Clinical Utility of GlioSeq Next-Generation Sequencing Test in Pediatric and Young Adult Patients With Brain Tumors

Abstract

Brain tumors are the leading cause of death in children. Establishing an accurate diagnosis and therapy is critical for patient management. This study evaluated the clinical utility of GlioSeq, a next-generation sequencing (NGS) assay, for the diagnosis and management of pediatric and young adult patients with brain tumors. Between May 2015 and March 2017, 142 consecutive brain tumors were tested using GlioSeq v1 and subset using GlioSeq v2. Out of 142 samples, 63% were resection specimens and 37% were small stereotactic biopsies. GlioSeq sequencing was successful in 100% and 98.6% of the cases for the detection of mutations and copy number changes, and gene fusions, respectively. Average turnaround time was 8.7 days. Clinically significant genetic alterations were detected in 95%, 66.6%, and 66.1% of high-grade gliomas, medulloblastomas, and low-grade gliomas, respectively. GlioSeq enabled molecular-based stratification in 92 (65%) cases by specific molecular subtype assignment (70, 76.1%), substantiating a neuropathologic diagnosis (18, 19.6%), and diagnostic recategorization (4, 4.3%). Fifty-seven percent of the cases harbored therapeutically actionable findings. GlioSeq NGS analysis offers rapid detection of a wide range of genetic alterations across a spectrum of pediatric brain tumors using formalin-fixed, paraffin-embedded specimens and facilitates integrated molecular-morphologic classification and personalized management of pediatric brain tumors.

Characterization of low‐grade epilepsy‐associated tumor from implanted stereoelectroencephalography electrodes

“…At initial genetic testing for Noonan syndrome diagnosis, this PTPN11 mutation was also found. Both FGFR1 and PTPN11 mutations have been commonly seen in DNETs 7–10 . Regarding PTPN11, mutational rates of 54% (resected tissue) and 50% (electrode DNA) are consistent with suggesting a heterozygous germline mutation, consistent with the patient's previous diagnosis of Noonan syndrome.…”

“…Both FGFR1 and PTPN11 mutations have been commonly seen in DNETs. [7][8][9][10] Regarding PTPN11, mutational rates of 54% (resected tissue) and 50% (electrode DNA) are consistent with suggesting a heterozygous germline mutation, consistent with the patient's previous diagnosis of Noonan syndrome. The diagnostic conclusion could be interpreted that, while PTPN11 heterozygous deletion could predispose the patient to tumor development, FGFR1 mutation is somatic and contributes to tumor formation.…”

“…Genomic DNA isolated from sEEG electrode‐derived samples was used to prepare a next‐generation sequencing (NGS) library. GlioSeq next‐generation sequencing is a custom, amplification‐based, targeted method for molecularly profiling brain tumors 7,8 . The GlioSeq (v3) panel consists of DNA and RNA portions.…”

“…GlioSeq next-generation sequencing is a custom, amplification-based, targeted method for molecularly profiling brain tumors. 7,8 The GlioSeq this method was completed using Sanger sequencing, in situ hybridization, and RT-PCR. Sensitivity of this assay is 5% allele frequency for detection of SNVs and short indels.…”

“…Tumor DNA isolated and extracted from cells attached to sEEG electrodes can be used for GlioseqWe hypothesized that residual tissue on sEEG electrodes could be a potential source of diagnostic material for downstream sequencing applications. We extracted DNA from two sEEG electrodes that passed through tumor tissue (Figure1A,B), both having sufficient concentration of DNA for methylation analysis (Infinium Meth-ylationEPIC array) and GlioSeq (Figure1C,D) 12,13. We compared the performance of GlioSeq on DNA extracted from resected tumor tissue versus sEEG electrode.Gli-oSeq of resected tissue identified hotspot mutations in the Protein Tyrosine Phosphatase Non-Receptor Type 11 gene (PTPN11 [NG_007459.1] [NM_001330437.2] M405V), Fibroblast Growth Factor Receptor 1 (FGFR1 [NG_007729.1] [NM_001174064.2] N546K), and Neurofibromatosis type 1 (NF1 [NG_009018.1] [NM_000267.3] D2346Vfs*49), which are all observed in pediatric gliomas inclusive of DNETs (Figure…”