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Sequences for diagnosis of bladder cancer and methods of use and applications thereof

A technology of microarray and primer set, applied in the field of sequence diagnosis and evaluation of bladder cancer, can solve the problems of failure to meet the requirements of staging and detection accuracy, and easy recurrence

Active Publication Date: 2016-08-17
BGI SHENZHEN CO LTD +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

70% of patients showed early stage (NMI-TCCs, stage Ta or T1), generally not life-threatening, but easy to relapse
However, the above-mentioned genes alone are far from meeting the accuracy requirements of staging and detection. Therefore, it is necessary to simultaneously detect other important genes related to bladder cancer to improve the accuracy of detection, or to find more To accurately determine the detection target

Method used

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  • Sequences for diagnosis of bladder cancer and methods of use and applications thereof
  • Sequences for diagnosis of bladder cancer and methods of use and applications thereof
  • Sequences for diagnosis of bladder cancer and methods of use and applications thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0006] Example 1: Sequencing of samples

[0007] In this example, the inventors used the nimblegen chip (Roche Company, NimbleGen SequenceCapture Human Exome2.1M Array) and the Hiseq high-throughput sequencing system (Illumina Company, Hiseq2000) to analyze 97 cases of bladder cancer obtained from Peking University Shenzhen Hospital Exome sequencing was performed on samples from patients (cancerous tissue and corresponding blood).

[0008] The details of the samples from 97 bladder cancer patients are shown in Table 1.

[0009] Table 1: Details of samples from 97 bladder cancer patients.

[0010]

[0011]

[0012]

[0013]

[0014] (N in Table 1 means no detailed information)

[0015] 1. Fragmentation of genomic DNA

[0016] Genomic DNA was extracted from the samples of each patient using the kit QIAamp DNA Mini Kit (Qiagen, 51306), and the obtained genomic DNA was fragmented into fragments with a size of about 200 bp using the ultrasonic method (Covaris, S-2). ...

Embodiment 2

[0023] Example 2: Processing and Analysis of Exome Sequencing Data of Samples

[0024] The exome sequencing data of each sample obtained in Example 1 were processed and analyzed as follows to identify genes associated with chromatin modification that are highly mutated in bladder cancer samples, and the sites of mutations in these genes

[0025] 1. As described in Example 1, obtain the exome sequencing data of each sample;

[0026] 2. For the exome sequencing data of each sample, the sequencing fragments (reads) containing the adapter sequence (adapter connector) in step 4 of Example 1 were removed; the sequencing fragments were deduplicated for the off-machine data of each lane Processing, this step is to remove some data redundancy caused by sequencing.

[0027] Specific execution steps:

[0028] Firstly, according to the report of each lane off-line data, its specific linker sequence is obtained, and each sequenced fragment of the off-line data is traversed to remove the ...

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PUM

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Abstract

Disclosed is a sequence for bladder cancer diagnosis and evaluation and the application method and use thereof. In particular, the invention provides probe sets, primer sets, compositions and microarrays for detecting at least one mutation in gene selected from UTX, CREBBP, EP300, ARID1A, CHD6, MLL, NC0R1 and MLL3. The invention also provides a method for bladder cancer diagnosis by detecting changes in the abovementioned genes, and the application of the probe sets and primer sets in preparing a kit and microarray for detecting bladder cancer.

Description

technical field [0001] The present invention relates to the fields of pathology, genetics, genomics and the like. In particular, the invention relates to sequences, methods of use and applications thereof for the diagnostic assessment of bladder cancer. Background technique [0002] Bladder cancer is the ninth most common cancer in the world today [Parkin, D.M., Bray, F., Ferlay, J. & Pisani, P. Global cancer statistics, 2002. CA Cancer J Clin55, 74-108 (2005).]. Divided into two types: early and middle and late. 70% of patients showed early stage (NMI-TCCs, stage Ta or T1), generally not life-threatening, but easy to relapse. 30% of the patients showed late stage (MI-TCCs, stage T2–4), manifested as metastatic, life-threatening [Wu, X.R. Urothelial tumorigenesis: a tale of divergent pathways. Nat Rev Cancer 5, 713-25 (2005)]. Previous genome-based studies have found that the two subtypes of bladder cancer are genetically very different: early-stage cancers have particula...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/68
CPCC12Q1/6886C12Q2600/156
Inventor 郭广武胡学达桂耀庭蔡志明唐爱发李泽松高升杰黄毅贾文龙李贤新陈超周亮万胜青叶睿宋鹏飞黄培德樊帆赵鑫朱家楼陈家浩鲍莉刘智盛阳作权周峰周权于源李彦丽王勇孙亮江智茂陈静吴松张仲富杨锐林赵军徐丛杰尹卫华王俊
Owner BGI SHENZHEN CO LTD
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