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Model construction method for identifying tumour purity sample and application thereof

A construction method and tumor technology, which is applied in the field of model construction for identifying tumor purity samples, can solve problems such as difficulty in estimating tumor purity, fewer mutation sites in chip captured data, etc., and achieve high reliability results

Active Publication Date: 2020-02-18
SHENZHEN GENEPLUS CLINICAL LAB
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  • Description
  • Claims
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Problems solved by technology

[0005] Therefore, the technical problem to be solved by the present invention is to provide a model construction method and application for identifying tumor purity samples, which solves the problem that there are few mutation sites in the data captured by the chip and it is difficult to estimate the tumor purity, and can identify low-purity tumors more accurately Samples, to achieve multiple mutual cross-confirmations between different indicators, with high credibility

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  • Model construction method for identifying tumour purity sample and application thereof
  • Model construction method for identifying tumour purity sample and application thereof
  • Model construction method for identifying tumour purity sample and application thereof

Examples

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Embodiment 1

[0043] Construction of Example 1 Identification Model

[0044] (1) Take 40 microscopic examinations and use the microscopic examination results (the tumor purity is estimated by image analysis of hematoxylin and eosin stained sections) as tumor samples with known tumor purity and their paired paracancerous tissues (paired samples ), see Table 1-2 for specific information. Region-capture sequencing of target probes (OncoD-C1021 tumor drug gene detection product, OncoD-P1021 tumor drug gene detection product and OncoMRD tumor postoperative monitoring product) of Beijing Jinjia Technology Co., Ltd. was carried out respectively. The sequencing platform was Illumina NovaSeq sequencing, and the sequencing The data includes the sequencing data of the target capture area (on target) and the non-target capture area (off target). The above sequencing data is GC-corrected on the target capture sequencing data using the LOESS algorithm, and then compared with the reference genome ( The h...

Embodiment 2

[0052] Identification of embodiment 2 tumor purity

[0053] Select tumor tissue sample A (No. 180028560F) and sample B (No. 180027591F) of known purity after microscopic examination and the microscopic examination results (estimation of tumor purity by image analysis of hematoxylin and eosin stained sections) And its paired paracancerous tissues (No. 190004260 BCD and 180027591BCD), according to the implementation of step (1)-step (4) in Example 1, the obtained index data CNA score, BAF score and VAF mode value are shown in the following table 3.

[0054] Table 3 Data of each index

[0055]

[0056] In this example, it is assumed that the purity 0.4 (40%) is regarded as high tumor purity.

[0057] When single-index identification is used, any one of the index data CNA score, BAF score, and VAF mode value in Table 3 above can be substituted into the corresponding linear model in step (5) in Example 1 to obtain tumor purity and qualitative Identifying tumor samples as low...

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Abstract

The invention belongs to the field of tumor purity detection, and especially relates to a model construction method for identifying a tumour purity sample and application thereof. The method comprisesthe steps of: based on targeted capture sequencing data of a tumor sample with known tumor purity, acquiring index data including a somatic cell copy number variation amplitude, heterozygote germlinemononucleotide variation and a somatic cell allele variation fraction; and associating the index data with the tumor purity of the tumor sample with known purity to construct an identification model.In the method, somatic mutation and germ cell variation are combined, the index data such as the somatic cell copy number variation amplitude, the heterozygote germline mononucleotide variation, themodel constructed by integrating the index data such as the somatic cell allele variation fraction and the like is used to solve the problem that the purity of tumors is difficult to identify due to few mutation sites in interval chip capture sequencing such as panel sequencing is solved, low-purity samples can be accurately identified, multiple cross confirmation among different indexes is achieved, and the reliability is high.

Description

technical field [0001] The invention belongs to the field of tumor purity detection, and in particular relates to a model construction method and application for identifying tumor purity samples. Background technique [0002] The cellular structure of tumor tissue is complex. In addition to tumor cells, it also includes stromal cells, immune cells, fibroblasts, vasculature, and extracellular matrix, which together constitute the tumor microenvironment. Tumor purity refers to the proportion of tumor cells in tumor tissue. Estimates of tumor purity may alter biological and clinical interpretation of results. Studies have shown that tumor purity is significantly correlated with clinical characteristics, genome expression, and biological characteristics of tumor patients. Neglecting the impact of tumor purity can lead to systematic bias in tumor genotyping, recurrence risk, and efficacy prediction. Accurate assessment of tumor purity is helpful. Helps objectively analyze tumor...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B5/00G16B20/20
CPCG16B5/00G16B20/20
Inventor 黄毅易鑫林浩翔刘久成吴玲清
Owner SHENZHEN GENEPLUS CLINICAL LAB
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