Molecular diagnostic test for cancer

A technique for cancer, testing samples, applied in the field of molecular diagnostic testing

Inactive Publication Date: 2015-11-25
ALMAC DIAGNOSTICS LIMITED
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Hypertension and VEGF polymorphisms are so far the only biomarkers showing potential, but important questions remain about their use in the clinical setting

Method used

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  • Molecular diagnostic test for cancer
  • Molecular diagnostic test for cancer
  • Molecular diagnostic test for cancer

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0356] Example 1 : Tissue processing, hierarchical clustering, subtype identification and classifier development

[0357] tumor material

[0358] Identification of exemplary expression signatures from gene expression analysis of a cohort of grossly dissected epithelial serous ovarian tumor FFPE tissue samples from NHS Lothian and University of Edinburgh.

[0359] The protocol for histological classification of epithelial ovarian cancer to define serous, endometrioid, clear cell, and mucinoid histology was recently updated. One consequence of this progression is that many tumors previously classified as endometrioid are now classified as serous. (McCluggage, W.G. "Morphological subtypes of ovarian cancer: a review with the mphasison new developments and pathogenesis," Pathology 2011 Aug; 43(5):420-32). The serous samples used in this study belonged to a larger collection of epithelial ovarian cancer samples with full histology collected between 1984 and 2006. Pathology t...

Embodiment 2

[0410] Example 2 : In silico validation of angiogenic subtypes and angiogenic classifier models

[0411]The 25-gene (initial protocol) angiogenesis classifier model and the 45-gene (reclassified scheme) performance of an angiogenesis classifier model. AUC is a statistic calculated based on observed disease scores and is a measure of the power of using a classifier model to predict a phenotype (Wray et al., PLoS Genetics Vol. 6, 1-9). AUC0.5 is common for random classifiers, and AUC1.0 would represent perfect class separation. Therefore, to determine whether an angiogenic subtype classifier model could predict patients who would respond to and be selected for an antiangiogenic ovarian cancer drug class as monotherapy or in combination with standard of care therapy, the following assumptions were made: The AUC after internal application of these data sets should be higher than 0.5, and the lowest confidence interval is higher than 0.5.

[0412] Classifier Models Applied...

Embodiment 3

[0414] Example 3 : Identification and in silico validation of the "non-angiogenic" subgroup of ovarian cancer

[0415] Classification of tumors into 'non-angiogenesis' sample groups

[0416] The expression of angiogenic genes in probeset cluster 2 was downregulated in all samples in sample cluster 1 of the hierarchical clustering of 265 samples newly classified as serous ( Image 6 , the blue scale marked at the bottom). from such as Figure 10 Of the samples from cluster 1 and cluster 3 pooled together as shown in , these samples in cluster 2 had a better prognosis than the remaining serous samples. This suggests that this group is defined by the downregulation of expression of the angiogenic genes identified in Table 1B. Patients with down-regulated genes involved in angiogenesis and thus this subgroup were referred to as the "non-angiogenesis" group. This phenotype has also been identified in ER+ and ER- breast cancers, as can be found in Figure 11A The intermedia...

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PUM

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Abstract

Methods and compositions are provided for the identification of a molecular diagnostic test for cancer. The test identifies cancer subtypes that have an up-regulation or a down- regulation in biomarker expression related to angiogenesis and vascular development. The present invention can be used to determine whether patients with cancer are clinically responsive or non-responsive to a therapeutic regimen prior to administration of any anti- angiogenic agent. This test may be used in different cancer types and with different drugs that directly or indirectly affect angiogenesis or angiogenesis signalling. In addition, the present invention may be used as a prognostic indicator for certain cancer types. In particular, the present invention is directed to the use of certain combinations of predictive markers, wherein the expression of the predictive markers correlates with responsiveness or non-responsiveness to a therapeutic regimen.

Description

[0001] Cross References to Related Applications [0002] This application claims the benefit of US Provisional Patent Application No. 61 / 732,761, filed December 3, 2012, entitled "Molecular Diagnostic Tests for Cancer." technical field [0003] The present invention relates to a molecular diagnostic test that can be used to diagnose cancers from different anatomical sites, including the use of common subtypes associated with angiogenesis. The present invention includes deriving gene classification models from gene expression levels. One application is to rank the response of cancer therapy drug classes and to select cancer therapy drug classes for patients and thus guide patients in their choice of treatment. Another application is to divide cancer patients into those who respond to anti-angiogenic therapeutics and those who do not. The present invention provides tests that can guide therapy selection during clinical trials evaluating new therapeutics and select patient grou...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68G16B25/10G16B40/20G16B40/30
CPCC12Q1/6886C12Q2600/106C12Q2600/158G16B25/00G16B40/00G16B40/30G16B40/20G16B25/10
Inventor D·P·哈金F·帕特森C·特林德E·J·奥布赖恩C·米奇C·古尔利L·A·希尔K·E·基廷J·奥唐纳M·拜尔斯乔S·德哈罗V·普劳特斯基R·肯尼迪T·戴维森A·温特A·麦克卡维甘
Owner ALMAC DIAGNOSTICS LIMITED
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