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Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
sequence data can be analyzed by next-generation sequencing (NGS).  ...  In this article, we review the recent advances in computational methods pertaining to CNV detection using whole genome and whole exome sequencing data.  ...  This article has been published as part of BMC Bioinformatics Volume 14 Supplement 11, 2013: Selected articles from The Second Workshop on Data Mining of Next-Generation Sequencing in conjunction with  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s11-s1">doi:10.1186/1471-2105-14-s11-s1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24564169">pmid:24564169</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3846878/">pmcid:PMC3846878</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i2y25xfa4jhqfmyxl5ol2y4zza">fatcat:i2y25xfa4jhqfmyxl5ol2y4zza</a> </span>
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Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing Data

Haiyong Zhao, Shuang Wang, Xiguo Yuan
<span title="2020-11-30">2020</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
In this paper, we propose a new computational method, PGMicroD, for the detection of pathogenic microbial composition in a sample using NGS data.  ...  Next-generation sequencing (NGS) technologies have provided great opportunities to analyze pathogenic microbes with high-resolution data.  ...  In future work, we intend to integrate mutations such as single nucleotide variations and copy number variations (Xi et al., 2019; Zhao et al., 2020) to improve the detection of microbial composition  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2020.603093">doi:10.3389/fgene.2020.603093</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33329748">pmid:33329748</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7734255/">pmcid:PMC7734255</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5g5vdkcqf5c7ncqvb52kfhr77u">fatcat:5g5vdkcqf5c7ncqvb52kfhr77u</a> </span>
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G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods

Andrea Manconi, Emanuele Manca, Marco Moscatelli, Matteo Gnocchi, Alessandro Orro, Giuliano Armano, Luciano Milanesi
<span title="2015-03-10">2015</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tkuhrcyiufdxtkdmjqvay6f2ua" style="color: black;">Frontiers in Bioengineering and Biotechnology</a> </i> &nbsp;
G-CNV can be efficiently used as a third-party tool able to prepare data for the subsequent read-depth signal generation and analysis.  ...  Copy number variations (CNVs) are the most prevalent types of structural variations (SVs) in the human genome and are involved in a wide range of common human diseases.  ...  ACKNOWLEDGMENTS We thank Dario Deledda for his advice and comments on the manuscript. In addition, we thank the reviewers for their very useful and constructive comments and suggestions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2015.00028">doi:10.3389/fbioe.2015.00028</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25806367">pmid:25806367</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4354384/">pmcid:PMC4354384</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j5r437d2bzgq5npzv23rhm3weq">fatcat:j5r437d2bzgq5npzv23rhm3weq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809052545/https://iris.unica.it/retrieve/handle/11584/134252/76586/fbioe-03-00028.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/1a/d5/1ad557b697bee86392848206012b6c6bfe04ac5f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2015.00028"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4354384" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

HBOS-CNV: A New Approach to Detect Copy Number Variations From Next-Generation Sequencing Data

Yang Guo, Shuzhen Wang, Xiguo Yuan
<span title="2021-06-07">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
Accurate detection of CNVs from next-generation sequencing (NGS) data is still a challenging task due to artifacts such as uneven mapped reads and unbalanced amplitudes of gains and losses.  ...  Copy number variation (CNV) is a genomic mutation that plays an important role in tumor evolution and tumor genesis.  ...  Different from traditional methods, the short reads generated by next-generation sequencing (NGS) technologies have a higher resolution that provides potential advantages for the accurate detection of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2021.642473">doi:10.3389/fgene.2021.642473</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34163521">pmid:34163521</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8215577/">pmcid:PMC8215577</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/27wfg4s4czdqjhbvxklwitgrtq">fatcat:27wfg4s4czdqjhbvxklwitgrtq</a> </span>
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CIRCNV: Detection of CNVs Based on a Circular Profile of Read Depth from Sequencing Data

Hai-Yong Zhao, Qi Li, Ye Tian, Yue-Hui Chen, Haque A. K. Alvi, Xi-Guo Yuan
<span title="2021-06-25">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j5h4zct24vcofi5scx6ttoapnq" style="color: black;">Biology</a> </i> &nbsp;
Copy number variation (CNV) is a common type of structural variation in the human genome.  ...  In this paper, we propose an alternative approach, called CIRCNV, for the detection of CNVs from sequencing data.  ...  Currently, there are a number of simulation tools that can be used to generate NGS data and simulate genomic variations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/biology10070584">doi:10.3390/biology10070584</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tnrq3il4qbc2rc5o42tapnoyce">fatcat:tnrq3il4qbc2rc5o42tapnoyce</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210629062125/https://res.mdpi.com/d_attachment/biology/biology-10-00584/article_deploy/biology-10-00584.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/3d/8f/3d8f3073a946017f0f0df1dbbd54d4242f5e9411.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/biology10070584"> <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>

SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data

Zhongyang Zhang, Ke Hao, Edwin Wang
<span title="2015-11-19">2015</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;
normal cells, making it difficult for the methods well tailored for the detection of germline copy number variation (CNV) to fit in tumor SCNA detection.  ...  SAAS-CNV: A Joint Segmentation Approach to Detect SCNA PLOS Computational Biology |  ...  Acknowledgments We thank Michael Linderman and Hardik Shah for their generous help in data pre-processing. We also thank Andrew Uzilov for helpful discussion.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1004618">doi:10.1371/journal.pcbi.1004618</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26583378">pmid:26583378</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4652904/">pmcid:PMC4652904</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zfndw27vujaxvfvudr37tekjl4">fatcat:zfndw27vujaxvfvudr37tekjl4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015151208/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004618&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/38/a0/38a09d0abf7b0e437514194c2649f7c78fb8ed25.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1004618"> <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/PMC4652904" 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 Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation

Armand Valsesia, Aurélien Macé, Sébastien Jacquemont, Jacques S. Beckmann, Zoltán Kutalik
<span title="2013-05-30">2013</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
In this review we discuss the progress, challenges, and limitations that occur at different stages of CNV analysis from the detection (using DNA microarrays and next-generation sequencing) and identification  ...  Hence there is a need for better-tailored and more robust tools for the detection and genome-wide analyses of CNVs.  ...  ACKNOWLEDGMENTS We are grateful to Sven Bergmann and James King for useful comments on our manuscript; to Andres Metsapalu for discussions regarding CNV false-discovery estimation; and to Fiona Cunningham  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2013.00092">doi:10.3389/fgene.2013.00092</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23750167">pmid:23750167</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3667386/">pmcid:PMC3667386</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2aj7jxhkcrac3jl2vflyxk57i4">fatcat:2aj7jxhkcrac3jl2vflyxk57i4</a> </span>
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Constructing a database for the relations between CNV and human genetic diseases via systematic text mining

Xi Yang, Zhuo Song, Chengkun Wu, Wei Wang, Gen Li, Wei Zhang, Lingqian Wu, Kai Lu
<span title="">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The detection and interpretation of CNVs are of clinical importance in genetic testing.  ...  Results: The resulting CNVdigest database includes 440,485 sentences for CNV-disease relationship. A total number of 1582 CNVs and 2425 diseases are involved.  ...  Discussion With the widely-spread use of array-based comparative genomic hybridization and next generation sequencing (NGS) copy number variant calling, the identification of CNVs became easier and easier  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2526-2">doi:10.1186/s12859-018-2526-2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/okaclo7w2nf5phu4ayu5tifpmy">fatcat:okaclo7w2nf5phu4ayu5tifpmy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427155553/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2526-2" 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/d9/d3/d9d353809625177a7d089560d9cb39cf5ff8b952.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2526-2"> <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>

CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly

Julien Prunier, Alexandra Carrier, Isabelle Gilbert, William Poisson, Vicky Albert, Joëlle Taillon, Vincent Bourret, Steeve D Côté, Arnaud Droit, Claude Robert
<span title="2021-12-15">2021</span> <i title="Life Science Alliance, LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n52qe5bgffhupjgphw3dmag6vq" style="color: black;">Life Science Alliance</a> </i> &nbsp;
As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain).  ...  Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified.  ...  We also thank ComputeCanada and CalculQu ébec for access to large computing resources.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.26508/lsa.202101207">doi:10.26508/lsa.202101207</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34911809">pmid:34911809</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8711850/">pmcid:PMC8711850</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/euwzrb7qjzcshcogyh3o2qbcxu">fatcat:euwzrb7qjzcshcogyh3o2qbcxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211216144034/https://www.life-science-alliance.org/content/lsa/5/3/e202101207.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/cc/10/cc10d66bf319acf3afe88a9aa3c92e0dbde1566c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.26508/lsa.202101207"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8711850" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients

