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Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data

Layla Oesper, Gryte Satas, Benjamin J. Raphael
2014 Computer applications in the biosciences : CABIOS  
whole-genome (WGS) and whole-exome (WXS) high-throughput DNA sequencing data.  ...  This intra-tumor heterogeneity complicates the analysis of somatic aberrations in DNA sequencing data from tumor samples.  ...  ACKNOWLEDGEMENTS The results published here are in whole or part based on data generated by TCGA research network established by the National Cancer Institute and the National Human Genome Research Institute  ... 
doi:10.1093/bioinformatics/btu651 pmid:25297070 pmcid:PMC4253833 fatcat:eowee2ax3rhgnfzqz7763ys3si

Next Generation Sequencing in Cancer Research and Clinical Application [chapter]

Derek Shyr, Qi Liu
2014 Omics in Clinical Practice  
The wide application of next-generation sequencing (NGS), mainly through whole genome, exome and transcriptome sequencing, provides a high-resolution and global view of the cancer genome.  ...  , and discuss the challenge and future directions in the research and clinical application of cancer genomic sequencing.  ...  Acknowledgements This work was supported by National Cancer Institute grants U01 CA163056, P30 CA068485, P50 CA098131, and P50 CA090949 and QL's work was partially supported by the State Key Program of  ... 
doi:10.1201/b17137-5 fatcat:2nl2wlqsr5h6vo7urlernmn44u

Next generation sequencing in cancer research and clinical application

Derek Shyr, Qi Liu
2013 Biological Procedures Online  
The wide application of next-generation sequencing (NGS), mainly through whole genome, exome and transcriptome sequencing, provides a high-resolution and global view of the cancer genome.  ...  , and discuss the challenge and future directions in the research and clinical application of cancer genomic sequencing.  ...  Acknowledgements This work was supported by National Cancer Institute grants U01 CA163056, P30 CA068485, P50 CA098131, and P50 CA090949 and QL's work was partially supported by the State Key Program of  ... 
doi:10.1186/1480-9222-15-4 pmid:23406336 pmcid:PMC3599179 fatcat:7qnr22ut6netlfe332wirmj35i

Open Access to Large Scale Datasets Is Needed to Translate Knowledge of Cancer Heterogeneity into Better Patient Outcomes

Andrew H. Beck
2015 PLoS Medicine  
Previously, these investigators used a publicly available data set of whole exome sequencing data in head and neck squamous cell carcinoma (HNSCC) from Stransky et al.  ...  Since the MATH score can be computed from whole exome sequencing data obtained from a single tumor sample (which is a data type that can be obtained from formalin-fixed, paraffin-embedded tumor tissue,  ... 
doi:10.1371/journal.pmed.1001794 pmid:25710538 pmcid:PMC4339838 fatcat:lwsc4ibrtnembbgwdufbdxtiti

Identification of Variants in Primary and Recurrent Glioblastoma Using a Cancer-Specific Gene Panel and Whole Exome Sequencing

Selene M. Virk, Richard M. Gibson, Miguel E. Quinones-Mateu, Jill S. Barnholtz-Sloan, Javier S Castresana
2015 PLoS ONE  
In this pilot study, comprised of triplet samples of normal blood, primary tumor, and recurrent tumor samples from three patients; we compared the ability of Illumina whole exome sequencing (ExomeSeq)  ...  genomic profiling of brain tumors.  ...  The results published here are in whole or part based upon The Cancer Genome Atlas project established by the NCI and NHGRI.  ... 
doi:10.1371/journal.pone.0124178 pmid:25950952 pmcid:PMC4423782 fatcat:36vj5hmuijfazdikxyslrgwqqe

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

Ronglai Shen, Venkatraman E. Seshan
2016 Nucleic Acids Research  
We demonstrate the application of FACETS using The Cancer Genome Atlas (TCGA) whole-exome sequencing of lung adenocarcinoma samples.  ...  tumor purity-, ploidyand clonal heterogeneity-adjusted integer copy number calls are greatly needed to more reliably interpret NGS-based cancer gene copy number data in the context of clinical sequencing  ...  Taylor, and Dr. Charlotte K.Y. Ng for their valuable input.  ... 
doi:10.1093/nar/gkw520 pmid:27270079 pmcid:PMC5027494 fatcat:ve6whnrsdfdrlen4m37vdchopu

