Tumor profiling from whole-genome and whole transcriptome sequencing to uncover gene fusions and structural variations in clinically relevant cancer genes.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e23118-e23118
Author(s):  
Alexandra E Gylfe ◽  
Eve Shinbrot ◽  
Boyko Kakaradov ◽  
Wayne Delport ◽  
Corine K Lau ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Transcriptome Sequencing ◽  
Whole Genome ◽  
Gene Fusions ◽  
Cancer Genes ◽  
Rna Seq ◽  
Structural Variations ◽  
Whole Transcriptome Sequencing ◽  
Somatic Alterations ◽  
Whole Transcriptome

e23118 Background: Current targeted cancer therapies rely on the identification of clinically relevant somatic alterations in the tumor. Hotspot gene-panels and exome sequencing are designed to quickly assess somatic variations in frequently mutated regions and/or the coding regions of relevant genes, but they have limited ability to detect complex genomic rearrangements or novel structural variations. Here, we describe an integrative and comprehensive approach to fully characterize the genomic complexity of solid tumors using high throughput whole genome sequencing (WGS) and whole transcriptome sequencing (RNA Seq). Methods: We performed WGS and high-depth sequencing of known cancer genes in 14 paired tumor-normal samples of a variety of tumor types. Tumor-specific somatic alteration assessments included protein-coding mutations, copy number variations, gene fusions and structural variants. In addition, RNA Seq data was analyzed to identify expressed somatic alterations. Results: We identified 2 novel fusion genes as well as important structural alterations which could have clinical and therapeutic implications. We described a novel BRAF fusion gene in a cholangiocarcinoma devoid of other known driver mutations. BRAF fusions have not been described previously in cholangiocarcinoma; this fusion may represent an alternative mechanism for MAPK activation and could be a useful drug target. We also identified a novel NTRK3 fusion partner in a glioblastoma tumor. This fusion may imply a novel mechanism for NTRK3 activation. Finally, we identified numerous tandem duplications in an ovarian cancer. Recent advances describe tandem duplication hotspots in ovarian cancer as a potential driver mechanism characterizing a specific mutational signature. Conclusions: Comprehensive genomics assessment of paired tumor-normal samples through whole-genome and transcriptome sequencing can yield additional clinically actionable genomic characteristics that may not be detected in whole-exome or hotspot gene-panel sequencing. These findings have the potential to aid in clinical decision making.

Abstract B93: Gene fusions detected by whole transcriptome sequencing of lung adenocarcinoma.

2011 ◽  
Author(s):  
Takashi Kohno ◽  
Hitoshi Ichikawa ◽  
Yasushi Totoki ◽  
Kazuki Yasuda ◽  
Masaki Hiramoto ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Transcriptome Sequencing ◽  
Gene Fusions ◽  
Whole Transcriptome Sequencing ◽  
Whole Transcriptome

Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology

2021 ◽  
Author(s):  
Vaidehi Jobanputra ◽  
Kazimierz O. Wrzeszczynski ◽  
Reinhard Buttner ◽  
Carlos Caldas ◽  
Edwin Cuppen ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Precision Oncology ◽  
Whole Genome ◽  
Clinical Interpretation ◽  
Whole Transcriptome Sequencing ◽  
Whole Transcriptome

scholarly journals Investigating the Responses of Cronobacter sakazakii to Garlic-Drived Organosulfur Compounds: a Systematic Study of Pathogenic-Bacterium Injury by Use of High-Throughput Whole-Transcriptome Sequencing and Confocal Micro-Raman Spectroscopy

2013 ◽  
Vol 80 (3) ◽  
pp. 959-971 ◽  
Author(s):  
Shaolong Feng ◽  
Tyson P. Eucker ◽  
Mayumi K. Holly ◽  
Michael E. Konkel ◽  
Xiaonan Lu ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Transcriptome Sequencing ◽  
Organosulfur Compounds ◽  
Cronobacter Sakazakii ◽  
Rna Seq ◽  
Diallyl Sulfide ◽  
Content Type ◽  
Micro Raman Spectroscopy ◽  
Whole Transcriptome Sequencing ◽  
Whole Transcriptome

ABSTRACTWe present the results of a study using high-throughput whole-transcriptome sequencing (RNA-seq) and vibrational spectroscopy to characterize and fingerprint pathogenic-bacterium injury under conditions of unfavorable stress. Two garlic-derived organosulfur compounds were found to be highly effective antimicrobial compounds againstCronobacter sakazakii, a leading pathogen associated with invasive infection of infants and causing meningitis, necrotizing entercolitis, and bacteremia. RNA-seq shows changes in gene expression patterns and transcriptomic response, while confocal micro-Raman spectroscopy characterizes macromolecular changes in the bacterial cell resulting from this chemical stress. RNA-seq analyses showed that the bacterial response to ajoene differed from the response to diallyl sulfide. Specifically, ajoene caused downregulation of motility-related genes, while diallyl sulfide treatment caused an increased expression of cell wall synthesis genes. Confocal micro-Raman spectroscopy revealed that the two compounds appear to have the same phase I antimicrobial mechanism of binding to thiol-containing proteins/enzymes in bacterial cells generating a disulfide stretching band but different phase II antimicrobial mechanisms, showing alterations in the secondary structures of proteins in two different ways. Diallyl sulfide primarily altered the α-helix and β-sheet, as reflected in changes in amide I, while ajoene altered the structures containing phenylalanine and tyrosine. Bayesian probability analysis validated the ability of principal component analysis to differentiate treated and controlC. sakazakiicells. Scanning electron microscopy confirmed cell injury, showing significant morphological variations in cells following treatments by these two compounds. Findings from this study aid in the development of effective intervention strategies to reduce the risk ofC. sakazakiicontamination in the food production environment and on food contact surfaces, reducing the risks to susceptible consumers.

