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A model construction method and application for identifying tumor purity samples

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: 2022-07-08
SHENZHEN GENEPLUS CLINICAL LAB
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  • Abstract
  • Description
  • Claims
  • Application Information

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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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  • A model construction method and application for identifying tumor purity samples
  • A model construction method and application for identifying tumor purity samples
  • A model construction method and application for identifying tumor purity samples

Examples

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Embodiment 1

[0043] Example 1 Construction of the identification model

[0044] (1) Take 40 microscopic examination results (estimated tumor purity by image analysis of hematoxylin and eosin stained sections) as tumor samples of known tumor purity and their paired paracancerous tissues (paired samples) ), see Table 1-2 for details. The target probes (Beijing Gene Plus Technology Co., Ltd. OncoD-C1021 tumor drug gene detection product, OncoD-P1021 tumor drug gene detection product and OncoMRD tumor postoperative monitoring product) were captured and sequenced respectively, and the sequencing platform was Illumina NovaSeq sequencing. The data includes the sequencing data of the target capture region (on target) and the non-target capture region (off target). The above sequencing data is GC-corrected using the LOESS algorithm to the target capture sequencing data, and then compared with the reference genome ( Human reference genome, USCS hg19) is compared to obtain the comparison result file...

Embodiment 2

[0052] Example 2 Identification of tumor purity

[0053] Select tumor tissue samples A (No.: 180028560F) and B (No. 180027591F) that have undergone microscopy and the results of microscopy (estimated tumor purity by image analysis of hematoxylin and eosin-stained sections) as known purity. And its paired adjacent tissue (numbering 190004260 BCD and 180027591 BCD), according to the step (1)-step (4) in the embodiment 1 implementation, 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 indicator

[0055]

[0056] In this example, it is assumed that the purity is < 0.4 (40%) as low tumor purity, and the purity ≥ 0.4 (40%) is considered as high tumor purity.

[0057] When single-index identification is adopted, any one of the index data CNA score, BAF score and VAF mode value in Table 3 is substituted into the corresponding linear model in step (5) in Example 1, and the tumor purity can be obtained...

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Abstract

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. Variation range, heterozygous germline single nucleotide variation and somatic allelic variation fraction; the above index data are correlated with the tumor purity of known purity tumor samples to construct an identification model; in the above method, the combination of somatic mutation and reproductive Cell variation, comprehensive somatic copy number variation amplitude, heterozygous germline single nucleotide variation and somatic allele variation fraction and other indicator data to build a model, which solves the problem of interval chip capture sequencing such as panel sequencing, which has fewer mutation sites and tumor purity For difficult identification problems, low-purity samples can be more accurately identified, and multiple cross-confirmations between different indicators can be realized, with high reliability.

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 components of tumor tissue are complex in structure. In addition to tumor cells, they also include 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. Tumor purity estimation results may alter biological and clinical interpretation of results. Studies have shown that tumor purity is significantly related to the 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. Facilitates objective analysis of tumor samples. TCGA beli...

Claims

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Application Information

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Patent Type & Authority Patents(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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