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SomaticSniper: identification of somatic point mutations in whole genome sequencing data

David E. Larson, Christopher C. Harris, Ken Chen, Daniel C. Koboldt, Travis E. Abbott, David J. Dooling, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, Li Ding
<span title="2011-12-06">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Results: In this article, we describe the mathematical basis of our SomaticSniper software for comparing tumor and normal pairs.  ...  Despite this fact, there remains a dearth of available software tools designed to compare sequences in pairs of samples and identify sites that are likely to be unique to one sample.  ...  ACKNOWLEDGEMENTS We would especially like to thank Heather Schmidt and Joelle Kalicki for their assistance in manual review and identification of potential false positives, Dr Michael Wendl for critical  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr665">doi:10.1093/bioinformatics/btr665</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22155872">pmid:22155872</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3268238/">pmcid:PMC3268238</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mutwonrdv5cz5hxojkcrhkgfg4">fatcat:mutwonrdv5cz5hxojkcrhkgfg4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190309045110/http://pdfs.semanticscholar.org/fe9a/3f2ce59442eca7c2708869fb3a685ad16620.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fe/9a/fe9a3f2ce59442eca7c2708869fb3a685ad16620.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr665"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268238" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Improving somatic variant identification through integration of genome and exome data

Vinaya Vijayan, Siu-Ming Yiu, Liqing Zhang
<span title="">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Conclusion: Using machine learning approach to combine results from multiple calling methods on multiple data platforms (e.g., genome and exome) enables more accurate identification of somatic variants  ...  used alone or using variants identified from only whole genome data or only whole exome data.  ...  Availability of data and materials The training set, A0BW.A15K.A152.MV.arff, and the steps to run the software is made available at https://bioinformatics.cs.vt.edu/zhanglab/software.html.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-017-4134-3">doi:10.1186/s12864-017-4134-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29513195">pmid:29513195</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2nggi34fezholo5ixsvzxfcqem">fatcat:2nggi34fezholo5ixsvzxfcqem</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720153351/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-017-4134-3?site=bmcgenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/85/0a/850a1d576d9f30f258f9eda09a14451cb719c6a7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-017-4134-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

The hidden genomic landscape of acute myeloid leukemia: subclonal structure revealed by undetected mutations

M. Bodini, C. Ronchini, L. Giaco, A. Russo, G. E. M. Melloni, L. Luzi, D. Sardella, S. Volorio, S. K. Hasan, T. Ottone, S. Lavorgna, F. Lo-Coco (+10 others)
<span title="2014-12-12">2014</span> <i title="American Society of Hematology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xnhkf6jpofento6hh7wd7pktv4" style="color: black;">Blood</a> </i> &nbsp;
The analyses carried out using two different bioinformatics pipelines (SomaticSniper and MuTect) on the same set of genomic data from 133 Acute Myeloid Leukemia (AML) patients, sequenced inside the Cancer  ...  Our findings raise the possibility that landscapes of AML genomes might be more complex than previously reported and characterized by the presence of hundreds of genes mutated at low variant allele frequency  ...  Introduction Whole genome sequencing (WGS) and whole exome sequencing (WES) are widely used for mutational analysis in cancer samples.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1182/blood-2014-05-576157">doi:10.1182/blood-2014-05-576157</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25499761">pmid:25499761</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4304104/">pmcid:PMC4304104</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cczfs3qb6rcnbaqdhzqcgcyux4">fatcat:cczfs3qb6rcnbaqdhzqcgcyux4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226042125/http://pdfs.semanticscholar.org/6892/10e6d9f7929cfbe2d7b8715330be53db815a.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/68/92/689210e6d9f7929cfbe2d7b8715330be53db815a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1182/blood-2014-05-576157"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304104" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Whole Exome Sequencing Data Analysis Algorithms in Cancer Diagnostics [chapter]

Áron Bartha, Balázs Gyorffy
<span title="">2020</span> <i title="Vide Leaf, Hyderabad"> Prime Archives in Cancer Research </i> &nbsp;
Whole exome sequencing (WES) enables the analysis of all protein coding sequences in the human genome.  ...  Here, we review analysis tools enabling utilization of WES data in clinical and research settings.  ...  Tools marked with an asterisk (*) are suitable for both whole genome sequencing (WGS) and whole exome sequencing (WES) data analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.37247/pacr.1.2020.5">doi:10.37247/pacr.1.2020.5</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fb3xwm2drbhqhinmehksj3dgai">fatcat:fb3xwm2drbhqhinmehksj3dgai</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201105125559/https://videleaf.com/wp-content/uploads/2020/06/Whole-Exome-Sequencing-Data-Analysis-Algorithms-in-Cancer-Diagnostics.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/90/62/9062314abab1b252bfcaa024e5469b19c70e6f70.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.37247/pacr.1.2020.5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

