scholarly journals INNV-40. TARGETED NEXT GENERATION SEQUENCING OF PEDIATRIC HIGH-GRADE GLIOMA AND ITS THERAPEUTIC IMPLICATIONS, MD ANDERSON EXPERIENCE

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi138-vi138
Author(s):  
David McCall ◽  
Agda Eterovic ◽  
Tyler Moss ◽  
Muhammed Baig ◽  
Greg Fuller ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Pediatric Patients ◽  
Initial Diagnosis ◽  
Cancer Center ◽  
Molecular Testing ◽  
Common Mutation ◽  
High Grade ◽  
Next Generation ◽  
Md Anderson ◽  
Generation Sequencing

Abstract INTRODUCTION The new understanding of molecular pathways in cancer is paving the way towards personalized cancer medicine, especially in refractory disease. High-grade gliomas (HGG) are common pediatric brain tumors that tend to recur, with no available standard therapy upon recurrence. HGG are challenging tumors with illusive biology and poor outcome. We report here the molecular testing of 27 pediatric HGG patients. MATERIALS AND METHODS An analysis of pediatric patients with HGG treated at UT MD Anderson Cancer Center (MDACC) who underwent molecular genetic profiling using next generation sequencing with different genomic panels (AmpliSeq™Cancer Hotspot and Oncomine Panels – by Thermo Fisher Scientific). RESULTS 27 patients with HGG (median age 14 years, range 3–18 years old) underwent genomic profiling. Primary diagnoses were glioblastoma multiforme (n=22), anaplastic astrocytoma (n = 2), gliosarcoma (n= 1), anaplastic pleomorphic xanthoastrocytoma (n= 1) and anaplastic oligoastrocytoma (n= 1). There are 46 genes common to the panels used. The most common mutation was in TP53 (73%). Other mutations included PIK3CA (19%), IDH1 (11.5%), 7.7% for ATM, EGFR and PTEN, and 3.8% for BRAF, FGFR1 and FGFR2. 24 out of 27 patients were tested at initial diagnosis and 3 upon relapse/progression. Patients at initial diagnosis received standard of care therapy of radiation and temozolomide. Only 5 patients received targeted therapy upon progression/recurrence. Some challenges of genomically-matched therapy included lack of clinical trials accepting pediatric patients, unavailability of a liquid form of a drug, and insurance disapproval for off-label use. CONCLUSION The next generation of therapy for childhood cancers will be based upon in-depth molecular phenotyping that may facilitate the development of rational risk-adapted and target-based therapies. This cohort, though limited by sample size, highlights the opportunity to perform molecular testing and identification of alterations in actionable genes.

Next-generation sequencing yields promising targets in advanced cholangiocarcinoma (CCA).

2014 ◽  
Vol 32 (3_suppl) ◽  
pp. 209-209
Author(s):  
Rachna T. Shroff ◽  
Chaitanya Churi ◽  
Asif Rashid ◽  
Lopa Mishra ◽  
Mingxin Zuo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Kras Mutation ◽  
Cancer Center ◽  
Next Generation ◽  
Illumina Hiseq ◽  
Md Anderson ◽  
Genetic Profiles ◽  
Next Generation Sequencing Ngs ◽  
Parp 1 ◽  
Generation Sequencing

209 Background: The incidence of CCA is rising and the clinical efficacy of systemic therapy is suboptimal. Next generation sequencing (NGS) technology offers potential for targeted therapeutics against genetically heterogenous solid tumors including cholangiocarcinoma (CCA). Methods: DNA was extracted from biopsy specimens of 61 patients (pts) with CCA seen at MD Anderson Cancer Center Houston, TX. DNA sequencing was performed for 3,769 exons of 236 cancer-related genes plus 47 introns from 19 genes to an average depth of 1000X using the Illumina HiSeq 2000 platform (performed by Foundation Medicine, Cambridge, MA). Results: 174genomic alterations (GA) were identified from 61 pt samples with an average of 2.85 GAs/pt (range 0-10). GAs identified were mutations (75%), amplifications (16%), loss/deletions (7%) and others (2%). 6 (10%) tumors showed no GAs. Most frequent GAs were TP53 (34%), KRAS (30%), ARID1A (15%), PBRM1 (11%), BAP1 (8%), ERBB2 (8%), FBXW7 (8%), SMAD4 (8%) and IDH1 (8%). ERBB2 GAs included 4 mutations and 1 amplification. KRAS mutation was associated with a statistically significant reduction in overall survival (OS). Mean OS in pts with KRAS mutation was 32 weeks vs. 63 weeks in KRAS wt (t = -2.126, p = 0.039). Ingenuity Pathway Analysis indicated disruption in cell cycle, proliferation, development, death and DNA repair pathways. Targetable signaling pathways from this study are described in the Table. Targetable GAs were noted in 62% of pts. These are potentially targetable by inhibitors to ERBB2, FGF, mTOR, MEK, BRAF and PARP-1. Conclusions: These data are the single largest compilation of NGS analysis on CCA pts and demonstrate the range of GAs that are eligible for investigational targeted therapies. These results can be used as a basis to develop personalized treatments for CCA pts based on individual genetic profiles. [Table: see text]

