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Tumor mutational load detecting method, device and storage medium

A technology of mutation load and tumor, which is applied in the field of tumor detection, can solve the problems of large differences, the inability to make accurate descriptions of mutation backgrounds, and the inability to guarantee the precise removal of germline gene mutations, so as to reduce dependence, reduce manpower consumption, and reduce Calculate the effect of resource consumption

Active Publication Date: 2019-06-28
裕策医疗器械江苏有限公司
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  • Summary
  • Abstract
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  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

First of all, TMB differences between different cancer types are large, and the same database filtering method cannot guarantee the accurate removal of germline gene mutations in all cancer types; secondly, this method is highly dependent on the quality and diversity of public databases. Unable to make precise descriptions of the mutant backgrounds of races not in the database

Method used

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  • Tumor mutational load detecting method, device and storage medium
  • Tumor mutational load detecting method, device and storage medium
  • Tumor mutational load detecting method, device and storage medium

Examples

Experimental program
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Effect test

Embodiment 1

[0084] In the following examples, the training data: 360 cases of healthy population control samples passed through Shenzhen Yuce Biotechnology Co., Ltd. YuceOne Plus chip sequencing generated single nucleotide mutation frequency data and 110 cases of healthy population control samples passed through Shenzhen Yuce Biotechnology Co., Ltd. Indel mutation frequency data generated by YuceOne Plus chip sequencing. Test data: Mutation results obtained from 11 lung cancer patient tissue samples sequenced by YuceOne Plus chip of Shenzhen Yuce Biotechnology Co., Ltd., including single nucleotide mutation frequency data and Indel mutation frequency data.

[0085] 360 healthy control samples were sequenced by the YuceOne Plus chip of Shenzhen Yuce Biotechnology Co., Ltd., and the reads obtained from the sequencing were compared with the human reference genome to obtain the comparison results in BAM format. Then use Samtools software to convert the BAM format file into a pileup format fil...

Embodiment 2

[0092] 23 cases of various cancer tissue test samples were sequenced through the YuceOne Plus chip of Shenzhen Yuce Biotechnology Co., Ltd., and the obtained single nucleotide mutation frequency data and Indel mutation frequency data were calculated by the method of the present invention. TMB, and then the same samples and The paired control samples were used to calculate TMB by whole exome double-sample sequencing method. Fit the TMB obtained by the two methods, the fitting result R-square is 0.72, the Adjusted R-square is 0.68, and the Pearson correlation coefficient is 0.85 ( Figure 6 ). Comparison with the results of 11 cases of lung cancer in Example 1 shows that the method of the present invention can also be applied to TMB detection of other cancer types.

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Abstract

The invention provides a tumor mutational load detecting method, a device and a storage medium. The method comprises the steps of acquiring mutation frequency data of a single testing sample, whereinthe mutation frequency data comprise the site mutation frequency of a sample target area, comparing the site mutation frequency with a preset threshold for obtaining a mononucleotide mutation which ishigher than the threshold, and eliminating meaningless mutation in mononucleotide mutation for obtaining the number of effective mononucleotide mutations; acquiring Indel mutation frequency data of the single testing sample, wherein the Indel mutation frequency data comprises the Indel mutation frequency of the sample target area, comparing the Indel mutation frequency with a preset threshold forobtaining the number of the Indel mutations which are higher than the threshold; calculating the number of the tumor mutational load according to a number evaluation formula of the tumor mutational load, wherein the number estimation formula comprises the weight item of the number of the effective mononucleotide mutations and the weight item of the number of the Indel mutations. The method according to the invention accurately detects the TMB index of the lung cancer sample under a precondition of no dependence to a common database and a normal pairing comparison sample.

Description

technical field [0001] The invention relates to the technical field of tumor detection, in particular to a method, device and storage medium for detecting tumor mutation load. Background technique [0002] Programmed Cell Death protein 1 (PD-1) is a protein usually expressed on the surface of cells, which regulates the immune system by reducing the inflammatory response of immune cells to cells and prevents the occurrence of autoimmunity. The ligand of PD-1, PD-L1, can specifically neutralize PD-1, thereby restarting the killing effect of the immune system on cells. This phenomenon is also known as immune checkpoint inhibition. Drugs developed through immune checkpoint inhibitory mechanisms such as CTLA-4 and PD-L1 have been found to have encouraging therapeutic effects in cancer treatment in recent years. [0003] Cell cancer is usually the result of long-term accumulation of gene mutations in somatic cells, but not all somatic cell mutations will lead to cell cancer. Th...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16B20/50G16B30/00
Inventor 倪帅李淼陈龙昀张艳鹏但旭陈超
Owner 裕策医疗器械江苏有限公司
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