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Methods, kits and compositions for providing a clinical assessment of prostate cancer

A prostate cancer and prostate-specific technology, applied in the field of prostate cancer signatures, can solve problems such as lack of effective control markers

Inactive Publication Date: 2015-05-06
DIAGNOCURE
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Another issue is the lack of valid control markers that can be used to standardize and / or validate prostate cancer marker assays

Method used

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  • Methods, kits and compositions for providing a clinical assessment of prostate cancer
  • Methods, kits and compositions for providing a clinical assessment of prostate cancer
  • Methods, kits and compositions for providing a clinical assessment of prostate cancer

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0295] Gene expression profiling of whole urine samples

[0296] We determined the technical feasibility of gene expression profiling in whole urine samples from men with or suspected of having prostate cancer. Urine samples were collected from 90 men who underwent a digital rectal examination (DRE) prior to transrectal ultrasound-guided prostate biopsy, and the results of the biopsy were used to divide the subjects into two groups: (1) men with prostate cancer and (2) men without prostate cancer, with or without benign prostatic symptoms. Biopsy results were used to assign subjects to one of the two groups described above. Symptoms of benign prostate cancer include: benign prostatic hyperplasia (BPH), high-grade prostatic intraepithelial neoplasia (HG-PIN), atypical small acinar proliferation (ASAP), and / or atypical prostate cells (Atypia). In all cases, the classification or stratification of samples was based on the interpretation of biopsies assessed by pathologists. ...

Embodiment 2

[0303] Gene expression profiling of urine sediment

[0304]On urine samples obtained after DRE from 77 subjects, the study described in Example 1 was repeated and the genes listed in Table 1 were analyzed by quantitative RT-PCR, except that whole urine was not used, but instead Urine samples were centrifuged to pellet cells prior to nucleic acid extraction. The whole process took about 15 minutes in a clinical centrifuge at 2,500 rpm. The obtained urinary sediment containing epithelial cells from the urogenital tract was then extracted as described in Example 1. Table 3B provides the mean normalized expression values ​​of normal subjects and cancer subjects and performance characteristics based on ROC curve analysis for each gene. Genes significantly associated with the presence of prostate cancer cells were either upregulated or downregulated. Genes whose expression levels differ significantly between normal subjects and prostate cancer subjects were determined to be use...

Embodiment 3

[0306] A machine-learning approach for studying genes significantly associated with prostate cancer

[0307] Here, we analyzed normalized gene expression data from 90 whole urine samples from Example 1 using machine learning to select and weight individual genes, gene pairs, or groups according to their ability to distinguish prostate cancer patients from non-prostate cancer individuals Gene. There are a number of different ways to combine genes individually to optimally separate a large number of data sources, one of which is to design class predictions (also known as classifiers) based on a preselected subset of genes. We supplemented this set of single gene signatures with a set of pairwise gene signatures obtained by taking the maximum of two ΔCts (eg "maxERG CACNA1D") or by subtracting the ΔCts of two pairs of genes (eg ERG-SNAI2). Although some selected genes were found to be associated with cancer and / or prostate in Examples 1 and 2, their association with the prosta...

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PUM

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Abstract

The present invention relates to prostate cancer signatures which are useful for providing a clinical assessment of prostate cancer from a biological sample of a subject. By performing initial gene expression studies on urine samples from prostate cancer and non-prostate cancer subjects, and using the PCA3 / PSA prostate cancer test as a performance benchmark, the present inventors have surprisingly discovered multiple signatures that are informative in urine-based prostate cancer tests, as well as in tissue-based tests. The signatures relate to combinations of at least two prostate cancer markers whose expression pattern in urine has been validated as being associated (either positively or negatively) with a clinical assessment of prostate cancer. The prostate cancer markers can be used in conjunction with bioinformatics approaches to generate a prostate cancer score, which correlates with a clinical assessment of prostate cancer. Methods, kits and compositions relating to the aforementioned signatures are also described.

Description

field of invention [0001] The present invention relates to prostate cancer. More specifically, the present invention relates to methods, kits and compositions for providing a clinical assessment of prostate cancer in a subject based on a biological sample from the subject. In particular, the invention relates to a prostate cancer signature comprising at least two prostate cancer markers for providing a clinical assessment of prostate cancer. Background of the invention [0002] Prostate cancer is the most common form of cancer affecting men. In the United States, more than 241,000 men are diagnosed with prostate cancer each year, and nearly 28,000 die from the disease each year. Although the lifetime risk of developing prostate cancer is estimated at 16% (and the risk of dying from the disease is estimated at 2.9%), autopsies show that prostate cancer is actually present in about two-thirds of men over the age of 80. These results highlight an important problem in the fie...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C40B30/00C40B30/04G01N33/48G01N33/68G06F19/12G16B25/10G16B40/20
CPCG16B40/00C12Q1/6886G01N33/57434C12Q2600/118C12Q2600/112C12Q2600/158G16B25/00G16B40/20G16B25/10G16H50/30Y02A90/10G06F18/2411G06F18/24323C12Q2600/16C12Q2600/166
Inventor J-F·海伊斯G·博德里Y·弗雷德E·帕克特
Owner DIAGNOCURE
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