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Device and method for identifying and evaluating tumor progression

A technology for tumors and patients, applied in biochemical equipment and methods, biochemical cleaning devices, enzymology/microbiology devices, etc., can solve problems such as cancer progression or difficult prognosis

Active Publication Date: 2018-09-07
TURING AI INST NANJING CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Therefore, it is often difficult to evaluate the progression or prognosis of cancer by only a single indicator
Reliable biological indicators that can be correlated with clinical features (eg, disease progression) are also lacking in the art

Method used

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  • Device and method for identifying and evaluating tumor progression
  • Device and method for identifying and evaluating tumor progression
  • Device and method for identifying and evaluating tumor progression

Examples

Experimental program
Comparison scheme
Effect test

Embodiment approach

[0210] 1. A device for identifying biological indicators capable of evaluating tumor progression, said device comprising:

[0211] 1) a clinical feature module capable of providing clinical features of a patient suffering from the tumor, the clinical features comprising the patient's tumor stage and / or the patient's survival time;

[0212] 2) a biological indicator module, which can provide at least one biological indicator derived from the patient;

[0213] 3) a correlation judging module, which can determine the correlation between the at least one biological indicator of each patient and the clinical characteristics of the corresponding patient; and

[0214] 4) An identification module, which can identify the biological indicators determined to be related to the clinical features in module 3) as being able to evaluate the progress of the tumor.

[0215] 2. A device for identifying biological indicators capable of evaluating tumor progression, said device comprising a compu...

Embodiment 1

[0304] Example 1 Patient and Tumor Sample Data Sources

[0305] Most of the genomic and clinical datasets of BLCA patients used in this application were downloaded from "NCI GDC DataPortal Legacy Archive". Among them, the clinical information of BLCA patients comes from TCGA-BLCA clinical files. The obtained BLCA patient RNA-seq dataset contained 419 samples, including 400 tumor samples and 19 normal samples. All gene expression values ​​were normalized.

[0306] Somatic mutation data at TCGA level 2 using the Mutation Annotation Format (MAF file). TCGA level 3 methylation data was downloaded from "jhu-usc_BLCA.HumanMethylation450". Correlation data between mRNA expression and DNA methylation at TCGA level 4 came from Broad GDAC Firehose. Copy number variation (CNV) data for TCGA Level 4 was downloaded from BroadGDAC Firehose.

[0307] The following discrete indices are used to represent the level of amplification and deletion of CNVs: severe deletion=-2; deletion=1; no c...

Embodiment 2

[0310] Example 2 Screening key genes based on survival rate analysis

[0311] Use survival analysis to study the relationship between survival status and different potential influencing factors (eg, key genes).

[0312] experimental method:

[0313] Cox proportional hazards regression

[0314] Univariate and multivariate Cox proportional hazards regression models were applied to identify key genes that may affect the survival of BLCA patients. The expression values ​​of individual genes in all BLCA samples were first normalized according to their z-scores. Genes expressed only in less than 20 samples were removed.

[0315] In univariate Cox proportional hazards regression, gene expression value was used as the only predictor variable; whereas in multivariate Cox proportional hazards regression, age, sex, tumor stage, and gene expression value were all used as predictor variables. p-values ​​were adjusted using the 'Benjamini & Hochberg' method.

[0316] Thresholds for sta...

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PUM

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Abstract

The invention relates to a device and method for identifying and evaluating tumor progression. The device or method can comprise the modules or steps as follows: 1) a module or step capable of providing clinical characteristics of patients suffering from tumor; 2) a module or step capable of providing at least one biological index derived from the patients; 3) a module or step capable of determining correlation between the at least one biological index of each patient and the clinical characteristics of the corresponding patients; 4) a module or step capable of evaluating the progress of the tumor or identifying relevant evaluation indexes. The device or method can provide guidance for studying the potential molecular mechanism of tumor progression and providing treatment strategies for tumor progression.

Description

technical field [0001] The present application relates to the detection and treatment of diseases, in particular to a device and method for identifying biological indicators that can be used to evaluate tumor progression, and a device and method for judging tumor progression. Background technique [0002] Elucidating the molecular mechanisms underlying tumorigenesis is one of the most important issues in oncology. Genomic characteristics of patients with dysregulated gene expression can be obtained by high-throughput DNA sequencing. For example, it has been found that copy number variation (CNV) can be used as an important indicator of colorectal cancer and other cancers (see Zhao S, et al,. Proc Natl Acad Sci USA 2013, 110(8):2916-2921). DNA methylation is an important epigenetic mechanism. In bladder cancer cells, abnormal DNA methylation levels have been shown to be related to the dysfunction of certain genes, and thus also to the occurrence of bladder cancer (see RoseM ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12M1/34C12Q1/6886
CPCC12Q1/6886C12Q2600/154C12Q2600/156C12Q2600/158C12Q2600/178G16H50/20G16H50/30G16B20/00G16B20/10G16B40/30Y02A90/10G16B20/20
Inventor 曾坚阳周斌
Owner TURING AI INST NANJING CO LTD