Identification of molecular sequence signatures and methods involving the same

• US 7,323,307 B2
• Filed: 08/04/2004
• Issued: 01/29/2008
• Est. Priority Date: 09/19/1996
• Status: Expired due to Fees

• 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:
  US10/911,065
• Publication Number:
  US 20050069927A1
• Time in Patent Office: 1,273 Days
• Field of Search: 435/6, 536/23.1, 536/24.3
• 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 analyzing a mRNA, said mRNA comprising one or more exons having an order, said order defined by one or more sequence signatures, each said one or more sequence signatures comprising a sequence spanning two exons, said method comprising;

providing said mRNA;

processing said mRNA to provide labeled nucleic acid fragments corresponding to said exons and said sequence signatures;

hybridizing said labeled fragments to a nucleic acid array, wherein said nucleic acid array comprises probes corresponding to said one or more exons and to said one or more sequence signatures; and

determining the identity of said sequence signatures and order of each said one or more exons to analyze the mRNA.

2. A method according to claim 1 further comprising generating data concerning which probes have bound to which labeled fragments and using computer programs to process said data to determine the identity and order of each said one or more exons.

3. A method according to claim 1 wherein said nucleic acid array is a high density polynucleotide array.

4. A method according to claim 1, wherein said step of processing is accomplished by in vitro transcription of a reverse transcribed double stranded DNA having a promoter with labeled bases incorporated during the incorporation step.

5. A method according to claim 4, wherein following said in vitro transcription the labeled RNA is fragmented.

6. A method according to claim 3 wherein said high density oligonucleotide array has a density selected from the group of 625, 1000, 10,000, 1,000,000 and 10,000,000 features per square cm.

7. A method according to claim 1 wherein said sequence signature includes sequences at most 300, 250, 200, 150, 100, 75, 50, 30, 25 or at most 15 nucleotides.

8. A method according to claim 1 wherein said sequence signatures include sequences less than 10, 15, 25, 30, 35, 45, 50, 60, 70, 80, 90, 100, 120, 135, 150, 175, 200, 250 and 300 nucleotides long.

9. A method according to claim 1 wherein said sequence signature includes the Hogness box, the TATA box, a homeobox, the CAAT box and ALU repeat sequences.