期刊
ACTA NEUROPATHOLOGICA COMMUNICATIONS
卷 8, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s40478-020-00963-0
关键词
Glioblastoma; MGMT; IDH; Targeted sequencing; CRISPR; Cas9; Long-read sequencing; Nanopore; Molecular marker; Methylation
资金
- University of Arkansas for Medical Sciences (UAMS) Department of Neurosurgery, College of Medicine
- Arkansas Biosciences Institute
- UAMS Winthrop P. Rockefeller Cancer Institute Seeds of Science Grant
- Helen Adams AMP
- Arkansas Research Alliance Endowed Chair
- National Institute of General Medical Sciences of the National Institutes of Health [P20GM125503]
Molecular biomarkers provide both diagnostic and prognostic results for patients with diffuse glioma, the most common primary brain tumor in adults. Here, we used a long-read nanopore-based sequencing technique to simultaneously assessIDHmutation status andMGMTmethylation level in 4 human cell lines and 8 fresh human brain tumor biopsies. Currently, these biomarkers are assayed separately, and results can take days to weeks. We demonstrated the use of nanopore Cas9-targeted sequencing (nCATS) to identifyIDH1andIDH2mutations within 36 h and compared this approach against currently used clinical methods. nCATS was also able to simultaneously provide high-resolution evaluation ofMGMTmethylation levels not only at the promoter region, as with currently used methods, but also at CpGs across the proximal promoter region, the entirety of exon 1, and a portion of intron 1. We compared the methylation levels of all CpGs toMGMTexpression in all cell lines and tumors and observed a positive correlation between intron 1 methylation andMGMTexpression. Finally, we identified single nucleotide variants in 3 target loci. This pilot study demonstrates the feasibility of using nCATS as a clinical tool for cancer precision medicine.
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