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- The analysis of somatic mutations across multiple genes in cancer specimens may be used to aid clinical decision making. The analytical validation of targeted next-generation sequencing panels is important to assess accuracy and limitations. - To report the development and validation of OncoPanel, a custom targeted next-generation sequencing assay for cancer. - OncoPanel was designed for the detection of single-nucleotide variants, insertions and deletions, copy number alterations, and structural variants across 282 genes with evidence as drivers of cancer biology. We implemented a validation strategy using formalin-fixed, paraffin-embedded, fresh or frozen samples compared with results obtained by clinically validated orthogonal technologies. - OncoPanel achieved 98% sensitivity and 100% specificity for the detection of single-nucleotide variants, and 84% sensitivity and 100% specificity for the detection of insertions and deletions compared with single-gene assays and mass spectrometry-based genotyping. Copy number detection achieved 86% sensitivity and 98% specificity compared with array comparative genomic hybridization. The sensitivity of structural variant detection was 74% compared with karyotype, fluorescence in situ hybridization, and polymerase chain reaction. Sensitivity was affected by inconsistency in the detection of FLT3 and NPM1 alterations and IGH rearrangements due to design limitations. Limit of detection studies demonstrated 98.4% concordance across triplicate runs for variants with allele fraction greater than 0.1 and at least 50× coverage. - The analytical validation of OncoPanel demonstrates the ability of targeted next-generation sequencing to detect multiple types of genetic alterations across a panel of genes implicated in cancer biology.

Pleomorphic xanthoastrocytoma (PXA) is low-grade glial neoplasm principally affecting children and young adults. Approximately 40% of PXA are reported to recur within 10 years of primary resection. Upon recurrence, patients receive radiation therapy and conventional chemotherapeutics designed for high-grade gliomas. Genetic changes that can be targeted by selective therapeutics have not been extensively evaluated in PXA and ancillary diagnostic tests to help discriminate PXA from other pleomorphic and often more aggressive astrocytic malignancies are limited. In this study, we apply the SNaPshot multiplexed targeted sequencing platform in the analysis of brain tumors to interrogate 60 genetic loci that are frequently mutated in 15 cancer genes. In our analysis we detect BRAF V600E mutations in 12 of 20 (60%) WHO grade II PXA, in 1 of 6 (17%) PXA with anaplasia and in 1 glioblastoma arising in a PXA. Phospho-ERK was detected in all tumors independent of the BRAF mutation status. BRAF duplication was not detected in any of the PXA cases. BRAF V600E mutations were identified in only 2 of 71 (2.8%) glioblastoma (GBM) analyzed, including 1 of 9 (11.1%) giant cell GBM (gcGBM). The finding that BRAF V600E mutations are common in the majority of PXA has important therapeutic implications and may help in differentiating less aggressive PXAs from lethal gcGBMs and GBMs.

ABSTRACT Objectives ERBB2 (human epidermal growth factor receptor 2 [HER2]) amplification/overexpression in colorectal carcinomas (CRCs) may predict response to HER2 inhibitors. We correlated ERBB2 amplification by next-generation sequencing (NGS) with HER2 overexpression by immunohistochemistry. Methods NGS was performed on specimens containing 20% or more tumor. HER2 immunohistochemistry (clone SP3) was scored semiquantitatively by H-score. ERBB2 fluorescence in situ hybridization (FISH) was performed to examine copy alterations in one HER2-heterogeneous tumor. Results ERBB2 amplification was detected in 2% of 1,300 CRCs analyzed by NGS. HER2 immunohistochemistry was examined in 15 cases with ERBB2 amplification (six or more copies), 10 with low gain (three to five copies), and 77 copy neutral. ERBB2 amplification and HER2 immunohistochemistry showed perfect concordance at an H-score of 105 or more. FISH confirmed homogeneous ERBB2 amplification in a tumor showing HER2 protein expression heterogeneity. ERBB2 amplification anticorrelated with RAS/RAF mutations (P = .0001). No ERBB2-amplified cases showed mismatch repair deficiency. Conclusions NGS-detected ERBB2 amplification highly correlates with HER2 overexpression in CRC, but immunohistochemistry is required to capture protein-level heterogeneity.

