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A method and device for predicting the type of met gene copy number change

A gene copy number and type technology, applied in the field of bioinformatics, can solve the problems of improper baseline and threshold line settings, reduced accuracy, incorrect and other problems, to improve the sensitivity and specificity, to avoid the effect of bias

Active Publication Date: 2021-07-20
SHENZHEN GENEPLUS CLINICAL LAB
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

There are many pitfalls in the operation process of this method, such as: improper setting of baseline and threshold line, low amplification efficiency, use of incorrect range to make standard curve, use of inappropriate normalization control, etc., resulting in inaccurate results decreased sex

Method used

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  • A method and device for predicting the type of met gene copy number change
  • A method and device for predicting the type of met gene copy number change

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0076] MET amplification refers to an increase in the copy number of the MET gene caused by amplification of a local region of chromosome 7.

[0077] MET polyploidy refers to an increase in the copy number of the MET gene caused by polyploidy on chromosome 7.

[0078] The method for calculating the proportion of MET amplification and MET polyploidy (also known as MET polysomy) in the population is as follows:

[0079] Select 250 tumor tissue samples (including paraffin-embedded tissue samples and fresh tissue samples) with MET copy number increase (without distinguishing MET amplification or MET polyploidy) after manual review, and combine the bam files of 250 samples with the capture interval (Gene increases the panel, the chip name is cd3) bed file, human reference genome sequence (the human reference genome used in this embodiment is hs37d5) fastq file as input file, adopts default parameter, utilizes CNVkit software to analyze each sample respectively The copy number of e...

Embodiment 2

[0087] Methods for identifying MET amplification and MET polysomy are as follows:

[0088] Randomly screen 45 cancer patient tissue samples, and combine the bam files of 45 samples with the bed files of the capture interval (Gene's large panel, the chip name is cd3), the human reference genome sequence (the human reference genome used in this example is hs37d5 ) fastq file as the input file, using the default parameters, using CNVkit software to identify the copy number of each sample respectively, and obtain the ratio of each sample relative to the copy number of the reference sample group. Each sample was processed using the CNV annotation filtering system to obtain the Status value of each gene. Based on the analysis results of the CNVKit software, the T test was used to identify MET amplification and MET polysomy. The specific results are as follows:

[0089] Table 2

[0090]

[0091]

[0092] For the results of FISH, use the ratio of cMET / CEP7 (that is, the ratio o...

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Abstract

A method and device for predicting the change type of MET gene copy number, the method comprising: a gene copy number ratio analysis step, analyzing the ratio of the gene copy number according to the baseline; a capture area analysis step, based on the ratio, the capture area of ​​the sample to be tested is analyzed Copy number variation annotation, according to the annotation results, predict whether the copy number of the MET gene in the test sample has changed; the MET gene copy number change type prediction step, for the test sample whose prediction result is an increase in the copy number of the MET gene, obtain the gene copy number Ratio, the statistics of whether there is a significant difference in the gene copy number ratio, predict the type of MET gene copy number increase. The normal control samples at the same time point were used to establish a baseline to avoid bias in the results of the CNV analysis of the samples to be tested, and significantly improve the sensitivity and specificity of the prediction of the copy number change type of the MET gene.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular to a method and device for predicting the type of copy number change of the MET gene. Background technique [0002] Mesenchymal to epithelial transition factor (MET) protein, as a receptor tyrosine kinase, exists in epithelial cells and can participate in many biological functions. It is located on the seventh human chromosome (7q21-q31) The region, with a total length of more than 120kb, contains 21 exons and 20 introns. With the deepening of research, MET has been confirmed to be amplified in a variety of malignant tumors, and has become one of the important drug resistance mechanisms of EGFR-TKIs, especially in non-small cell lung cancer (NSCLC) , has become an important tumor driver gene and therapeutic target. There are currently two ways to increase the copy number of the MET gene. One is chromosome 7 polyploidy (polysomy), which refers to the increase in the copy number of the...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/20
CPCG16B20/20
Inventor 管彦芳方欢李彩琴刘涛易鑫杨玲
Owner SHENZHEN GENEPLUS CLINICAL LAB