A simple consensus approach improves somatic mutation prediction accuracy

David L Goode, Sally M Hunter, Maria A Doyle, Tao Ma, Simone M Rowley, David Choong, Georgina L Ryland, Ian G Campbell
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/odidfbcgarekjpyyfxpdptajxa" style="color: black;">Genome Medicine</a> </i> &nbsp;
Differentiating true somatic mutations from artifacts in massively parallel sequencing data is an immense challenge.  ...  , MuTect, JointSNVMix2 and SomaticSniper, by Sanger sequencing.  ...  (such as whole-genome sequencing).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gm494">doi:10.1186/gm494</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24073752">pmid:24073752</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3978449/">pmcid:PMC3978449</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/edlln2wacjeu5hu2iskigsphpu">fatcat:edlln2wacjeu5hu2iskigsphpu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718004203/https://minerva-access.unimelb.edu.au/bitstream/handle/11343/265696/PMC3978449.pdf;jsessionid=83484D99F49571AEC2FCB963DAC71802?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e4/78/e478add2f0f9a5d75545838096dd815b07135a34.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gm494"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978449" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Quantifying the influence of mutation detection on tumour subclonal reconstruction

Lydia Y. Liu, Vinayak Bhandari, Adriana Salcedo, Shadrielle M. G. Espiritu, Quaid D. Morris, Thomas Kislinger, Paul C. Boutros
<span title="2020-12-07">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
We show that predictions of subclonal architecture and timing of somatic mutations vary extensively across pipelines.  ...  AbstractWhole-genome sequencing can be used to estimate subclonal populations in tumours and this intra-tumoural heterogeneity is linked to clinical outcomes.  ...  This work was funded by the Government of Canada through Genome Canada (OGI-125). V.B., L.Y.L. and A.S. were supported by Fellowships from the Canadian Institutes of Health Research.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-020-20055-w">doi:10.1038/s41467-020-20055-w</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33288765">pmid:33288765</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g6ayrcoojncydj6pi3kxu55wsm">fatcat:g6ayrcoojncydj6pi3kxu55wsm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429052041/https://www.nature.com/articles/s41467-020-20055-w.pdf?error=cookies_not_supported&amp;code=1dbc980e-c326-4abf-9f46-2465d133e1c9" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/84/b0/84b0114296b09b73965c8c57d4977296280ae667.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-020-20055-w"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a>

An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data

Yuichi Shiraishi, Yusuke Sato, Kenichi Chiba, Yusuke Okuno, Yasunobu Nagata, Kenichi Yoshida, Norio Shiba, Yasuhide Hayashi, Haruki Kume, Yukio Homma, Masashi Sanada, Seishi Ogawa (+1 others)
<span title="2013-03-06">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Recent advances in high-throughput sequencing technologies have enabled a comprehensive dissection of the cancer genome clarifying a large number of somatic mutations in a wide variety of cancer types.  ...  Using 13 whole-exome sequencing data with 87.5-206.3 mean sequencing depths, we demonstrate that our method not only outperforms several existing methods in the calling of mutations with moderate allele  ...  ACKNOWLEDGEMENT The super-computing resource was provided by Human Genome Center, Institute of Medical Science, the University of Tokyo. The authors also thank H. Tanaka, Y. Mori and N.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt126">doi:10.1093/nar/gkt126</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23471004">pmid:23471004</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3627598/">pmcid:PMC3627598</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qg6mdgvl3vekhd2kizhookiohm">fatcat:qg6mdgvl3vekhd2kizhookiohm</a> </span>
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Confidence-based Somatic Mutation Evaluation and Prioritization

Martin Löwer, Bernhard Y. Renard, Jos de Graaf, Meike Wagner, Claudia Paret, Christoph Kneip, Özlem Türeci, Mustafa Diken, Cedrik Britten, Sebastian Kreiter, Michael Koslowski, John C. Castle (+2 others)
<span title="2012-09-27">2012</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Using sequencing data generated from triplicate exome profiling of C57BL/6 mice and B16-F10 melanoma cells, we used the existing algorithms GATK, SAMtools and SomaticSNiPer to identify somatic mutations  ...  All of the high confidence somatic mutations validated (50 of 50), none of the 44 low confidence somatic mutations validated, and 15 of 45 mutations with an intermediate FDR validated.  ...  Here we present our development of a confidence score for mutations calls and apply the method to the identification of somatic mutations in B16 melanoma.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002714">doi:10.1371/journal.pcbi.1002714</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23028300">pmid:23028300</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3459886/">pmcid:PMC3459886</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ueoxb24uufcuvlktvl7i27l3bi">fatcat:ueoxb24uufcuvlktvl7i27l3bi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015135910/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002714&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ec/8c/ec8cd60ac504ce36be6a9b690aa7c3c9067a410d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002714"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459886" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools

