Exomic Sequencing of Four Rare Central Nervous System Tumor Types

Abstract

A heterogeneous population of uncommon neoplasms of the central nervous system (CNS) cause significant morbidity and mortality. To explore their genetic origins, we sequenced the exomes of 12 pleomorphic xanthoastrocytomas (PXA), 17 non-brainstem pediatric glioblastomas (PGBM), 8 intracranial ependymomas (IEP) and 8 spinal cord ependymomas (SCEP). Analysis of the mutational spectra revealed that the predominant single base pair substitution was a C:G>T:A transition in each of the four tumor types. Our data confirm the critical roles of several known driver genes within CNS neoplasms, including TP53 and ATRX in PGBM, and NF2 in SCEPs. Additionally, we show that activating BRAF mutations play a central role in both low and high grade glial tumors. Furthermore, alterations in genes coding for members of the mammalian target of rapamycin (mTOR) pathway were observed in 33% of PXA. Our study supports the hypothesis that pathologically similar tumors arising in different age groups and from different compartments may represent distinct disease processes with varied genetic composition.

Detection of tumor-derived DNA in cerebrospinal fluid of patients with primary tumors of the brain and spinal cord

“…Initially, a PCR-based approach testing for mutations in codons 130-139 of IDH1; codons 126-155, 144-178, and 250-262 of IDH2; all coding exons of TP53; and the TERT promoter was used (44)(45)(46)(47)(48). If no mutations were present within these genes, paired-end libraries of DNA from the tumors and WBC pellets were prepared and captured (SureSelect; Agilent) as previously described (47). Massively parallel sequencing was carried out on an Illumina HiSeq Instrument at either the Goldman Sequencing Facility at Johns Hopkins Medical Institutions or Personal Genome Diagnostics.…”

“…Massively parallel sequencing was carried out on an Illumina HiSeq Instrument at either the Goldman Sequencing Facility at Johns Hopkins Medical Institutions or Personal Genome Diagnostics. Mutations were identified as previously described (47,(49)(50)(51)(52).…”

“…For this purpose, primers were designed to amplify an ∼100-bp region surrounding each mutation. The two primers had universal sequences at their 5′ ends, allowing a second round of PCR to be performed using a second set of primers containing these sequences (19,47). The sequences of the primers used to assess each mutation are listed in Table S5.…”

Somatic mutations of SUZ12 in malignant peripheral nerve sheath tumors

“…Genomic DNA libraries were prepared and captured according to the protocol suggested by Illumina and as previously described 9,20 . DNA libraries were sequenced with the Illumina HiSeq Genome Analyzer, yielding 100 bp of sequence from the final library fragments for whole-exome and whole-genome analyses.…”

The genetic basis of intradural spinal tumors and its impact on clinical treatment

“…104 Similarly, another study of 8 spinal and 8 intracranial ependymomas reported significant losses of chromosome 22, on which NF2 resides, in spinal ependymoma. 8 In addition, an unexpected partial loss of chromosome 13 was observed. In addition, loss of chromosome 10q has been reported in a study of a small number of spinal ependymomas.…”