first assay being selected to provide a determination of the presence or the absence of a first sequence signature, or the presence of a variant of a first sequence signature and said second assay being selected to provide a determination of the presence or the absence of a second sequence signature, or the presence of a variant of a second sequence signature;

wherein at least one of said assays employs a high-density nucleic acid array;

analyzing said nucleic acid sample using said first assay; and

determining whether said nucleic acid is a member of said gene family based on the results of said first and second assays.

8. The method of claim 7, wherein said first sequence signature is a highly conserved region of the gene family.

9. The method of claim 7, wherein said second sequence signature is a non-conserved region of the gene family.

10. The method of claim 7, further comprising determining the full length sequence of said nucleic acid sample.

11. The method of claim 7, wherein said gene family is the TGF-beta family.

12. The method of claim 7, wherein said first or second sequence signature is between 9 and 100 nucleotides in length.

14. The method of claim 12, wherein said first or second sequence signature is between 18 and 30 nucleotides in length.

13. A method of narrowing a sample for analysis, comprising:

providing a sample containing nucleic acids;

analyzing whether said sample contains a sequence signature using a high-density nucleic acid array with a density of at least four hundred different polynucleotides sequences per square centimeter; and

further analyzing said nucleic acid sample only if said sequence signature is not present.