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Detecting hepatocellular carcinoma

A methylation, sample technology, applied in the field of detection of hepatocellular carcinoma

Active Publication Date: 2019-05-21
MAYO FOUND FOR MEDICAL EDUCATION & RES +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0009] The present invention addresses this need

Method used

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  • Detecting hepatocellular carcinoma
  • Detecting hepatocellular carcinoma
  • Detecting hepatocellular carcinoma

Examples

Experimental program
Comparison scheme
Effect test

Embodiment I

[0205] This example describes the identification of 311 differentially methylated regions (DMRs) that were used to discriminate HCC DNA samples from DNA derived from normal controls (eg, non-HCC individuals with or without cirrhosis).

[0206] Experiments were performed in four phases.

[0207] First, DNA methylation was performed using RRBS on DNA extracted from frozen tumor HCC tissue (with and without cirrhosis) and from frozen normal liver tissue (with and without cirrhosis) as well as buffy coat samples from healthy volunteers. Kylation marker discovery. Discriminatory differentially methylated regions (DMRs) were identified by stringent filtering criteria and the same or extended samples were re-analyzed using real-time methylation-specific quantitative PCR analysis (qMSP) to ensure reproducibility of results (technical validation).

[0208] Second, candidate markers were selected by blinded qMSP analysis of DNA extracted from independent archival case and control tissu...

Embodiment II

[0265]Tissue samples (75 HCC, 20 cirrhotic, and 30 normal) were run in QuARTs format on a real-time PCR instrument (Roche LC480) (see US Patent No. 8,361,720) using primers and probes generated from DMR sequences (see Table 5), GoTaq DNA polymerase (Promega), Lyase 2.0 (Hologic) and fluorescence resonance energy transfer reporter kit (FRET) (Biosearch Technologies) containing FAM, HEX and Quasar 670 dyes. Table 6 shows the ability of each marker to discriminate HCC from cirrhotic and normal samples with 100% sensitivity.

[0266] table 5.

[0267]

[0268]

[0269] Table 6.

[0270]

Embodiment III

[0272] The main objective of this example is to identify a panel of markers predictive of hepatocellular carcinoma (HCC). Plasma from 244 subjects (95 HCC and 149 controls) was adjusted to 2 mL and extracted. The 149 controls consisted of 51 cirrhotic patients and 98 normal patients.

[0273] Figure 9 The relative importance of each of the methylation markers considered in this analysis is shown. The cross-validated estimates for sensitivity and specificity for the entire marker panel were 75% and 96%, respectively.

[0274] The following marker panel (Chr12.133, CLEC11A, EMX1, HOXA1, CCNJ_3707) yielded a sensitivity of 85.3% for HCC at a specificity of 88.6% in controls versus normal patients (Table 7).

[0275] Table 7.

[0276]

[0277] The same group (Chr12.133, CLEC11A, EMX1, HOXA1, CCNJ_3707) produced the following specific reductions for normal and cirrhotic (control group) patients (Table 8).

[0278] Table 8.

[0279]

[0280] An exemplary procedure for i...

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Abstract

Provided herein is technology for hepatocellular carcinoma screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of hepatocellular carcinoma.

Description

[0001] Cross References to Related Applications [0002] This application claims the benefit of priority to U.S. Provisional Patent Application 62 / 383,165, filed September 2, 2016, which is hereby incorporated by reference in its entirety. field of invention [0003] Provided herein are techniques for hepatocellular carcinoma screening and relate in particular, but not exclusively, to methods, compositions and related uses for detecting the presence of hepatocellular carcinoma. Background technique [0004] Hepatocellular carcinoma (HCC) is a primary liver malignancy and occurs mainly in patients with underlying chronic liver disease and cirrhosis. The cells of origin are considered to be hepatic stem cells (see Alison MR. Stem Cell Rev. 2005.1(3):253-60). Tumors progress with local expansion, intrahepatic spread, and distant metastasis. [0005] HCC is currently the third leading cause of cancer death worldwide, affecting more than 500,000 people. The incidence of HCC is...

Claims

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Application Information

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IPC IPC(8): C07H21/04C12Q1/68G16C60/00G16C20/00
CPCC12Q1/6886C12Q2600/154C12Q2600/166C12Q2600/16C12Q1/6827C12Q2565/627C12Q2521/331
Inventor 威廉·R·泰勒大卫·A·阿尔奎斯特道格拉斯·W·马奥尼约翰·B·基谢尔特蕾西·C·亚卜哈特姆·T·阿拉维玛丽亚·贾库莫普洛斯格雷厄姆·P·利德加德
Owner MAYO FOUND FOR MEDICAL EDUCATION & RES
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