scholarly journals Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

2010 ◽  
Vol 11 (5) ◽  
pp. R57 ◽  
Author(s):  
Elizabeth T Cirulli ◽  
Abanish Singh ◽  
Kevin V Shianna ◽  
Dongliang Ge ◽  
Jason P Smith ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Whole Genome ◽  
Whole Transcriptome Sequencing ◽  
Whole Transcriptome

scholarly journals No observable guide-RNA-independent off-target mutation induced by prime editor

2021 ◽  
Author(s):  
Runze Gao ◽  
Zhi-Can Fu ◽  
Xiangyang Li ◽  
Ying Wang ◽  
Jia Wei ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
High Specificity ◽  
Human Cells ◽  
Whole Genome ◽  
Guide Rna ◽  
Genome Wide ◽  
Target Sites ◽  
Whole Transcriptome Sequencing ◽  
Whole Transcriptome ◽  
Target Effects

Prime editor (PE) has been recently developed to induce efficient and precise on-target editing, whereas its guide RNA (gRNA)-independent off-target effects remain unknown. Here, we used whole-genome and whole-transcriptome sequencing to determine gRNA-independent off-target mutations in cells expanded from single colonies, in which PE generated precise editing at on-target sites. We found that PE triggered no observable gRNA-independent off-target mutation genome-wide or transcriptome-wide in transfected human cells, highlighting its high specificity.

Structural Variations Identified By Whole Transcriptome Sequencing (RNA-Seq) in Childhood ALL with Different Response to Therapy

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 3768-3768 ◽  
Author(s):  
Grazia Fazio ◽  
Marco Severgnini ◽  
Ingrid Cifola ◽  
Silvia Bungaro ◽  
Andrea Biondi ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Chromosomal Rearrangements ◽  
Response To Therapy ◽  
Normal Blood ◽  
Rna Seq ◽  
Childhood All ◽  
Blood Samples ◽  
Genome Wide ◽  
Whole Transcriptome Sequencing ◽  
Whole Transcriptome

Abstract Introduction. Acute Lymphoblastic Leukemia (ALL) is the most frequent type of childhood leukemia. It is a multi-step process, characterized by the expansion of a pre-leukemic clone, accumulating cooperative genetic events required for the full transformation and clinical manifestation. Recently, the technological advances in genome-wide profiling techniques have allowed a better understanding of its molecular basis and heterogeneity. However, incidence and cure rates greatly differ among children, reflecting diverse responses to drug treatment and distinguishing risk groups. This defines the need for molecular investigations to better understand leukemia biology and improve risk prediction. Aim. We applied a whole-transcriptome sequencing approach (RNA-seq) to characterize low- (LR) versus high-risk (HR) patients, to identify new genetic lesions associated to different early response to therapy. Methods. Total RNA was extracted from primary leukemic blast samples of 10 pediatric ALL patients (4LR and 6 HR, according to minimal residual disease monitoring), included in the Italian AIEOP-BFM ALL2000 protocol. Genome-wide DNA profiling was performed by Affymetrix Cyto2.7M Arrays, RNA-seq was carried out by Illumina GAIIx platform, and validations were performed using independent approaches, such as RT-PCR and FISH. Fusion events were detected using FusionMap software, followed by a custom computational pipeline for the reduction of false positives and the identification of the most likely fusion candidates. Potential interest for leukemia was explored by testing the occurrence of these candidate fusions and con-joined genes in other RNA-seq datasets from different tumors and normal blood samples (i.e.: 15 melanomas, 2 melanocytes, 45 CEU individuals from 1K Genomes Project, plus 25 AML and 12 ALL). Results. We sequenced the transcriptome of 10 childhood ALL cases, not carrying other clinical or genetic risk factors. We performed a comprehensive whole-transcriptome analysis, comprising identification of fusion transcripts, alternative splicing and SNPs. Priority was given to fusion transcripts, which could originate from intra- or inter-chromosomal rearrangements, since they might represent potential prognostic markers or therapeutic targets for personalized treatments. We identified 127 fusion candidates. Strikingly, 123 out of 127 events were identified as intra-chromosomal, 119 of which were involving two contiguous genes or with overlapping loci (the so-called “con-joined genes”). Among the four intra-chromosomal events, the NUP214-ABL1 fusion, previously found in T-ALL and responsive to kinase inhibitors, was here identified and validated in one HR B-ALL patient, thus opening new perspectives for targeted treatment options. Finally, among the four inter-chromosomal events, the novel PAX5-POM121C fusion was identified and validated in one LR patient. Both intra- and inter-chromosomal fusions resulted private or low-frequent events, not recurrent in other tumor types, nor in normal blood samples. Among the con-joined genes, we identified a subset of 22 events not present in melanoma nor in normal blood samples, but common to the external AML and ALL datasets. Conclusion. RNA-seq represents one of the most comprehensive approaches to identify genetic alterations carried by leukemia clones. Our analyses identified novel fusion genes, originated by either inter- or intra-chromosomal rearrangements, as well as a considerable number of con-joined genes. Further evaluations will address SNPs, mutations, gene expression changes and splice variants that could be related to a different risk of relapse, and the feasibility of the screening of these candidates on a larger population of consecutive clinical cases. Disclosures No relevant conflicts of interest to declare.

Sign in / Sign up

Export Citation Format

Share Document