Cellular arrays and methods of detecting and using genetic disorder markers

• US 9,284,610 B2
• Filed: 11/14/2012
• Issued: 03/15/2016
• Est. Priority Date: 10/28/1998
• Status: Expired due to Fees

• Current Assignee: Abbott Molecular Incorporated (Abbott Laboratories)
• Original Assignee: Abbott Molecular Incorporated (Abbott Laboratories)
• Inventors: Kallioniemi, Olli-P, Muller, Uwe Richard, Sauter, Guido, Kononen, Juha, Barlund, Maarit
• Primary Examiner(s): Haney, Amanda
• Application Number:
  US13/676,382
• Publication Number:
  US 20130143770A1
• Time in Patent Office: 1,217 Days
• Field of Search: None
• US Class Current: 1/1
• 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 characteristic 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.

Claims

1. A composition suitable for detecting the presence of cancerous cells in a human breast tissue specimen, said composition comprising nucleic acids, wherein said nucleic acids consist of (i) a labeled probe suitable for detecting expression of PDGF-β

, said probe obtained by PCR screening of a human genomic library and suitable for detecting expression of PDGF- β

in the human breast cancer specimen;

(ii) a labeled locus specific probe for chromosomal region 7q31;

(iii) a labeled locus specific probe for chromosomal region 8p11-p12; and

(iv) a labeled locus specific probe for chromosomal region 10q25-26, wherein probes (ii), (iii), and (iv) are suitable for detecting their target chromosomal regions in the human breast cancer specimen, and wherein probes (i), (ii), (iii), and (iv) are labeled with a fluorescent dye.

2. The composition of claim 1 used in a method to detect breast cancer, wherein probes (i), (ii), (iii), and (iv) are detected by polymerase chain reaction (PCR).

3. The composition of claim 1 used in a method to detect breast cancer, wherein probes (i), (ii), (iii), and (iv) are detected by fluorescence in situ hybridization (FISH).

4. The composition of claim 1 used in a method to detect breast cancer, wherein probes (i), (ii), (iii), and (iv) are detected using a cDNA microarray.

5. The composition of claim 1 wherein probes (i), (ii), (iii), and (iv) are each labeled with fluorescent dye of a unique emission wave length.

6. A composition suitable for detecting the presence of cancerous cells in a human breast tissue specimen, said composition comprising nucleic acids, wherein said nucleic acids consist of (i) a labeled probe suitable for detecting expression of PDGF-β

, said probe obtained by PCR screening of a human genomic library and suitable for detecting expression of PDGF-β

in the human breast cancer specimen;

(ii) a labeled locus specific probe for chromosomal region 7q31; and

(iii) a labeled locus specific probe for chromosomal region 8p11-p12, wherein probes (ii) and (iii) are suitable for detecting their target chromosomal regions in the human breast cancer specimen, and wherein probes (i), (ii), and (iii) are labeled with a fluorescent dye.

7. A composition suitable for detecting the presence of cancerous cells in a human breast tissue specimen, said composition comprising nucleic acids, wherein said nucleic acids consist of (i) a labeled probe suitable for detecting expression of PDGF-β

, said probe obtained by PCR screening of a human genomic library and suitable for detecting expression of PDGF-β

in the human breast cancer specimen;

(ii) a labeled locus specific probe for chromosomal region 7q31; and

(iii) a labeled locus specific probe for chromosomal region 10q25-26, wherein probes (ii) and (iii) are suitable for detecting their target chromosomal regions in the human breast cancer specimen, and wherein probes (i), (ii), and (iii) are labeled with a fluorescent dye.