Genomic landscapes of canine splenic angiosarcoma (hemangiosarcoma) contain extensive heterogeneity within and between patients [article]

Shukmei Wong, EJ Ehrhart, Samuel Stewart, Victoria Zismann, Jacob Cawley, Rebecca Halperin, Natalia Briones, Keith Richter, Karthigayini Sivaprakasam, Nieves Perdigones, Tania Contente-Cuomo, Salvatore Facista (+4 others)
2020 bioRxiv   pre-print
Multi-platform genomic analysis included matched tumor/normal cancer gene panel and exome sequencing. We found candidate somatic cancer driver mutations in 14/28 (50%) HSAs.  ...  We also identified significant intratumoral genomic heterogeneity, consistent with a branched evolution model, through multi-region exome sequencing of three distinct tumor regions from selected primary  ...  in Primary Analysis of CanineHemangiosarcoma Whole Exome Data Somatic SNVs Identified by Panel Sequencing in Canine Splenic Lesions Somatic SNVs Identified by Exome Sequencing in HSA 309 310 311  ... 
doi:10.1101/2020.11.15.380048 fatcat:kfontqtbk5fdzjmnzvb2frqteq

A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine

Eliezer M. Van Allen, Dan Robinson, Colm Morrissey, Colin Pritchard, Alma Imamovic, Scott Carter, Mara Rosenberg, Aaron McKenna, Yi-Mi Wu, Xuhong Cao, Arul Chinnaiyan, Levi Garraway (+1 others)
2016 OncoTarget  
We sought to determine the reproducibility of ascertaining tumor genome aberrations using whole exome sequencing (WES) and RNAseq.  ...  Though providers offering various cancer genomics assays have multiplied, the level of reproducibility in terms of the technical sensitivity and the conclusions resulting from the data analyses have not  ...  In addition to the issues faced in interpreting and reporting germline WGS/WES data, cancer genomics must consider tissue quality and quantity, intra-tumor heterogeneity, inter-tumor heterogeneity, gains  ... 
doi:10.18632/oncotarget.9184 pmid:27167109 pmcid:PMC5288156 fatcat:g4yethyfcrfxbjgenqjkcfotsm

Mining mutation contexts across the cancer genome to map tumor site of origin

Saptarshi Chakraborty, Axel Martin, Zoe Guan, Colin B. Begg, Ronglai Shen
2021 Nature Communications  
We accomplish this using a projection-based statistical method that achieves a highly effective signal condensation, by leveraging DNA sequence and epigenetic contexts using a set of meta-features that  ...  These constitute a hidden genome that contrasts the relatively small number of mutations that occur frequently, the properties of which have been studied in depth.  ...  ., TCGA whole exome and MSK-IMPACT targeted gene panel datasets, that are used in our analysis.  ... 
doi:10.1038/s41467-021-23094-z pmid:34031376 fatcat:ipa54rexsfbejn5es3ji32sixq

The Impact of Tumor Heterogeneity on Patient Treatment Decisions

C. J. Farhangfar, F. Meric-Bernstam, J. Mendelsohn, G. B. Mills, A. K. Lucio-Eterovic
2012 Clinical Chemistry  
The use of flow-sorted nuclei and whole-genome amplification followed by next-generation sequencing allowed the authors to identify and quantify genomic copy number within an individual nucleus at a robustly  ...  Achieving a substantially greater depth is possible with targeted exome sequencing, whereas achieving that goal for whole-exome sequencing (let alone for the entire genome) would be very challenging, owing  ... 
doi:10.1373/clinchem.2012.194712 pmid:23143327 fatcat:y3bz6a4oojh2dlxjcftc75vrqm

