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Method and system for detecting degree of tumor heterogeneity

A heterogeneity, tumor technology, applied in the field of bioinformatics, can solve the problem of inability to detect the degree of tumor heterogeneity

Pending Publication Date: 2020-07-10
深圳裕策生物科技有限公司
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0006] Therefore, the existing technology cannot detect the degree of tumor heterogeneity

Method used

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  • Method and system for detecting degree of tumor heterogeneity
  • Method and system for detecting degree of tumor heterogeneity
  • Method and system for detecting degree of tumor heterogeneity

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Embodiment 1

[0118] In this embodiment, the samples used are a batch of tumor tissue samples and control blood samples from a lung cancer immunotherapy cohort of 69 patients in total, and the control blood samples are specifically white blood cell samples separated from peripheral blood. The sampling method of the tumor tissue sample in this embodiment is a formalin-fixed paraffin-embedded (FFPE) sample prepared by sampling the pathological puncture of each patient's lung lesion at a single point, and the sampling unit is the Cancer Prevention and Control Center of Sun Yat-sen University.

[0119] The specific steps of detecting tumor heterogeneity of paired samples in this embodiment are as follows:

[0120] 1) Obtain tumor tissue samples and control blood samples, and perform whole exome sequencing. This sequencing is provided by Nanjing Shihe Gene Biotechnology Co., Ltd. After obtaining the sequencing sequence data, use the variation detection software VarScan (v2.4.1) to detect the var...

Embodiment 2

[0137] In this embodiment, the samples used are a batch of tumor tissue samples and control blood samples from a nasopharyngeal carcinoma immunotherapy cohort of a total of 56 patients, and the control blood samples are specifically white blood cell samples separated from peripheral blood. The sampling method of the tumor tissue sample in this embodiment is sampling at a single point in each patient's lung lesion. The sampling method of the tumor tissue sample in this embodiment is the pathological puncture single-point sampling of the lung lesions of each patient and the prepared formalin-fixed paraffin-embedded (FFPE) sample, and the sampling unit is the Cancer Prevention and Control Center of Sun Yat-sen University.

[0138] The specific steps of detecting tumor heterogeneity of paired samples in this embodiment are as follows:

[0139] 1) Obtain tumor tissue samples and control blood samples for whole exome sequencing, which is provided by Nanjing Shihe Gene Biotechnology ...

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Abstract

The invention provides a method and system for detecting the degree of tumor heterogeneity. The method comprises the following steps: acquiring sequencing data of a tumor tissue sample and a control sample, carrying out somatic variation detection, and acquiring somatic variation sites; clustering the somatic cell variation sites according to clusters; judging a main cloning mutation cluster and asubcloning mutation cluster according to a clustering result; and calculating a ratio of the number of somatic cell variations in the subcloning mutation cluster in the tumor tissue sample to the number of all the somatic cell variations, wherein the ratio is the value of tumor heterogeneity. According to the method, mutation frequency detected at each mutation site of the sample is fully utilized to estimate the cell proportion of corresponding tumor cloning, so the specific numerical value of a tumor heterogeneity degree is calculated; and thus, a numerical reference basis is provided for subsequent prediction of immunotherapy effect.

Description

technical field [0001] The invention relates to the technical field of bioinformatics, in particular to a method and system for detecting the degree of tumor heterogeneity. Background technique [0002] Cancer is one of the most important non-communicable diseases in the world, and it is also a disease with a high mortality rate. In my country, nearly 4.3 million people are diagnosed with cancer every year, and more than 2.8 million people die of cancer. [0003] Anti-tumor targeted drugs and immune checkpoint inhibitors are currently more effective means of treating cancer. The currently recognized potential indicators for evaluating the efficacy of immune checkpoint inhibitors anti-PD-(L)1, such as TMB (tumor mutation burden), MSI (Microsatellite instability), etc. cannot completely screen out patients who benefit from immune checkpoint inhibitors. Recent studies have suggested that ITH (tumor heterogeneity) may be used as a potential indicator for evaluating the efficacy...

Claims

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Application Information

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IPC IPC(8): G16B20/30G16B20/50G16B40/00
CPCG16B20/30G16B20/50G16B40/00
Inventor 金皓玄方文峰陈龙昀苏小凡廖裕威
Owner 深圳裕策生物科技有限公司
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