A gene set for liver cancer detection and its panel detection design method

A technology of liver cancer and genes, which is applied to the gene set for liver cancer detection and its panel detection design. The application field of this gene set in gene chips can solve the cumbersome process of information analysis methods, the omission of important sites, and the single technical process, etc. low cost of detection and analysis, convenient analysis, and high overall coverage

Active Publication Date: 2022-06-17
ZHONGSHAN HOSPITAL FUDAN UNIV +1
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The technology of diagnosing liver cancer by high-throughput sequencing of the genome in biological samples has made great progress, but the existing liver cancer detection has the following defects: 1. The detection content is single and the function is limited
At present, most panel designs are only aimed at drug guidelines, labels, and limited literature collection, and there are few comprehensive analyzes based on the results of large-scale sequencing platforms, public databases, and text mining techniques
3. At present, the technical process of panel design and synthesis method is single, and there are always areas that cannot be designed according to the fixed algorithm, so it is inevitable to omit some important sites
4. There are few applicable platforms. For the developed panel detection, there is already a set of detection system schemes on common platforms, but for new detection platforms, such as BGISEQ-500, there is no suitable detection scheme yet
5. The process of information analysis method is cumbersome
The bioinformatics analysis of off-machine data needs to be evaluated step by step, and the results are completed step by step. The steps are cumbersome, time-consuming, and the portability is not high, which cannot meet the current analysis needs.

Method used

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  • A gene set for liver cancer detection and its panel detection design method
  • A gene set for liver cancer detection and its panel detection design method
  • A gene set for liver cancer detection and its panel detection design method

Examples

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preparation example Construction

[0052] As a preferred embodiment, the preparation method of the gene panel of the present application mainly comprises the following steps:

[0053] 1. Screening of liver cancer information and related genes. Including the collection of liver cancer information and its related genes in at least three aspects. The first aspect is to collect liver cancer information and related genes obtained by sequencing liver cancer patient samples in local databases. The second aspect is to collect liver cancer information disclosed in public databases and its related genes. Gene; thirdly, collect the liver cancer information and its related genes disclosed in the literature; merge and de-redundancy the liver cancer information and its related genes collected in the three aspects, and determine the standard gene name through HGNCapproved Official Symbol to form a gene set ;

[0054] 2. Detection target area selection. Based on the gene set obtained in step 1, select the target region; exte...

Embodiment 1

[0069] Example 1 Panel sequencing

[0070] 1) Sample collection

[0071] According to the collection standards of the "Chinese Standards for the Diagnosis and Treatment of Primary Liver Cancer", medical institutions collected samples from 110 patients with liver cancer.

[0072] 2) Extraction of sample DNA, library preparation

[0073] Liver cancer individualized genetic testing uses liver cancer tumor FFPE as the experimental group for each sample, and blood samples collected during the same period as the control group. Considering the influence of tag adapters, hybridization, and data volume utilization, the number of libraries to be established is evaluated, and the number of established libraries is confirmed. 4 pairs of library samples are the best. Use FFPE nucleic acid extraction kit and blood cell extraction kit for sample extraction, and use Qubit DNA Fluorometer and Qubit dsDNA HS Assay kit for quantitative detection. The extraction concentration is required to be ...

Embodiment 2

[0087] Example 2 Data Analysis of Disembarkation

[0088] The information analysis process is used for the paired sample analysis of the liver cancer project. It takes the downloaded Fastq file of the sequencing platform (for example, BGI-Seq500 in this case) as input, and goes through the steps of filtering, alignment, deduplication, duplicate alignment, and mutation detection. The final mutation results and basic statistics of the data are displayed.

[0089] This procedure is used for paired sample analysis of the liver cancer project. For the fastq after the BGI-Seq500 is off the machine, it is first filtered by SOAPnuke to filter out reads with a ratio of low-quality bases (≦10) higher than 50%, or N (undetermined bases) ratio of more than 10%. , and count the relevant indicators before and after filtering, including the amount of initial data, the amount of effective data, CG content, N content, Q20, Q30, etc.; compare the clean fastq obtained after filtering to the hum...

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Abstract

The invention discloses a method for preparing a liver cancer gene detection panel, comprising the following steps: screening liver cancer information and related genes to obtain a gene set; selecting a gene target region; designing a panel probe; synthesizing an RNA single-stranded probe to obtain a gene detection panel. The gene detection panel designed by the present invention can be used for the diagnosis, typing and prognosis of liver cancer, has wide gene coverage and strong portability, and is suitable for newly developed detection platforms.

Description

technical field [0001] The invention belongs to the field of gene detection, in particular to a gene set used for liver cancer detection and a panel detection design method thereof, and also relates to the application of the gene set in a gene chip. Background technique [0002] Liver cancer is one of the most common malignant tumors in clinical practice. According to statistics, there are about 740,000 new liver cancer cases and 700,000 liver cancer deaths worldwide each year, about half of which occur in China. Due to the high morbidity and high mortality of liver cancer, liver cancer is paid special attention in the world, and the incidence and mortality of liver cancer in my country are also increasing year by year. It seriously endangers human health and has become a global and serious public health problem. The occurrence and development of liver cancer is a complex biological process. In addition to the patient's own susceptibility to genetic factors, various extrace...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6886
CPCC12Q1/6886
Inventor 周俭樊嘉安娜于竞杨欣荣阳作权王向东林木飞黄傲谢颖朱师达吴逵
Owner ZHONGSHAN HOSPITAL FUDAN UNIV
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