Method and device for detecting single sample body cell mutation sites in abnormal tissue and storage medium

A somatic cell mutation and mutation site technology, which is applied to the detection method, device and storage medium of a single sample of somatic cell mutation site in abnormal tissues, can solve the problem of not being able to contain reproductive genetic mutation information, and achieve high sensitivity and high specificity sexual effect

Active Publication Date: 2017-12-19
深圳裕康医学检验实验室
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  • Abstract
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  • Claims
  • Application Information

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Problems solved by technology

It can be seen that the current somatic mutation detection method based on unpaired samples has great challenges. How to identify reproductive genetic mutations is the key, but the current database, whether it is the human polymorphic genetic site database dbSNP (https:// www.ncbi.nlm.n...

Method used

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  • Method and device for detecting single sample body cell mutation sites in abnormal tissue and storage medium
  • Method and device for detecting single sample body cell mutation sites in abnormal tissue and storage medium
  • Method and device for detecting single sample body cell mutation sites in abnormal tissue and storage medium

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Embodiment 1

[0110] For 26 exome tumor samples with a sequencing depth of 100X or more, the single-sample somatic mutation site detection method of the embodiment of the present invention was used for somatic cell mutation detection, and the detection method based on paired samples was used for somatic cell mutation detection.

[0111] In this embodiment, the single-sample somatic mutation site detection method, specific methods and parameters include:

[0112] Data preprocessing: the abnormal sample is a tumor sample; the simulated normal sample is to extract more than a dozen original sequences obtained by next-generation sequencing and combine them into a 100X deep sample; the reference genome is a human reference genome; the filtering of effective sequencing sequences includes: Filter out non-human genome sequences and sequencing repeats; filter out sequences whose sequence comparison quality value is less than 1; for paired sequences in the overlapping region: if two paired sequences h...

Embodiment 2

[0124] According to the specific method and parameters of Example 1, the mutation of the important gene (CGC) of the tumor sample is detected by the single-sample somatic mutation site detection method of the embodiment of the present invention, and the mutation of the important gene (CGC) is analyzed Get back the situation.

[0125] Such as Image 6 As shown, the column represents the number of CGC gene mutations (No.of mutations in CGC genes) of true positive and true negative (true negative) of the sample, showing that more than 90% of the mutations can be retrieved, and the TP53 and NOTCH1 genes are in The frequencies of mutations in esophageal squamous cell carcinoma of the test data are 85% and 12%, respectively, and the single-sample somatic mutation site detection method in the embodiment of the present invention can find 100%.

[0126] Such as Figure 7 As shown, one of the samples T99, the mutation retrieved using the single-sample somatic mutation site detection m...

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Abstract

The invention provides a method and device for detecting single sample body cell mutation sites in abnormal tissue and a storage medium. The method includes the following steps that the effective sequencing sequence of an abnormal sample and the effective sequencing sequence of a simulated normal sample are obtained; in the effective sequencing sequences, basic groups, different from basic groups of the simulated normal sample, of the abnormal sample are obtained, according to the mutation basic group frequency, the types of the basic groups of the abnormal sample and the simulated normal sample are judged, the FISHER is then used for accurately detecting the difference of the types of the basic groups, and according to the difference, the mutation type is judged; by filtering the mutation types, false positive mutation and germ cell mutation are removed, and high-reliability somatic cell mutation sites are obtained. The method has the advantages of being high in sensitivity and specificity, has high sensitivity in mutation detection of known mutation genes, and new mutation genes can be found.

Description

technical field [0001] The invention relates to the technical field of mutation detection, in particular to a method, device and storage medium for detecting mutation sites in single-sample somatic cells in abnormal tissues. Background technique [0002] Genome sequencing technology provides new directions and opportunities for cancer research. In recent decades, researchers have discovered a large number of new tumor driver genes through sequencing technology, which has accelerated the discovery of cancer molecular markers and the process of personalized medicine. . The conventional experimental design is to collect tumor samples and control samples at the same time, and find somatic mutations by comparing the differences between tumor samples and control samples. This is an ideal experimental design, but in fact, some tumor tissues are difficult to obtain control samples or are lost during preservation. These samples still have high research value, so for unpaired samples...

Claims

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Application Information

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IPC IPC(8): G06F19/18G06F19/22
CPCG16B20/00G16B30/00
Inventor 王佳茜高志博陈超李淼杨洁
Owner 深圳裕康医学检验实验室
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