scholarly journals Detection of EGFR Mutation Distribution and Transcriptional Variants in IDH-Wildtype High-Grade Gliomas Using a Next-Generation Sequencing Oncopanel

2021 ◽  
Author(s):  
Nayuta Higa ◽  
Toshiaki Akahane ◽  
Taiji Hamada ◽  
Hajime Yonezawa ◽  
Hiroyuki Uchida ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Receptor Gene ◽  
Kinase Domain ◽  
The Cancer Genome Atlas ◽  
Cancer Center ◽  
High Grade ◽  
Next Generation ◽  
Transcriptional Variants ◽  
High Grade Gliomas ◽  
Generation Sequencing

Abstract \Purpose: To detect the epidermal growth factor receptor gene (EGFR) mutation profile and transcriptional variants in high-grade gliomas (HGGs), we sequenced EGFR and evaluated the EGFR splicing profile using a next-generation sequencing (NGS) oncopanel. Methods: We analyzed 124 HGGs—10 grade Ⅲ IDH-wildtype anaplastic astrocytomas (AAs) and 114 grade Ⅳ IDH-wildtype glioblastomas (GBMs). Results: The EGFR mutations were observed in 6.0% of grade Ⅳ GBMs and in 33% of grade Ⅲ AAs. Four cases harbored missense mutations in the EGFR kinase domain (L747A, S768I, V774M, and T790M). A total of 25% of the GBMs showed EGFR amplification. Moreover, 27% of the EGFR mutations occurred in the kinase domain. EGFRvⅢ positivity was detected in 8.0% of EGFR-amplified GBMs. We identified two other EGFR variants in GBM cases with deletions of exons 6–7 (Δe 6-7) (one case) and exons 2–14 (Δe 2-14) (two cases). Interestingly, in one case, the initial EGFRvIII mutation transformed into an EGFR Δe 2-14 mutation during recurrence. The frequency of EGFR alterations in our cohort was lower but the frequency of EGFR mutations in the kinase domain in our cohort was higher than that in The Cancer Genome Atlas and Memorial Sloan Kettering Cancer Center cohorts. Conclusions: We suggested that the EGFR gene profiles of GBM differ among cohorts and identified rare EGFR variants with longitudinal and temporal transformations of EGFRvⅢ.

scholarly journals Detection of EGFR Mutation Distribution and Transcriptional Variants in IDH-wildtype High-grade Gliomas using a Next-generation Sequencing Oncopanel

2021 ◽  
Author(s):  
Nayuta Higa ◽  
Toshiaki Akahane ◽  
Taiji Hamada ◽  
Hajime Yonezawa ◽  
Hiroyuki Uchida ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Receptor Gene ◽  
Kinase Domain ◽  
The Cancer Genome Atlas ◽  
Cancer Center ◽  
High Grade ◽  
Next Generation ◽  
Transcriptional Variants ◽  
High Grade Gliomas ◽  
Generation Sequencing

Abstract Purpose: To detect the epidermal growth factor receptor gene (EGFR) mutation profile and transcriptional variants in high-grade gliomas (HGGs), we sequenced EGFR and evaluated the EGFR splicing profile using a next-generation sequencing (NGS) oncopanel. Methods: We analyzed 124 HGGs—10 grade Ⅲ IDH-wildtype anaplastic astrocytomas (AAs) and 114 grade Ⅳ IDH-wildtype glioblastomas (GBMs). Results: The EGFR mutations were observed in 6.0% of grade Ⅳ GBMs and in 33% of grade Ⅲ AAs. Four cases harbored missense mutations in the EGFR kinase domain (L747A, S768I, V774M, and T790M). A total of 25% of the GBMs showed EGFR amplification. Moreover, 27% of the EGFR mutations occurred in the kinase domain. EGFRvⅢ positivity was detected in 8.0% of EGFR-amplified GBMs. We identified two other EGFR variants in GBM cases with deletions of exons 6–7 (Δe 6-7) (one case) and exons 2–14 (Δe 2-14) (two cases). Interestingly, in one case, the initial EGFRvIII mutation transformed into an EGFR Δe 2-14 mutation during recurrence. The frequency of EGFR alterations in our cohort was lower but the frequency of EGFR mutations in the kinase domain in our cohort was higher than that in The Cancer Genome Atlas and Memorial Sloan Kettering Cancer Center cohorts. Conclusions: We suggested that the EGFR gene profiles of GBM differ among cohorts and identified rare EGFR variants with longitudinal and temporal transformations of EGFRvⅢ.

