Methods for functional analysis of high-throughput experimental data and gene groups identified therefrom

• US 9,353,415 B2
• Filed: 12/19/2007
• Issued: 05/31/2016
• Est. Priority Date: 12/19/2006
• Status: Active Grant

• Current Assignee: Camelot UK Bidco Limited (Clarivate Plc)
• Original Assignee: Thomson Reuters LLC (The Woodbridge Co. Ltd.)
• Inventors: Nikolsky, Yuri, Bugrim, Andrej, Nikolskaya, Tatiana
• Primary Examiner(s): Woolwine, Samuel
• Assistant Examiner(s): OYEYEMI, OLAYINKA A
• Application Number:
  US12/520,441
• Publication Number:
  US 20100216660A1
• Time in Patent Office: 3,086 Days
• Field of Search: 435/6.1, 435/91.2
• US Class Current: 1/1
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks

Abstract

The present invention relates generally to groups of genes that can be used to diagnose and differentiate between types of specific diseases such as breast cancer. The groups of genes can be further used to develop diagnostic kits for the specific diseases. The diagnostic kits can also differentiate between sub-categories of a disease to help identify the appropriate treatment regimen for a patient.

Claims

1. A method for categorizing a breast cancer tissue sample, said method comprising:

a) providing an article of manufacture, said article comprising oligonucleotides for measuring gene expression of genes in the following descriptor groups;

(1) PSMD3, TCAP, ERBB2, THRAP4, GRB7, CRK7, GSDML, LENEP, PPARBP;

(2) DNALI1, XBP1, AR, FOXA1;

(3) GATA3, TFF3, ACADSB, ESR1, CAl2;

(4) KRT17, SERPINB5, KRT5, GABRP, ANXA8, TRIM29, S100A2;

(5) KRT18, KRT8, PPP2CA, KRT8L2;

(6) COL11A1, WNT2, MMP14, PLAU, PLAUR;

(7) FN1, THY1, BAPX1, COL5A2;

(8) PSMB9, STAT1, PDCD1LG2, GBP1, CXCL10, UBE2L6, TAP1, LAP3; and

(9) CEACAM3, CEACAM5, CEACAM6, CEACAM7,

said oligonucleotides comprising primer pairs suitable for reverse-transcriptase polymerase chain reaction (RT-PCR) of the genes in the descriptor groups, wherein the primer pairs comprise primers having the sequences of SEQ ID NOs;

1-100;

b) measuring expression of genes of the descriptor groups in the tissue sample using the primer pairs to carry out an RT-PCR amplification of the genes;

c) assigning a positive or negative status for each of the descriptor groups based on whether a majority of genes in a group are overexpressed in the sample; and

d) categorizing the breast cancer tissue sample based on a combination of the positive and/or negative statuses so determined,

wherein SEQ ID NOs;

1-100 are;