Method and device for detecting somatic variation in samples based on single-sample next-generation sequencing

A next-generation sequencing, single-sample technology, applied in the field of bioinformatics, can solve the problems of inability to accurately find somatic cell variation, lack of white blood cells, etc.

Active Publication Date: 2022-05-27
BEIJING USCI MEDICAL LAB CO LTD
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Problems solved by technology

However, for many retrospective samples, the lack of white blood cell control samples often prevents accurate identification of somatic variants

Method used

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  • Method and device for detecting somatic variation in samples based on single-sample next-generation sequencing
  • Method and device for detecting somatic variation in samples based on single-sample next-generation sequencing
  • Method and device for detecting somatic variation in samples based on single-sample next-generation sequencing

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[0025] According to a typical embodiment of the present invention, the method further includes the step of annotating the detected variation, preferably, the annotation includes annotating amino acid changes, 1000 genome population frequency, ExAC according to the genomic position of the variation and the variation base Population frequency and information recorded in the dbSNP database, etc. Annotate public database information on all variants so that variants can be filtered using the public database information on the annotation. In one embodiment of the present invention, variant filtering includes: removing strand-preferred sites, preferably, strand-preferential sites refer to variants that support mutation reads in the positive or negative strands to be 0, so as to remove mutations due to amplification False positive variants due to bias.

[0026] According to a typical embodiment of the present invention, variant filtering further includes: removing variants annotated ...

Embodiment 1

[0048] In this embodiment, the specific operations are mainly divided into two parts, the first part is the part completed outside the detection program, and the second part is the part completed in the detection program.

[0049] In this embodiment, the sample to be tested is a single-sample lung cancer pathological sample.

[0050] In the embodiment of the present invention, the main reagent supplies are commercially available, and the information is as follows in Table 1:

[0051] Table 1

[0052]

[0053]

[0054] The specific operation steps are as follows:

[0055] 1. The sample was pretreated and DNA was extracted, and quantified with a fluorescence quantitative meter (Qubit) at a concentration of 3.8 ng / μl and a volume of 130 μl; the sample was fragmented with a sonicator (Covaris) to make the DNA fragment size within 200 μl. Between ~400bp, and then use agarose gel electrophoresis to check whether the fragment size meets the requirements.

[0056] 2. The frag...

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Abstract

The invention discloses a method and a device for detecting somatic cell variation of a sample based on single-sample next-generation sequencing. Wherein, the method includes the following steps: S1, obtaining the sequence information of the target gene of the sample to be detected; and S2, analyzing the sequence information, realizing somatic cell variation through variation detection, variation filtering according to known databases, and background noise filtering status determination. According to the biological characteristics of somatic cell mutations, they are generally harmful mutations, so they should not appear in most healthy people (population frequency database filtering). In addition, most somatic cell mutations are generally low in frequency due to the limitation of tumor purity. (It can be filtered by mutation frequency). Therefore, by applying the technical solution of the present invention, the state of somatic cell variation can be determined, thus realizing somatic cell variation detection using a single sample using a known database filtering method, and solving the problem of single sample detection of somatic cell variation.

Description

technical field [0001] The present invention relates to the technical field of bioinformatics, in particular, to a method and device for detecting somatic cell variation of a sample based on single-sample second-generation sequencing. Background technique [0002] Somatic variants are mutations that occur in normal body cells, such as those in the skin or organs. Such mutations are not passed on to offspring. Somatic mutations are distinct from germline mutations, which occur in cells that will become gametes (sperm and eggs). Mutations in germ cells can be passed on to offspring. [0003] In the clinical practice of next-generation sequencing, the detection of somatic variation is an important content. Pathological tissue samples and control samples are used for detection, and the variation that exists specifically in the pathological tissue samples is found, that is, somatic variation. However, for many retrospective samples, the lack of white blood cell control sample...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6869C12Q1/6883C12Q1/6886
CPCC12Q1/6869C12Q1/6883C12Q1/6886C12Q2535/122
Inventor 单光宇张静波刘文伍启熹王建伟刘倩唐宇
Owner BEIJING USCI MEDICAL LAB CO LTD
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