scholarly journals Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Suguru Takeuchi ◽  
Jun-ichi Kawada ◽  
Kazuhiro Horiba ◽  
Yusuke Okuno ◽  
Toshihiko Okumura ◽  
...  
Keyword(s):  
Respiratory Failure ◽  
Next Generation Sequencing ◽  
Bronchoalveolar Lavage ◽  
Bronchoalveolar Lavage Fluid ◽  
Pediatric Patients ◽  
Respiratory Infections ◽  
Sequence Data ◽  
Lavage Fluid ◽  
Next Generation ◽  
Generation Sequencing

Abstract Next-generation sequencing (NGS) has been applied in the field of infectious diseases. Bronchoalveolar lavage fluid (BALF) is considered a sterile type of specimen that is suitable for detecting pathogens of respiratory infections. The aim of this study was to comprehensively identify causative pathogens using NGS in BALF samples from immunocompetent pediatric patients with respiratory failure. Ten patients hospitalized with respiratory failure were included. BALF samples obtained in the acute phase were used to prepare DNA- and RNA-sequencing libraries. The libraries were sequenced on MiSeq, and the sequence data were analyzed using metagenome analysis tools. A mean of 2,041,216 total reads were sequenced for each library. Significant bacterial or viral sequencing reads were detected in eight of the 10 patients. Furthermore, candidate pathogens were detected in three patients in whom etiologic agents were not identified by conventional methods. The complete genome of enterovirus D68 was identified in two patients, and phylogenetic analysis suggested that both strains belong to subclade B3, which is an epidemic strain that has spread worldwide in recent years. Our results suggest that NGS can be applied for comprehensive molecular diagnostics as well as surveillance of pathogens in BALF from patients with respiratory infection.

scholarly journals MSIplus for Integrated Colorectal Cancer Molecular Testing by Next-Generation Sequencing

2015 ◽  
Vol 17 (6) ◽  
pp. 705-714 ◽  
Author(s):  
Jennifer A. Hempelmann ◽  
Sheena M. Scroggins ◽  
Colin C. Pritchard ◽  
Stephen J. Salipante
Keyword(s):  
Colorectal Cancer ◽  
Next Generation Sequencing ◽  
Molecular Testing ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Next-Generation Sequencing Technologies in Blood Group Typing

2019 ◽  
Vol 47 (1) ◽  
pp. 4-13 ◽  
Author(s):  
Daniel Fürst ◽  
Chrysanthi Tsamadou ◽  
Christine Neuchel ◽  
Hubert Schrezenmeier ◽  
Joannis Mytilineos ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Blood Group ◽  
Large Scale ◽  
Cost Effective ◽  
Molecular Testing ◽  
Blood Group Antigens ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Blood Group Typing ◽  
Generation Sequencing

Sequencing of the human genome has led to the definition of the genes for most of the relevant blood group systems, and the polymorphisms responsible for most of the clinically relevant blood group antigens are characterized. Molecular blood group typing is used in situations where erythrocytes are not available or where serological testing was inconclusive or not possible due to the lack of antisera. Also, molecular testing may be more cost-effective in certain situations. Molecular typing approaches are mostly based on either PCR with specific primers, DNA hybridization, or DNA sequencing. Particularly the transition of sequencing techniques from Sanger-based sequencing to next-generation sequencing (NGS) technologies has led to exciting new possibilities in blood group genotyping. We describe briefly the currently available NGS platforms and their specifications, depict the genetic background of blood group polymorphisms, and discuss applications for NGS approaches in immunohematology. As an example, we delineate a protocol for large-scale donor blood group screening established and in use at our institution. Furthermore, we discuss technical challenges and limitations as well as the prospect for future developments, including long-read sequencing technologies.

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