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Neuroendocrine Tumors

a neuroendocrine tumor and gene expression technology, applied in the field of gene expression to classify neuroendocrine tumors, can solve the problems of unknown or uncertain tumor site origin

Inactive Publication Date: 2014-11-27
BIOTHERANOSTICS
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

This patent is about using gene expression profiles to classify and identify unknown or occult cancers or tumors in cell samples obtained from a subject in a clinical setting. The method can be applied to both fresh and formalin-fixed paraffin-embedded samples. The gene expression profiles can be used to determine the subtype of neuroendocrine tumor cell in a patient, which can aid in the diagnosis and management of the cancer. The disclosed method can be performed with high accuracy in a clinical setting. The patent also includes a kit for use with tumor cells in vitro. Overall, the patent provides a way to better identify and classify cancer cells in a clinical setting.

Problems solved by technology

But in other cases, the tumor site of origin may remain unknown or uncertain, such as in a case of metastatic presentation.

Method used

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example 1

Materials and Methods

[0116]Seventy-five (44 metastatic, 31 primary) formalin-fixed, paraffin-embedded neuroendocrine tumor samples were selected after 2-institution pathologist adjudication. The samples included subtypes gastrointestinal (n=12), pulmonary (n=22), Merkel cell (n=10), pancreatic (n=10), pheochromocytoma (n=10), and medullary thyroid carcinoma (n=11).

[0117]The following tumors were considered to have neuroendocrine differentiation: Merkel cell carcinoma, medullary thyroid carcinoma, pheochromocytoma, paraganglioma, pulmonary NEC (carcinoid, small cell carcinoma, large cell NEC), pancreatic NEC (all grades), and gastrointestinal NEC (all grades; stomach, small intestine, appendix, and colorectum). Both primary and metastatic cases were included. Excluded were some sites of “epithelial” neuroendocrine tumors (thymus, pituitary, kidney, bladder, cervix, ovary), carcinomas with occult / mixed neuroendocrine differentiation, and most of the rarer “neural” types of neuroendocr...

example 2

Classification of Neuroendocrine Tumors

[0120]Blinded samples were tested by the CancerType ID® 92-gene classifier (bioTheranostics, Inc), which makes tumor type predictions based upon quantitative PCR expression measurement for 87 gene targets and 5 reference genes. Briefly, a selected formalin fixed, paraffin embedded block was sectioned in RNase free conditions to produce one hematoxylin and eosin stained section and three unstained 7-micron sections for molecular testing. The freshly prepared slides included only a research ID. Samples were macrodissected using the H&E stained template or laser capture microdissected for tumor enrichment. Total RNA was extracted and DNase treated.

[0121]First strand cDNA was synthesized and then was pre-amplified (PreAmp, Life Technologies, Carlsbad, Calif.). Real-time PCR was then performed using an ABI 7900HT instrument quantitatively measuring the expression of 87 tumor-associated genes and 5 reference genes as previously described (Ma et al. 2...

example 3

Characteristics of Classification

[0125]All 75 neuroendocrine tumors met quality control parameters and were classified by the assay. The cohort included 44 females and 31 males, with a mean age of 62 years (range 29 to 86). Tumor characteristics are provided in Table 4. Cases were comprised of 59% metastatic tumors and 41% primary tumors. The most common biopsy site was liver, followed by lung and lymph node (FIG. 1). The performance characteristics for the 92-gene assay predictions of neuroendocrine subtype are shown in Table 5.

TABLE 5Neuroendocrine subtypenMatchesSensSpecPPVNPVGastrointestinal12121.001.001.001.00Merkel cell10101.000.970.831.00Pancreatic1080.800.980.910.97Pheo / paraganglioma10101.001.001.001.00Pulmonary22200.911.001.000.98Thyroid Medullary11111.001.001.001.00Total75710.95

[0126]Assay sensitivities were 99% (95% CI: 0.93-0.99) for accurate classification of neuroendocrine tumors and 95% (95% CI:0.87-0.98) for identification of tumor subtype for site of origin. Positiv...

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Abstract

The disclosure provides methods for the use of gene expression measurements to classify or identify neuroendocrine cancer in samples obtained from a subject in a clinical setting, such as in cases of formalin fixed, paraffin embedded (FFPE) samples.

Description

RELATED APPLICATIONS[0001]This application claims benefit of priority from U.S. Provisional Patent Application No. 61 / 802,063, filed Mar. 25, 2013, which is hereby incorporated in its entirety as if fully set forth.FIELD OF THE DISCLOSURE[0002]This disclosure relates to the use of gene expression to classify neuroendocrine tumors. The classification is performed by use of gene expression profiles, or patterns, of expressed sequences as disclosed herein. The expression levels of the sequences are expressed in patterns that permit the classification of neuroendocrine tumors even though expression occurs in more than one type of tumor. The gene expression profiles, whether embodied in nucleic acid expression, protein expression, or other expression formats, may be used to classify a cell containing sample of neuroendocrine tumor cells. This permits a more accurate identification of neuroendocrine cancer, treatment of the cancer, and determination of the prognosis of the subject from wh...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/68
CPCC12Q1/6886C12Q2600/112C12Q2600/158C12Q2600/16
Inventor SCHNABEL, CATHERINE A.ZHANG, YIERLANDER, MARK G.
Owner BIOTHERANOSTICS
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