Francisco Requena, Hamza Hadj Abdallah, Alejandro García, Patrick Nitschké, Sergi Romana, Valérie Malan, Antonio Rausell
<span title="2021-05-21">2021</span> <i title="Oxford University Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Copy Number Variants (CNVs) are an important cause of rare diseases.  ...  CNVxplorer mines a comprehensive set of clinical, genomic, and epigenomic features associated with CNVs.  ...  Abbreviations: CNV: Copy Number Variants; aCGH: array comparative genomic hybridization; NGS: Next Generation Sequencing; WES:Whole Exome Sequencing; WGS: Whole Genome Sequencing; lncRNAs: long non-coding  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkab347">doi:10.1093/nar/gkab347</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34019647">pmid:34019647</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8262689/">pmcid:PMC8262689</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o72vsarzhbclfp4drwcqvn5tpa">fatcat:o72vsarzhbclfp4drwcqvn5tpa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210527105127/https://watermark.silverchair.com/gkab347.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAq8wggKrBgkqhkiG9w0BBwagggKcMIICmAIBADCCApEGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMHeRKzVisnL9G3Wg2AgEQgIICYsjTYDxeICfxFCT9XUPTFFwTyzHbmEHXrrsU-xaT6ITZtsNfwb0UBSjLBY4Fey23HInIIcmUftsyhRQZ3PVa0l67JDBYfyU3tX54muxxGCXiEWmv8c_gQkDXzIZU8ZpBPLFv4W_WZEiVv8LmiQYiJ4AGyZAO2-ewLtq9LlfyJGMPhaNwoJxAqGqR3vThbd3RlI1_BWkleOXY5reicUTnslFS9jSBW1MJCJJvTioy75XB6De1uuGl1klfuq_9vtNiw18q9EhEsp0s9cvdFAbsFB7LepETOrV6fla4jryoE09-U-1PuyByhUtOB6odHp1RXcWMQJe0lfjlomR2zf5YEb-tc9DiXfcXe-VvFBcpsBN78g9A7_-9mBDLlpa2OdPMYuJXtTpQmv3hrvi4hR17SRTw6uMiFafWGqMD7bZAvSwxDO3MwI3NeXsxBxejwpkCQFWGlgoEM8L9dnP_uQI6evT1GBpIok9RsiuaiKwDbdNpLC9Nu0beMljSvEqwe3FFvWY6p4ivwjt3EICDAB9L87D3-7zT2FauMcuYQtEQ3iCLgAO0JdQxP-EFLLroxwhNMZnMIZ3dQ8qBbChAK_N9nspBko8o45wgmkaecWLYZ55QjQmjZFGb5Stm09P58KP66a3c9mpINlsVL6zvN1TXhb77wr0abl9UlTfxRs86lCEn4-IEkuv_OR-uo491SBNynPknphN4CU-QjzcQJ-Jm57u5Q4lcrz6Ml0q4XWxCvHYNRyNbM_LOmG5NV5SMAjkrNeVsprGb53BpG7wyQZ2PRm18YL9BruO8q6E1pXNSHRKGLlM" 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/1b/40/1b4083a0b402b2e3aa564d2b5fe23bf11aa137e9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkab347"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262689" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

MFCNV: A New Method to Detect Copy Number Variations From Next-Generation Sequencing Data

Haiyong Zhao, Tihao Huang, Junqing Li, Guojun Liu, Xiguo Yuan
<span title="2020-05-15">2020</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
Next-generation sequencing (NGS) technique has provided a wealth of data for the detection of CNVs at base-pair resolution.  ...  Copy number variation (CNV) is a very important phenomenon in tumor genomes and plays a significant role in tumor genesis.  ...  This work was supported by the National Natural Science Foundation of China (61773192) and by the Fundamental Research Funds for the Central Universities (YJ20009).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2020.00434">doi:10.3389/fgene.2020.00434</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32499814">pmid:32499814</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7243272/">pmcid:PMC7243272</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zmjlh5yp5jfujdmvzp6bujb26a">fatcat:zmjlh5yp5jfujdmvzp6bujb26a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200606024424/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7243272&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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2020.00434"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7243272" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Cluster-Based Approach for the Discovery of Copy Number Variations From Next-Generation Sequencing Data

