Somatic mutation detection method and device for tumor tissue single samples

A technology for tumor tissue and mutation detection, which is applied in biochemical cleaning devices, biochemical equipment and methods, enzymology/microbiology devices, etc. , TMB similarity results are high, the effect of high accuracy

Pending Publication Date: 2020-09-29
SHENZHEN HAPLOX BIOTECH
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Problems solved by technology

[0003] The purpose of the present invention is to provide a method and device for detecting somatic mutations in a single tumor tissue sample based on high-thr...

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  • Somatic mutation detection method and device for tumor tissue single samples
  • Somatic mutation detection method and device for tumor tissue single samples
  • Somatic mutation detection method and device for tumor tissue single samples

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Embodiment 1

[0088] A. DNA was extracted from 45 paraffin-embedded FFPE samples of tumor tissues, and for comparison, DNA was extracted from corresponding 45 normal control samples (see Table 1). Then, use probes to capture tumor-related genes, and use the Novaseq6000 sequencer to sequence the tumor-related genes through high-throughput sequencing to obtain high-throughput sequencing raw data, that is, the original off-machine fastq data. Such as figure 1 (A) shown.

[0089] B. Use fastp software to filter the original fastq data, remove low-quality sequence information, remove sequences with high N base content, remove adapter sequences, obtain filtered sequence files, and count Q20 information, Q30 information, and GC content and other information. Such as figure 1 (B) shown.

[0090] C. Use the bwa mem software to compare the filtered clean fastq data to the human reference genome hg19 for data comparison, obtain the original comparison bam file, statistical comparison rate and othe...

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Abstract

The invention belongs to the technical field of tumor gene detection and provides a high-flux capture sequencing based somatic mutation detection method and device for tumor tissue single samples, andfurther provides a computer readable medium used for operating the method and detection equipment. According to the invention, a normal copy number base line is established by selecting detected normal control samples, and a model capable of accurately screening stable conditions of single sample microsatellite sites is established by selecting the detected normal control samples; and compared with the prior art, the problem that tumor tissue mutation detection is carried out under the condition of no control samples can be solved, besides, multiple types of mutation such as SNV, INDEL, CNV,Fusion and MSI can be detected better, and calculation of tumor mutation burden (TMB) can be performed. The somatic mutation detection of the tumor tissue single samples can be realized under the condition of no control samples.

Description

technical field [0001] The invention belongs to the technical field of tumor gene detection, in particular to a method and device for detecting somatic cell mutations in a single tumor tissue sample based on high-throughput capture sequencing. Background technique [0002] With the rapid development of high-throughput sequencing technology, gene detection based on high-throughput capture sequencing has been increasingly used to guide the detection and treatment of clinical tumors. Gene mutation plays an important role in the occurrence and development of tumors. Mutations are divided into somatic mutations and germline mutations. The former occurs in somatic cells and is not inherited to offspring, while the latter occurs in fertilized eggs and can be inherited to offspring. Often, tumors are the result of somatic mutations. Somatic mutations include single nucleotide variation (SNV), small insertion-deletion variation (INDEL), structural variation (SV), copy number variat...

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Application Information

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IPC IPC(8): C12Q1/6858C12M1/00C12M1/36C12M1/34G16B20/50
CPCC12Q1/6858G16B20/50C12Q2535/122C12Q2537/165
Inventor 许明炎陈亚如周衍庆王丹丹汪周阳陈实富
Owner SHENZHEN HAPLOX BIOTECH
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