Carlos A Garcia-Prieto, Francisco Martínez-Jiménez, Alfonso Valencia, Eduard Porta-Pardo, Can Alkan
<span title="2022-05-05">2022</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
For that purpose, a wide range of computational tools have been developed in recent years to detect somatic mutations in sequencing data from tumor samples.  ...  Overall, our results highlight the limitations of widespread practices within the cancer genomics community and point to important differences in critical analyses of tumor sequencing data depending on  ...  Acknowledgements We would like to thank the patients that donated the samples for The Cancer Genome Atlas, without them this work would not be possible.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btac306">doi:10.1093/bioinformatics/btac306</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35512388">pmid:35512388</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i5kfc7th4bgbno6lzf2wdudigu">fatcat:i5kfc7th4bgbno6lzf2wdudigu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220507055551/https://watermark.silverchair.com/btac306.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAv4wggL6BgkqhkiG9w0BBwagggLrMIIC5wIBADCCAuAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMwIwnmMiMiOGLH5zyAgEQgIICsYL0AzjMK4foyDdOf3vS9NMG4-TyFD--kLFPe41Za5jmhBOkRbI9YQ__V1-w48HqivfwOJ525Ab2t6jOhOlkunLfH9zL-auBF125UJQE4e1DXliOdCvXqxxUJZfo9fnzbLIH_1WbCd9B_djZbBqCyzTj_-9zlQSPgWVAgzY8bCVTAdOS-uETWCTpkxwiTDTP9DlXveGXxl5Sseum0DyJbaIsfpBWuhhbg_PJNnmq3tEozX__KA6L88OMQAq2psBwR1aG7BW42UdsRnB6S7ZSKGicKK_c44c3mfvMc5pMqhWDEJs6htgUB7HdQS0-5HNnILsFYfDVJDZ7TslY6KPx_kp-5DSsT-8ZyA-rg5BVBkMtO7INl-J2ryXRSbGN7mlP_K9QdpfumRll6zAa1S2yGpuezE1m_ru5jrK2OJHo1_XsaJfKKLvGsxjslGAYL7OSJiTRkAMBus_Fj6IjaHPdVI6PCGhmUNz32YdG-KlcoyXo7brzLZYuqcfWT5xsUkDp8xkgNsTBaEVxdlEgCJmPtMuKeCaM1kBy7oOefpXfEgTEbpO2luFy2bFVvxJYGF1PydkpOaJqzvzb6M1dErqVERmgrgY89672YjJSyygus6VaLaXDi7s63hKC39bUAktjEfRTg7T2HiRCw4K8y6W8kx0GTF59rswUiK94NuiByIrInTsdHMvC_L-jsQLf7iAPVAcASb2ee9Br_eEb1ok1YIJtCTmPtMRMio6gJpPtozGIUBWoZ1_JWs4SWv0lzxbHk81tO8jQ5LCUw7pYRODPukVZOT1CGVf_r919EVhwhm4vgzAYhXLVC3hYQEfqhi-2CXTsi4nIHOLNMQTLQRLWDVpJ2vDHtVJWcHBVX4RuTcRM0K8Z4OeJa-KN5VMoyNbLWcHGcry9LxP6Mjxq9IszkjYp" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/23/35/2335a6cd8dfd478f96311044011fd29ed5a48277.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btac306"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology

Bartha, Győrffy
<span title="2019-11-04">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2zwku6u6nfdcri773tpisi6ldi" style="color: black;">Cancers</a> </i> &nbsp;
Whole exome sequencing (WES) enables the analysis of all protein coding sequences in the human genome.  ...  Here, we review analysis tools enabling utilization of WES data in clinical and research settings.  ...  Tools marked with an asterisk (*) are suitable for both whole genome sequencing (WGS) and whole exome sequencing (WES) data analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers11111725">doi:10.3390/cancers11111725</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31690036">pmid:31690036</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6895801/">pmcid:PMC6895801</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s3lnry4r3ffqbeorfnuiigobtm">fatcat:s3lnry4r3ffqbeorfnuiigobtm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208062149/https://res.mdpi.com/d_attachment/cancers/cancers-11-01725/article_deploy/cancers-11-01725-v3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/18/cd/18cdab819c698560fd9ab495e8b04f40831ab7d3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers11111725"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895801" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Inter and Intra-Tumoural Heterogeneity of Subclonal Reconstruction [article]

