Genome for molecular typing of medulloblastoma and application thereof

A medulloblastoma, molecular typing technology, applied in recombinant DNA technology, microbial determination/examination, DNA/RNA fragment, etc. question

Active Publication Date: 2019-01-11
HANGZHOU CANHELP GENOMICS TECH CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Thus, the method is susceptible to interference from RNA degradation in paraffin-embedded tissue samples
At the same time, the NanoString nCounter Technology, which is based on this method, is a closed technology platform that requires specific detection equipment and reagent consumables. The operation and maintenance costs are extremely high, and the experimental operation process is complicated, so it is not suitable for large-scale clinical applications.

Method used

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  • Genome for molecular typing of medulloblastoma and application thereof
  • Genome for molecular typing of medulloblastoma and application thereof
  • Genome for molecular typing of medulloblastoma and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0099] Training set sample collection and processing:

[0100] The present invention first analyzes the clinical data of 103 patients with medulloblastoma and the gene chip detection data of their biological samples, including relevant clinical data of 8 cases of WNT type, 33 cases of SHH type, 27 cases of Group3 type and 35 cases of Group4 type. Data and expression abundance data of 20,250 genes were used to construct a medulloblastoma gene expression database.

[0101] Screening of 13 specific genes:

[0102] According to the measured value of gene expression abundance, the inventors selected 13 genes closely related to medulloblastoma type from 20,250 genes by means of statistical analysis method variance analysis. These genes were differentially expressed in different subtypes of medulloblastoma, which was statistically significant (P value < 0.0001), see Table 2.

[0103] Table 2: 13 Gene Sets

[0104]

[0105] 13 genes based on the construction of statistical analy...

Embodiment 2

[0108] High-throughput sequencing data verification:

[0109] In this example, the inventors analyzed the high-throughput sequencing data of 73 cases of medulloblastoma, including 8 cases of WNT type, 10 cases of SHH type, 16 cases of Group3 type and 39 cases of Group4 type. The 13-gene statistical analysis model was used to distinguish the subtype of each sample, and compared with the clinical diagnosis results, the diagnostic coincidence rate was 75.3%. Taking the SHH type as a reference, the sensitivity of typing was 100.0%, and the specificity was 93.7%. See Table 3 and Table 4 for details.

[0110] Table 3: Classification results of the 13-gene model in 73 cases of high-throughput sequencing data

[0111]

[0112] Table 4: Performance indicators of the 13-gene model in 73 cases of high-throughput sequencing data

[0113]

Embodiment 3

[0115] In this example, the inventors conducted molecular typing experiments on 285 paraffin tissue samples of medulloblastoma, including 51 cases of SHH type, 46 cases of Group3 type and 188 cases of Group4 type. Experimenters collected medulloblastoma-enriched regions from formalin-fixed, paraffin-embedded tissue blocks by hand scraping, and extracted total RNA; treated with DNase to ensure complete removal of genomic DNA contamination; reverse-transcribed After obtaining cDNA, real-time quantitative polymerase chain reaction (real-timequantitative polymerase chain reaction, RTQ-PCR) of 13 genes was carried out to detect the gene expression level in paraffin-embedded tumor tissue, and the analysis model was used to calculate the relationship between the sample and medulloblastoma subtype. similarity score.

[0116] The subtypes of each sample were discriminated by the 13-gene statistical analysis model, and compared with the clinical diagnosis results, the diagnostic coincid...

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Abstract

The invention discloses a genome for molecular typing of medulloblastoma. The genome for molecular typing of medulloblastoma includes the following 24 genes: EPHA7 gene, OTX2 gene, ROBO1 gene, TTR gene, LGR5 gene, IGF2BP3 gene, TBR1 gene, ZFPM2 gene, TRDC gene, TRAC gene, PEX5L gene, NKD1 gene, RALYL gene, GABRA5 gene, GAD1 gene, TNC gene, KCNA1 gene, EOMES gene, MAB21L2 gene, WIF1 gene, DKK2 gene, PDLIM3 gene, IMPG2 gene, and KHDRBS2 gene. In addition, the invention also discloses an application of the genome in preparing a kit and a gene chip for molecular typing of medulloblastoma. As proved by experience, the method can accurately distinguish the WNT type, the SHH type, the Group3 type and the Group4 type of medulloblastoma, and has the advantages of objective result interpretation, high accuracy and short experiment period, and has important clinical significance in carrying out precise treatment on patients.

Description

technical field [0001] The invention relates to the fields of cancer diagnosis and molecular biology, as well as the clinical application of diagnosis technology. Specifically, the present invention relates to a group of genes used for molecular typing of medulloblastoma and its application. Through the establishment of molecular typing of medulloblastoma and the detection of the expression of specific genes in medulloblastoma tissue, the identification of medulloblastoma Blastoma subtypes, including WNT type (WNTsubgroup), SHH type (Sonic Hedgehog Subgroup), Group3 type (Group3) and Group4 type (Group4). In addition, the present invention also relates to a kit for molecular typing of medulloblastoma. Background technique [0002] According to China's cancer statistics, in 2015, the number of new cases of brain and central nervous system cancer in my country reached about 101,600, and it was listed as the seventh among the top ten common tumors. The death toll was 61,000, a...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6886C12Q1/6837C12N15/11
CPCC12Q1/6837C12Q1/6886C12Q2600/158C12Q2600/112C12Q2600/16C12Q1/6806
Inventor 徐清华陈成书孙益丰陈金影王奇峰宋凯斌
Owner HANGZHOU CANHELP GENOMICS TECH CO LTD
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