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Method and device for detecting tumor mutation load based on single sample

A mutation load and detection method technology, applied in the field of biomedicine, can solve the problems of large differences, the inability to make accurate descriptions of mutation backgrounds, relying on the quality and diversity of public databases, etc., to achieve accurate detection results

Active Publication Date: 2020-06-23
苏州吉因加生物医学工程有限公司 +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, this method still has several shortcomings
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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  • Method and device for detecting tumor mutation load based on single sample
  • Method and device for detecting tumor mutation load based on single sample
  • Method and device for detecting tumor mutation load based on single sample

Examples

Experimental program
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Effect test

Embodiment 1

[0089] The present invention provides a probe composition, including probes that capture all 4847 exon regions of the 312 genes shown in Table 1, and capture the introns, promoters, and fusion breakpoint regions of the 38 genes shown in Table 2 probes, and probes that capture 1778 coding regions of 709 other related genes shown in Table 3. It can be understood that the key of the present invention lies in the design of the capture region of the probe. After the capture region is determined, the specific probe design can refer to the existing capture probe design scheme, which will not be repeated here.

[0090] Table 1 All 4847 exon regions of 312 genes

[0091] ABL1 ACVR1B AKT1 AKT2 AKT3 ALK APCs AR ARAF ARID1A ARID1B ARID2 ASXL1 ATMs ATR ATRX AURKA AURKB AXIN1 AXIN2 AXL B2M BAP1 BARD1 BCL2 BCL2L1 BCOR BLM BMPR1A BRAF BRCA1 BRCA2 BRD4 BRIP1 BTK CARD11 CASP8 CBFB CBL CCND1 ...

Embodiment 2

[0099] A multigene detection kit for human tumors, including target sequence capture components, nucleic acid purification components, library construction and quality control components. Among them, the target sequence capture components include probes that capture all 4847 exon regions of the 312 genes shown in Table 1, and probes that capture the introns, promoters, and fusion breakpoint regions of the 38 genes shown in Table 2 , and probes capturing 1778 coding regions of 709 other related genes shown in Table 3. The probe composition is named as cd3 probe. As for the probe composition, conventional methods can be selected for its design. Wherein, the target sequence capturing components also include hybridization reaction solution, elution reaction solution, primers and linkers, and DNA polymerase reaction solution.

[0100] In an exemplary embodiment, the kit includes components as shown in Table 4.

[0101] Table 4 Components of Human Tumor Multigene Detection Kit

[...

Embodiment 3

[0107] The flow chart of the single-sample-based tumor mutation burden detection method in this embodiment is as follows figure 1 shown, including the following steps:

[0108] (1) Experiment and sequencing steps

[0109] Select 241 cases of lung adenocarcinoma tumor samples, extract the DNA of the tumor samples to be tested, and use the nucleic acid purification components of the human tumor multigene detection kit (Table 4) in Example 2 to purify the DNA of the tumor samples to be tested, and use the library construction Realize library construction with quality control components, including DNA repair, DNA fragmentation, end repair and A base addition, adapter ligation and library amplification; use target sequence capture components to hybridize and capture the library, and the resulting capture products are amplified . The Gene+Seq-2000 sequencing platform was used to perform double-end sequencing with a sequence length of 100 bp to obtain the sequencing data of the tar...

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Abstract

The invention relates to the field of biomedicine, in particular to a method and a device for detecting tumor mutation load based on a single sample. According to the device, a probe combination comprises probes that capture the exon region of a gene shown in Table 1, an intron promoter fusion breakpoint region of a gene shown in Table 2, and a coding region region of a gene shown in Table 3. A human tumor polygene detection kit comprises the probe combination. The TMB detection method based on the single sample comprises the following steps: access to target area of the tumor samples under test sequencing data, with the reference genome comparison, based on comparing the results obtained, detecting mutation loci, filtering original variable results with normal sample normal baseline database coincidence loci, filtering the high frequency reproductive mutation locus of a first cell mutation data set, screening the clonal somatic cell mutation locus of a second somatic cell mutation data set and calculating TMB. This method can accurately detect TMB of tumor samples without pairing samples.

Description

technical field [0001] The present invention relates to the field of biomedicine, in particular to a method and device for detecting tumor mutation load based on a single sample. Background technique [0002] In recent years, immunotherapy has received more and more attention in the field of tumor treatment. 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 called immune checkpoint inhibition (immune checkpoint inhibitor, ICI). Drugs developed through immune checkpoint inhibitory mechanisms such as CTLA-4 and PD-L1 have achieved significant clinical efficacy in the treatment of various tumors. However, due to the lack of suitable clinica...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12N15/11C12Q1/6858G16B20/20G16B20/50G16B30/10
CPCC12Q1/6858G16B20/20G16B20/50G16B30/10C12Q2535/122C12Q2537/165
Inventor 黄毅易鑫裴士美吴玲清刘久成李俊王长希杨玲
Owner 苏州吉因加生物医学工程有限公司
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