Fusions involving neurotrophic tyrosine receptor kinase ( NTRK ) genes are detected in ≤2% of gliomas and can promote gliomagenesis. The remarkable therapeutic efficacy of TRK inhibitors, which are among the first Food and Drug Administration-approved targeted therapies for NTRK -fused gliomas, has generated significant clinical interest in characterizing these tumors. In this multi-institutional retrospective study of 42 gliomas with NTRK fusions, next generation DNA sequencing ( n  = 41), next generation RNA sequencing ( n  = 1), RNA-sequencing fusion panel ( n  = 16), methylation profile analysis ( n  = 18), and histologic evaluation ( n  = 42) were performed. All infantile NTRK -fused gliomas ( n  = 7) had high-grade histology and, with one exception, no other significant genetic alterations. Pediatric NTRK -fused gliomas ( n  = 13) typically involved NTRK2 , ranged from low- to high-histologic grade, and demonstrated histologic overlap with desmoplastic infantile ganglioglioma, pilocytic astrocytoma, ganglioglioma, and glioblastoma, among other entities, but they rarely matched with high confidence to known methylation class families or with each other; alterations involving ATRX , PTEN , and CDKN2A/2B were present in a subset of cases. Adult NTRK -fused gliomas ( n  = 22) typically involved NTRK1 and had predominantly high-grade histology; genetic alterations involving IDH1 , ATRX , TP53 , PTEN , TERT promoter, RB1 , CDKN2A/2B , NF1 , and polysomy 7 were common. Unsupervised principal component analysis of methylation profiles demonstrated no obvious grouping by histologic grade, NTRK gene involved, or age group. KEGG pathway analysis detected methylation differences in genes involved in PI3K/AKT, MAPK, and other pathways. In summary, the study highlights the clinical, histologic, and molecular heterogeneity of NTRK -fused gliomas, particularly when stratified by age group.

Chromosome-arm copy number alterations (CNAs) are an important component of cancer molecular classifiers. CNAs are often translated into binary chromosome arm calls (arm gain/loss) using an arm call threshold before integration into classification schemes. However, substantial variability exists in thresholds used to define arm calls from CNA data. Here, we analyze 1042 meningiomas with whole-genome microarray data and 13 meningiomas with multifocal sampling to characterize how CNA thresholds influence molecular classification and prognostication. Changing arm call thresholds shifts the association of chromosomal arm calls with meningioma recurrence in an arm-dependent manner and upgrades 21.5% of cases from low-grade to high-grade in a molecularly Integrated Grade (IG) scheme. The impact of threshold differences in IG prediction of recurrence is most evident amongst intermediate grade (IG-2) tumors and CNA call thresholds approaching whole-chromosome arm length (>95%). The designation of chromosome loss or gain remains stable across a majority of thresholds, although this varies in a chromosome-dependent manner. CNAs fluctuate among paired primary-recurrent tumors, mostly growing on recurrence, but cluster in discrete sizes within a tumor. Appreciation of the impact of chromosome arm call thresholds can help ensure robustness of molecular classification paradigms. Defining clinically meaningful criteria for copy number alterations (CNA) remains challenging. Here, the authors explore the distribution and prognostic impact of CNA features in a large clinically annotated cohort of meningiomas, determining arm call thresholds that enable consistent molecular classification and patient stratification.

In mouse models of patient-derived breast cancer brain metastases, combined inhibition of PI3K and mTOR resulted in regression, and therapeutic response was correlated with a reduction in 4EBP1 phosphorylation. Brain metastases represent the greatest clinical challenge in treating HER2-positive breast cancer. We report the development of orthotopic patient-derived xenografts (PDXs) of HER2-expressing breast cancer brain metastases (BCBM), and their use for the identification of targeted combination therapies. Combined inhibition of PI3K and mTOR resulted in durable tumor regressions in three of five PDXs, and therapeutic response was correlated with a reduction in the phosphorylation of 4EBP1, an mTORC1 effector. The two nonresponding PDXs showed hypermutated genomes with enrichment of mutations in DNA-repair genes, which suggests an association of genomic instability with therapeutic resistance. These findings suggest that a biomarker-driven clinical trial of PI3K inhibitor in combination with an mTOR inhibitor should be conducted for patients with HER2-positive BCBM.

