Dataset Information

Rapid detection of isocitrate dehydrogenase 1 mutation status in glioma based on Crispr-Cas12a.

ABSTRACT: The aim is to use Crispr-Cas12a for the rapid detection of the single nucleotide polymorphism (SNP) of isocitrate dehydrogenase 1 (IDH1)-R132H locus and explore the effectiveness and consistency of this method with direct sequencing method for detecting IDH1-R132H of glioma tissue samples. 58 previous frozen tissue and 46 recent fresh tissue samples of adult diffuse glioma were selected to detect IDH1-R132H using Crispr-Cas12a. The results of immunohistochemistry (IHC) and direct sequencing methods were analyzed. We calculated the efficiency index of Crispr-Cas12a and IHC, and analyzed the consistency among Crispr-Cas12a, IHC and direct sequencing method using paired Chi-sequare test and Kappa identity test. We accomplished the rapid detection of IDH1-R132H in 60 min using Crispr-Cas12a. Regarding direct sequencing method as the gold standard, the sensitivity, specificity and consistency rate of Crispr-Cas12a was 91.4%, 95.7% and 93.1% in the frozen sample group, while 96.1%, 89.7% and 92.0% in the fresh sample group, respectively. Kappa test showed good consistency between the two methods (k = 0.858). Crispr-Cas12a can quickly and accurately detect IDH1-R132H and has good stability. It is a promising method to detect IDH1 mutation status intraoperatively.

SUBMITTER: Feng Z

PROVIDER: S-EPMC10081818 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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Rapid detection of isocitrate dehydrogenase 1 mutation status in glioma based on Crispr-Cas12a.

Feng Zhebin Z Kong Dongsheng D Jin Wei W He Kunyu K Zhao Junyan J Liu Bin B Xu Hanyun H Yu Xin'guang X Feng Shiyu S

Scientific reports 20230407 1

The aim is to use Crispr-Cas12a for the rapid detection of the single nucleotide polymorphism (SNP) of isocitrate dehydrogenase 1 (IDH1)-R132H locus and explore the effectiveness and consistency of this method with direct sequencing method for detecting IDH1-R132H of glioma tissue samples. 58 previous frozen tissue and 46 recent fresh tissue samples of adult diffuse glioma were selected to detect IDH1-R132H using Crispr-Cas12a. The results of immunohistochemistry (IHC) and direct sequencing meth ...[more]

PMID: 37029174

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Project description:BackgroundAlthough much is known about molecular and chromosomal characteristics that distinguish glioma histological subtypes, DNA methylation patterns of gliomas and their association with other tumor features such as mutation of isocitrate dehydrogenase (IDH) genes have only recently begun to be investigated.MethodsDNA methylation of glioblastomas, astrocytomas, oligodendrogliomas, oligoastrocytomas, ependymomas, and pilocytic astrocytomas (n = 131) from the Brain Tumor Research Center at the University of California San Francisco, as well as nontumor brain tissues (n = 7), was assessed with the Illumina GoldenGate methylation array. Methylation data were subjected to recursively partitioned mixture modeling (RPMM) to derive methylation classes. Differential DNA methylation between tumor and nontumor was also assessed. The association between methylation class and IDH mutation (IDH1 and IDH2) was tested using univariate and multivariable analysis for tumors (n = 95) with available substrate for sequencing. Survival of glioma patients carrying mutant IDH (n = 57) was compared with patients carrying wild-type IDH (n = 38) using a multivariable Cox proportional hazards model and Kaplan-Meier analysis. All statistical tests were two-sided.ResultsWe observed a statistically significant association between RPMM methylation class and glioma histological subtype (P < 2.2 × 10(-16)). Compared with nontumor brain tissues, across glioma tumor histological subtypes, the differential methylation ratios of CpG loci were statistically significantly different (permutation P < .0001). Methylation class was strongly associated with IDH mutation in gliomas (P = 3.0 × 10(-16)). Compared with glioma patients whose tumors harbored wild-type IDH, patients whose tumors harbored mutant IDH showed statistically significantly improved survival (hazard ratio of death = 0.27, 95% confidence interval = 0.10 to 0.72).ConclusionThe homogeneity of methylation classes for gliomas with IDH mutation, despite their histological diversity, suggests that IDH mutation is associated with a distinct DNA methylation phenotype and an altered metabolic profile in glioma.

Dataset Information

Rapid detection of isocitrate dehydrogenase 1 mutation status in glioma based on Crispr-Cas12a.

Publications

Rapid detection of isocitrate dehydrogenase 1 mutation status in glioma based on Crispr-Cas12a.

Similar Datasets

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