Application of methylation sites in SHH myeloblastoma
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A medulloblastoma, methylation technology, applied in biochemical equipment and methods, microbial determination/inspection, DNA/RNA fragments, etc., can solve the problems of easy degradation, long analysis period and high cost
Active Publication Date: 2019-05-21
GUANGZHOU KINGMED DIAGNOSTICS CENT +2
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[0006] However, the current diagnosis of SHH medulloblastoma mainly refers to its gene expression profile, which requires RNA transcriptome sequencing, which is costly and takes a long period of experiment and analysis. Because RNA is easily degraded, the technical requirements for experimental operations are also high, so the experiment failed. Both the rate and the experimental error are relatively high
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Embodiment 1
[0041] Sample collection and testing.
[0042] 1. Sample collection.
[0043] Collect 223 postoperative tissue samples from patients with SHH-type medulloblastoma, and 540 postoperative tissue samples from patients with other types of medulloblastoma except SHH, that is, OTHERS samples (including other subtypes of medulloblastoma: WNT, Group3 and Group4).
[0044] 2. Sample testing.
[0045] The commercial Illumina HumanMethylation450 BeadChip chip was used to detect methylation, and the routine experimental procedures were followed. The main experimental procedures include:
[0046] 1. Extract sample DNA and amplify;
[0047] 2. Use enzymes to break DNA to fragment it;
[0048] 3. Separation and purification of DNA fragments and addition of adapters;
[0049] 4. Hybridization of DNA fragments with chips;
[0050] 5. On-chip detection on the chip.
Embodiment 2
[0052] Screening for methylation sites.
[0053] 1. Preliminary screening of methylation sites.
[0054] Using the data in Example 1 as the database, first establish a model based on a single methylation site, and then select highly differentiated methylation sites to build a comprehensive model based on a series of methylation sites. Then, according to the b-value value of the selected methylation site (one or more), the eigenvalue vector of a sample is constructed, and each sample corresponds to a tumor type (SHH type medulloblastoma or OTHERS), by This establishes a SVM classification model, and then obtains the methylation sites with significant differences, as shown in the following table.
[0055] Table 1. Methylation sites with significant differences between SHH medulloblastoma and OTHERS
[0056] site
Gene
Chromosome
Locus Chromosomal Coordinates
positive / negative chain
cg20419291
ROBO4
chr11
124767974
+
cg0968442...
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Abstract
The invention relates to an application of methylation sites in SHH medulloblastoma, belongs to the technical field of tumor typing detection, and particularly relates to an application of a methylation degree reagent of at least one gene site in ROBO4, OTX2OS1, AHRR, DKK4 and PART1 genes in a biological sample in preparation of a diagnostic reagent or diagnostic equipment for SHH type medulloblastoma. By analyzing and comparing data of a large number of SHH type myeloblastoma samples and other types of samples, the inventor finds that the methylation degree of the sites in the genes can be used as a reference index for diagnosing the SHH type myeloblastoma, and the SHH type of the myeloblastoma can be typed and confirmed only by directionally detecting a plurality of methylation sites, sothat the diagnosis difficulty of the SHH type myeloblastoma is reduced, and the cost is reduced.
Description
technical field [0001] The invention relates to the technical field of tumor typing and detection, in particular to the application of a SHH type medulloblastoma methylation site. Background technique [0002] Medulloblastoma is the most common malignant brain tumor in children. About 85% of medulloblastoma occurs in children under the age of 18, and 1 in every 5 children with brain tumors has medulloblastoma . In recent years, the survival rate of patients with medulloblastoma has improved, but the mortality rate is still high, and neurological and endocrine sequelae often occur in patients with successful treatment. [0003] The incidence of medulloblastoma is about 0.71 / 100,000 people. In the United States, 400 to 500 children suffer from the disease every year. The peak incidence of the disease is between 3 and 6 years old. It is very rare in people after the age of 50. There is no report on the influence of biochemical environment on the incidence of medulloblastoma. ...
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