Ependymomas show poor correlation between World Health Organization grade and clinical outcome. A subgroup of supratentorial ependymomas are characterized by C11orf95-RELA fusions, presumed to be secondary to chromothripsis of chromosome 11, resulting in constitutive activation of the NF-κB signaling pathway and overexpression of cyclin D1, p65, and L1 cell adhesion molecule (L1CAM). These RELA -fused ependymomas are recognized as a separate, molecularly defined World Health Organization entity and might be associated with poor clinical outcome. In this study, we show that immunohistochemistry for NF-κB signaling components, such as L1CAM, p65, and cyclin D1, can help distinguish RELA -fused from non- RELA -fused supratentorial ependymomas. Furthermore, these three markers can reliably differentiate RELA -fused ependymomas from a variety of histologic mimics. Lastly, we report that RELA -fused ependymomas may be associated with different chromosomal copy number changes and molecular alterations compared to their non- RELA -fused counterparts, providing additional insight into the genetic pathogenesis of these tumors and potential targets for directed therapies.

In a small series of patients with refractory Hodgkin's lymphoma, a substantial rate of tumor regression (87%) was documented in response to blockade of the programmed death 1 pathway. The programmed death 1 (PD-1) pathway serves as a checkpoint to limit T-cell–mediated immune responses. 1 Both PD-1 ligands, PD-L1 and PD-L2, engage the PD-1 receptor and induce PD-1 signaling and associated T-cell “exhaustion,” a reversible inhibition of T-cell activation and proliferation. 1 By expressing PD-1 ligands on the cell surface and engaging PD-1 receptor–positive immune effector cells, tumors can co-opt the PD-1 pathway to evade an immune response. 2 PD-1–blocking antibodies have been used to enhance immunity in solid tumors and obtain durable clinical responses with an acceptable safety profile. 2 – 5 Preliminary data also support empirical PD-1 blockade as a therapeutic strategy . . .

Whole-genome copy number analysis platforms, such as array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) arrays, are transformative research discovery tools. In cancer, the identification of genomic aberrations with these approaches has generated important diagnostic and prognostic markers, and critical therapeutic targets. While robust for basic research studies, reliable whole-genome copy number analysis has been unsuccessful in routine clinical practice due to a number of technical limitations. Most important, aCGH results have been suboptimal because of the poor integrity of DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues. Using self-hybridizations of a single DNA sample we observed that aCGH performance is significantly improved by accurate DNA size determination and the matching of test and reference DNA samples so that both possess similar fragment sizes. Based on this observation, we developed a novel DNA fragmentation simulation method (FSM) that allows customized tailoring of the fragment sizes of test and reference samples, thereby lowering array failure rates. To validate our methods, we combined FSM with Universal Linkage System (ULS) labeling to study a cohort of 200 tumor samples using Agilent 1 M feature arrays. Results from FFPE samples were equivalent to results from fresh samples and those available through the glioblastoma Cancer Genome Atlas (TCGA). This study demonstrates that rigorous control of DNA fragment size improves aCGH performance. This methodological advance will permit the routine analysis of FFPE tumor samples for clinical trials and in daily clinical practice.

Jason Locasale, Lewis Cantley, Matthew Vander Heiden and colleagues show that PHGDH is amplified in some human cancers and diverts a relatively large amount of glycolytic carbon into serine and glycine biosynthesis. They further show that PHGDH -amplified cancer cells become dependent on PHGDH for their growth, suggesting that the altered metabolic flux driven by this amplification contributes to oncogenesis. Most tumors exhibit increased glucose metabolism to lactate, however, the extent to which glucose-derived metabolic fluxes are used for alternative processes is poorly understood 1 , 2 . Using a metabolomics approach with isotope labeling, we found that in some cancer cells a relatively large amount of glycolytic carbon is diverted into serine and glycine metabolism through phosphoglycerate dehydrogenase (PHGDH). An analysis of human cancers showed that PHGDH is recurrently amplified in a genomic region of focal copy number gain most commonly found in melanoma. Decreasing PHGDH expression impaired proliferation in amplified cell lines. Increased expression was also associated with breast cancer subtypes, and ectopic expression of PHGDH in mammary epithelial cells disrupted acinar morphogenesis and induced other phenotypic alterations that may predispose cells to transformation. Our findings show that the diversion of glycolytic flux into a specific alternate pathway can be selected during tumor development and may contribute to the pathogenesis of human cancer.