Cellular arrays and methods of detecting and using genetic disorder markers

• US 20090092993A1
• Filed: 09/19/2008
• Published: 04/09/2009
• Est. Priority Date: 10/28/1998
• Status: Active Grant

• Current Assignee: Abbott Molecular Incorporated (Abbott Laboratories)
• Original Assignee: Abbott Molecular Incorporated (Abbott Laboratories)
• Inventors: Sauter, Guido, Barlund, Maarit, Miller, Uwe Richard, Kallioniemi, Olli-P., Kononen, Juha
• Granted Patent: US 9,260,758 B2
• Time in Patent Office: Days
• US Class Current: 435/6.14
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00743 Cells
• CPC Class Codes: B01L 3/5085 for multiple samples, e.g. microtitration plates
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2537/157 A reaction step characterised by the number of molecules incorporated or released
• CPC Class Codes: C12Q 2539/103 Serial analysis of gene expression [SAGE]
• CPC Class Codes: C12Q 2543/10 the purpose being "in situ" analysis
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• 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 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 1/08 involving an extracting tool, e.g. core bit
• CPC Class Codes: G01N 1/2813 Producing thin layers of samples on a substrate, e.g. smearing, spinning-on G01N1/30 takes precedence
• CPC Class Codes: G01N 1/312 for samples mounted on planar substrates
• CPC Class Codes: G01N 2001/282 with mapping; Identification of areas; Spatial correlated pattern
• CPC Class Codes: G01N 2001/288 : Filter punches
• CPC Class Codes: G01N 2001/368 : Mounting multiple samples in one block, e.g. TMA [Tissue Microarrays]
• CPC Class Codes: G01N 33/5005 : involving human or animal cells immunoassay G01N33/56966; immunoassays of protozoa G01N33/56905; protozoa in screening assays C12Q1/025
• CPC Class Codes: G01N 33/54306 : Solid-phase reaction mechanisms
• CPC Class Codes: G02B 21/34 : Microscope slides, e.g. mounting specimens on microscope slides

Abstract

A method is disclosed for rapid molecular profiling of tissue or other cellular specimens by placing a donor specimen in an assigned location in a recipient array, providing copies of the array, and performing a different biological analysis of each copy. The results of the different biological analyses are compared to determine if there are correlations between the results of the different biological analyses at each assigned location. In some embodiments, the specimens may be tissue specimens from different tumors, which are subjected to multiple parallel molecular (including genetic and immunological) analyses. The results of the parallel analyses are then used to detect common molecular characteristics of the genetic disorder type, which can subsequently be used in the diagnosis or treatment of the disease. The biological characteristics of the tissue can be correlated with clinical or other information, to detect characteristics associated with the tissue, such as susceptibility or resistance to particular types of drug treatment. Other examples of suitable tissues which can be placed in the matrix include tissue from transgenic or model organisms, or cellular suspensions (such as cytological preparations or specimens of liquid malignancies or cell lines).

Claims

1. A method of detecting the presence of cancerous cells in a specimen, the method comprising determining whether fibroblast growth factor receptor 2 (FGFR2) is amplified in the specimen, amplification indicating the presence of cancerous cells in the specimen.

2. The method of claim 1, wherein the specimen is selected from the group consisting of lung, breast, testicular, bladder, colon and endometrial tissues.

3. The method of claim 1, wherein said tissue is breast tissue.

4. The method of claim 1, wherein polymerase chain reaction (PCR) is performed to determine whether FGFR2 is amplified in the specimen.

5. The method of claim 1, wherein fluorescence in situ hybridization (FISH) is performed to determine whether FGFR2 is amplified in the specimen.

6. The method of claim 1, wherein said DNA amplification located at chromosomal region 10q25.