Applying high throughput to CLL

Chris Cain
2013 Science-Business eXchange  
1 However, no DNA mutations or translocations were found that could explain how the chimera is generated, and validation in additional samples will be needed before its significance becomes clear.  ...  ABSOLUTE, were essential to handle the complexity of quantifying populations of mutations in whole-exome sequencing data derived from bulk tumors.  ...  A joint team from the Dana-Farber Cancer Institute and the Broad Institute of MIT and Harvard focused on tumor DNA and used whole-exome sequencing to measure mutational heterogeneity in patient samples  ... 
doi:10.1038/scibx.2013.253 fatcat:qckbwczm7zdardtgdwfnadsle4

Patient-derived conditionally reprogrammed cells maintain intra-tumor genetic heterogeneity

Bruna R. S. Correa, Joanna Hu, Luiz O. F. Penalva, Richard Schlegel, David L. Rimm, Pedro A. F. Galante, Seema Agarwal
2018 Scientific Reports  
Whole exome sequencing and copy number variations are used for the first time to address the capability of CR cells to keep their tumor-derived heterogeneity.  ...  Whole exome sequencing (WES) and copy number variations (CNVs) were used to assess the level of ITH in cell cultures when compared with primary tumor and normal tissue materials from each patient.  ...  We also thank Yale University Keck facility to carry out exome sequencing and SNP arrays. We also would like to extend our thanks to Dr.  ... 
doi:10.1038/s41598-018-22427-1 pmid:29511269 pmcid:PMC5840339 fatcat:gtg3fnzm6jbr3hrhkivev4ikbq

Myxoid smooth muscle neoplasia of the uterus: comprehensive analysis by next-generation sequencing and nucleic acid hybridization

Ju-Yoon Yoon, Adrian Mariño-Enriquez, Natalie Stickle, Richard J. de Borja, Nadia Ismiil, Bojana Djordjevic, Carl Virtanen, Aastha Ravat, Marisa R. Nucci, Jelena Mirkovic, Carlos Parra-Herran
2019 Modern Pathology  
We performed whole exome next-generation sequencing and a pan-sarcoma RNA fusion assay in tumoral paraffin-embedded tissue from nine well-characterized uterine myxoid smooth muscle tumors (seven myxoid  ...  Copy number variation load, inferred from sequencing data, was variable with genomic indexes ranging from 2.2 to 74.7 (median 25.7), with higher indexes in myxoid leiomyosarcomas than myxoid smooth muscle  ...  Acknowledgements This work was supported in part by the SARC LMSARC research fund and the Brigham and Women's Hospital Program in Precision Medicine (AME).  ... 
doi:10.1038/s41379-019-0299-4 pmid:31189997 fatcat:fthziftrj5carbgwhjb37dyjxa

Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects

Xiaoyan Zhang, Sadie L. Marjani, Zhaoyang Hu, Sherman M. Weissman, Xinghua Pan, Shixiu Wu
2016 Cancer Research  
genome and transcriptome amplification, epigenome profiling, multi-dimensional sequencing, and next-generation sequencing and analysis.  ...  Here, we discuss the current methods for single cancer-cell sequencing, with a strong focus on those practically used or potentially valuable in cancer research, including single-cell isolation, whole  ...  Acknowledgments The authors thank Hongjin Wu and Ling Yang for their suggestions in singlecell RNA-seq and bioinformatic analysis, respectively. Grant Support  ... 
doi:10.1158/0008-5472.can-15-1907 pmid:26941284 fatcat:pb5wwn5rwbhstb4k32rxv7hbn4

High-throughput sequencing of the melanoma genome

Manfred Kunz, Michael Dannemann, Janet Kelso
2012 Experimental Dermatology  
Next-generation sequencing technologies are now common for whole-genome, whole-exome and wholetranscriptome sequencing (RNA-seq) of tumors to identify point mutations, structural or copy number alterations  ...  Whole-exome sequencing of seven melanoma cell lines identified overlapping gain of function mutations in MAP2K1 (MEK1) and MAP2K2 (MEK2) genes.  ...  All authors contributed equally in drafting and writing of the manuscript. M.D. and J.K. analysed the melanoma sequence mentioned in the Figure S1 .  ... 
doi:10.1111/exd.12054 pmid:23174022 fatcat:we565a5cara5pcthgm2qrrn6by
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