Identification of molecular sequence signatures and methods involving the same

• US 6,329,140 B1
• Filed: 09/18/1997
• Issued: 12/11/2001
• 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: Lockhart, David J., Wong, Gordon G., Langer-Safer, Pennina
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US08/933,219
• Time in Patent Office: 1,545 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 2219/00659 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 its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide or 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 of selecting clones for analysis comprising:

providing a support having a variety of clones associated therewith wherein said support is a high-density nucleic acid array with a density of at least four hundred different polynucleotides sequences per square centimeter;

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.