Vinayak Bhandari, Lydia Y Liu, Adriana Salcedo, Shadrielle MG Espiritu, Quaid D Morris, Paul C Boutros
<span title="2018-09-17">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Recent studies have used whole-genome sequencing data to estimate the origins of this clonal heterogeneity, and have linked it to clinical outcomes like response to curative treatment.  ...  Conclusions: Analysis of a large cohort of single- and multi-region tumour whole genomes shows that selection of variant detection and subclonal reconstruction algorithms significantly biases the results  ...  We used MuTect (v1.1.4) (23) and SomaticSniper (v1.0.2) (22) for the identification of somatic single nucleotide variants from whole-genome sequencing data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/418780">doi:10.1101/418780</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wv2pctdevfhxdptngwo44z5wme">fatcat:wv2pctdevfhxdptngwo44z5wme</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429133148/https://www.biorxiv.org/content/biorxiv/early/2018/09/17/418780.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/68/3e/683e1d5f8e20f598a90cfc6af09a86dd5c531994.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/418780"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data

Jennifer D. Hintzsche, William A. Robinson, Aik Choon Tan
<span title="">2016</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qe5jsynkezfovmnttfiupg7j3m" style="color: black;">International Journal of Genomics</a> </i> &nbsp;
Whole Exome Sequencing (WES) is the application of the next-generation technology to determine the variations in the exome and is becoming a standard approach in studying genetic variants in diseases.  ...  Understanding the exomes of individuals at single base resolution allows the identification of actionable mutations for disease treatment and management.  ...  This work is partly supported by the National Institutes of Health P50CA058187, Cancer League of Colorado, the David F. and Margaret T.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2016/7983236">doi:10.1155/2016/7983236</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28070503">pmid:28070503</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5192301/">pmcid:PMC5192301</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qtlmgypwxjbv7ewg5wskhqxs4a">fatcat:qtlmgypwxjbv7ewg5wskhqxs4a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209031837/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5192301&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c5/65/c565df86213cd2c321209e95ce1173e363ad3b61.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2016/7983236"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192301" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease

Britt-Sabina Petersen, Martina E Spehlmann, Andreas Raedler, Björn Stade, Ingo Thomsen, Raquel Rabionet, Philip Rosenstiel, Stefan Schreiber, Andre Franke
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Our goal was the identification of mutations present only in the affected twins, pointing to novel candidates for CD susceptibility loci.  ...  Results: We aimed to test if somatic mutations play a role in CD etiology by sequencing the genomes and exomes of directly affected tissue from the bowel and blood samples of one and the blood-derived  ...  Acknowledgements This work was in part supported by the DFG Cluster of Excellence "Inflammation at Interfaces" and received funding under the EU Seventh  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-564">doi:10.1186/1471-2164-15-564</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24996980">pmid:24996980</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4102722/">pmcid:PMC4102722</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/csfeb7azfjajljtcfmtkt77nqu">fatcat:csfeb7azfjajljtcfmtkt77nqu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428230407/http://diposit.ub.edu/dspace/bitstream/2445/130864/1/660866.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/92/09/92091870b7db3c011d31eaa9d3b5725d06ba3da0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-564"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102722" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations

Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt
<span title="">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
However, most of them are dedicated to a particular type of mutation, e.g. germline SNVs in normal cells, somatic SNVs in cancer/tumor cells, or indels only.  ...  Conclusions: SNVSniffers demonstrates the feasibility to develop integrated solutions to fast and efficient identification of germline and somatic variants.  ...  Publication of this article was funded by Georgia Institute of Technology.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-016-0300-5">doi:10.1186/s12918-016-0300-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27489955">pmid:27489955</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4977481/">pmcid:PMC4977481</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3tudsjrsjzdefntvjmg2nta7a4">fatcat:3tudsjrsjzdefntvjmg2nta7a4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171012060305/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/49b/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEyOTE4LTAxNi0wMzAwLTUucGRm.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/27/0a/270a54a1be1e989f2e2a58976ef6d033cda95f85.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-016-0300-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977481" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Whole-exome sequencing reveals recurrent somatic mutation networks in cancer

Xiaoping Liu, Jiguang Wang, Luonan Chen
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3nxjpygtrbechhvcm56vaxdcqi" style="color: black;">Cancer Letters</a> </i> &nbsp;
The whole-exome sequencing information can reflect the mutations of the protein-coding region in the genome and depict the causal relationship between the mutations and phenotypes.  ...  In this review, we focus on the recent advances on network-based methods for identifying cancer driver modules or pathways, including methods of whole-exome sequencing, somatic mutation detection, driver  ...  Acknowledgments This work was supported by the National Natural Science Foundation of China under Grants Nos. 91029301, 61134013 and 61072149; and by the Chief Scientist Program of Shanghai Institutes  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.canlet.2012.11.002">doi:10.1016/j.canlet.2012.11.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23153794">pmid:23153794</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/angjidrzlfa4fhnnb7anqnhcai">fatcat:angjidrzlfa4fhnnb7anqnhcai</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200320082003/http://www.escience.cn/system/download/64608" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/83/bf/83bfbc5f7fbdbd4c0902331215ea0d1df1ac6869.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.canlet.2012.11.002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>
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