Guojun Liu, Junying Zhang
<span title="2021-06-28">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
The next-generation sequencing technology offers a wealth of data resources for the detection of copy number variations (CNVs) at a high resolution.  ...  In this work, we propose a new CNV detection method, called CBCNV, for the detection of CNVs of different lengths from whole genome sequencing data.  ...  In recent years, most related tools for CNV detection using next-generation sequencing data have been developed based on paired-end mapping (PEM) (Korbel et al., 2007 ) and depth of coverage (DOC) (Yoon  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2021.699510">doi:10.3389/fgene.2021.699510</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hhr2ft5i5vgvddd27hxk6ouxii">fatcat:hhr2ft5i5vgvddd27hxk6ouxii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210701080650/https://fjfsdata01prod.blob.core.windows.net/articles/files/699510/pubmed-zip/.versions/2/.package-entries/fgene-12-699510-r1/fgene-12-699510.pdf?sv=2018-03-28&amp;sr=b&amp;sig=Hrl0p9VL5jyQzfxKlcdS5qkBj7fuXLbBLy3qg4ZTKWg%3D&amp;se=2021-07-01T08%3A07%3A19Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fgene-12-699510.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/27/7c/277c3b7dbdd8cd329fab40aec6a09c584b3b945e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2021.699510"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a>

Identification of copy number variations and translocations in cancer cells from Hi-C data [article]

Abhijit Chakraborty, Ferhat Ay
<span title="2017-08-21">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Making the scenario even more complex, cancer cells harbor chromosomal abnormalities (e.g., copy number variations (CNVs) and translocations) altering their genomes both at the sequence level and at the  ...  Our CNV predictions correlate very well with whole genome sequencing (WGS) data among chromosomes with CNV events for a breast cancer cell line (r=0.89) and capture most of the CNVs we simulate using Avesim  ...  Noble, Feng Yue, Jesse Dixon and members of their groups for valuable discussions and Feng Yue's group for sharing their unpublished whole genome sequencing data for the T47D cell line.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/179275">doi:10.1101/179275</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/anvbhqqx2rdfrd2x32svmpbjma">fatcat:anvbhqqx2rdfrd2x32svmpbjma</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503024451/https://www.biorxiv.org/content/biorxiv/early/2017/08/21/179275.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/8d/12/8d12cf222f64eb4d4b68eb555fea1cc407f2166b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/179275"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients [article]

Francisco Requena, Hamza Hadj Abdallah, Alejandro Garcia, Patrick Nitschke, Sergi Romana, Valerie Malan, Antonio Rausell
<span title="2021-03-20">2021</span> <i title="Cold Spring Harbor Laboratory"> medRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Copy Number Variants (CNVs) are an important cause of rare diseases.  ...  CNVxplorer mines a comprehensive set of clinical, genomic, and epigenomic features associated with CNVs.  ...  In addition, features of interest often involve heterogeneous high-dimensional omics data, scattered across multiple databases, often difficult to access and interpret from a clinical perspective.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.03.19.21253806">doi:10.1101/2021.03.19.21253806</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rn4thtowpjc4tep6w5fdwxfv2q">fatcat:rn4thtowpjc4tep6w5fdwxfv2q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715004439/https://www.medrxiv.org/content/medrxiv/early/2021/03/20/2021.03.19.21253806.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/2f/dd/2fdd5e8739fd6df4e9daa5b830429479d94ea6ce.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.03.19.21253806"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> medrxiv.org </button> </a>

Identification of copy number variations and translocations in cancer cells from Hi-C data

Abhijit Chakraborty, Ferhat Ay, Christina Curtis
<span title="2017-10-18">2017</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;
Making the scenario even more complex, cancer cells harbor chromosomal abnormalities (e.g., copy number variations (CNVs) and translocations) altering their genomes both at the sequence level and at the  ...  Our CNV predictions correlate very well with whole genome sequencing (WGS) data among chromosomes with CNV events for a breast cancer cell line (r=0.89) and capture most of the CNVs we simulate using Avesim  ...  Noble, Feng Yue, Jesse Dixon and members of their groups for valuable discussions and Feng Yue's group for sharing their unpublished whole genome sequencing data for the T47D cell line. .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btx664">doi:10.1093/bioinformatics/btx664</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29048467">pmid:29048467</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jzceznyumrfb3j5sgaqfm2vk2i">fatcat:jzceznyumrfb3j5sgaqfm2vk2i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190225143732/http://pdfs.semanticscholar.org/6f98/71faf08ff85af1eeebf6c25e7da29880ed7b.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/6f/98/6f9871faf08ff85af1eeebf6c25e7da29880ed7b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btx664"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>
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