Methods for diagnosing pancreatic cancer

• US 20080050726A1
• Filed: 09/19/2006
• Published: 02/28/2008
• Est. Priority Date: 09/19/2005
• Status: Abandoned Application

• Current Assignee: Veridex LLC (Johnson & Johnson)
• Original Assignee: Veridex LLC (Johnson & Johnson)
• Inventors: Talantov, Dmitri, Wang, Yixin
• Application Number:
  US11/523,496
• Publication Number:
  US 20080050726A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2600/158 Expression markers
• CPC Class Codes: G01N 33/5091 for testing the pathological state of an organism
• CPC Class Codes: G01N 33/57484 involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

The present invention provides a method of identifying origin of a metastasis of unknown origin by obtaining a sample containing metastatic cells; measuring Biomarkers associated with at least two different carcinomas; combining the data from the Biomarkers into an algorithm where the algorithm normalizes the Biomarkers against a reference; and imposes a cut-off which optimizes sensitivity and specificity of each Biomarker, weights the prevalence of the carcinomas and selects a tissue of origin determining origin based on highest probability determined by the algorithm or determining that the carcinoma is not derived from a particular set of carcinomas; and optionally measuring Biomarkers specific for one or more additional different carcinoma, and repeating the steps for additional Biomarkers.

Claims

1. A method of identifying pancreatic carcinoma comprising the steps of

a. obtaining a sample containing metastatic cells;

b. measuring Biomarkers associated with expression of F5, PSCA, ITGB6, KLK10, CLDN18, TR10 or FKBP10 Marker genes.

wherein the expression levels of the Marker genes above or below pre-determined cut-off levels are indicative of the presence of pancreatic cancer in the sample.

2. The method of claim 1 wherein the Marker genes are F5 and PSCA.

3. The method of claim 2 wherein the Marker genes further comprise or are replaced by ITGB6, KLK10, CLDN18, TR10 and/or FKBP10.

4. The method of one of claims 1-3 wherein gene expression is measured using at least one of SEQ ID NOs:

39-41 and 43-45.

6. A kit for conducting an assay according to one of claims 1-3 comprising:

Biomarker detection reagents.

7. A microarray or gene chip for performing the method of one of claims 1-3.

8. A diagnostic/prognostic portfolio comprising isolated nucleic acid sequences, their complements, or portions thereof of a combination of genes according to one of claims 1-3, or 1-3 where the combination is sufficient to measure or characterize gene expression in a biological sample having metastatic cells relative to cells from different carcinomas or normal tissue.

9. A method according to one of claims 1-3, or 1-3 further comprising measuring expression of at least one gene constitutively expressed in the sample.

5. A composition comprising at least one isolated sequence selected from SEQ ID NOs:

39-41 and 43-45.