Identification of molecular sequence signatures and methods involving the same

• US 20030129604A1
• Filed: 03/14/2002
• Published: 07/10/2003
• Est. Priority Date: 09/19/1996
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lockhart, David J., Wong, Gordon G., Langer-Safer, Pennina
• Granted Patent: US 7,135,285 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• 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

8. 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 a presence, absence, or variant of a first sequence signature and said second assay being selected to provide a determination of a presence, absence or 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.

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

10. The method of claim 8, wherein said second sequence signature is a non-conserved region of a gene family.

11. The method of claim 8, further comprising determining the full length sequence of said nucleic acid sample.

12. The method of claim 8, wherein said gene family is the TGF-beta family.

13-1. The method of claim 13, wherein said first or second sequence signature is between 18 and 30 nucleotides in length.

14. A method of selecting clones for analysis comprising:

providing a support having a variety of clones associated therewith;

exposing said support to one or more polynucleotides under low, medium, or high stringency conditions to permit at least some hybridization between said clones and said polynucleotides;

identifying said clones that hybridize with said polynucleotides ; and

selecting at least one of said clones not identified in said identifying step for analysis.

15. The method of claim 14, wherein said support is a high-density nucleic acid array.

16. 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; and

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

17. A high density nucleic acid array comprising sequence signatures from the TGF-beta gene family.