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TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

Yan W. Asmann, Sumit Middha, Asif Hossain, Saurabh Baheti, Ying Li, High-Seng Chai, Zhifu Sun, Patrick H. Duffy, Ahmed A. Hadad, Asha Nair, Xiaoyu Liu, Yuji Zhang (+3 others)
2011 Computer applications in the biosciences : CABIOS  
TREAT (Targeted RE-sequencing Annotation Tool) is a tool for facile navigation and mining of the variants from both targeted resequencing and whole exome sequencing.  ...  It provides a rich integration of publicly available as well as in-house developed annotations and visualizations for variants, variant-hosting genes and host-gene pathways.  ...  We are very grateful for the following investigators at Mayo Clinic who allowed us to use their exome sequencing data for the purpose of developing the work flow: Dr Stephen Thibodeau, Dr Ellen Goode and  ... 
doi:10.1093/bioinformatics/btr612 pmid:22088845 pmcid:PMC3259432 fatcat:mab7jmq7vzgllaqmb7btt4ide4

Targeted exome sequencing of Korean triple-negative breast cancer reveals homozygous deletions associated with poor prognosis of adjuvant chemotherapy-treated patients

Hae Min Jeong, Ryong Nam Kim, Mi Jeong Kwon, Ensel Oh, Jinil Han, Se Kyung Lee, Jong-Sun Choi, Sara Park, Seok Jin Nam, Gyung Yup Gong, Jin Wu Nam, Doo Ho Choi (+4 others)
2017 OncoTarget  
This study analyzed the genetic mutation landscape in 70 patients with triple-negative breast cancer by targeted exome sequencing of tumor and matched normal samples.  ...  Notably, homozygous deletion of three genes, EPHA5, MITF, and ACSL3, was significantly associated with an increased risk of recurrence or distant metastasis in adjuvant chemotherapy-treated patients.  ...  ACKNOWLEDGMENTS We would like to thank the patients who consented to participate in this study. CONFLICTS OF INTEREST The authors declare no competing interests.  ... 
doi:10.18632/oncotarget.18618 pmid:28977883 pmcid:PMC5617443 fatcat:3eqqgjyjszf5rggbuvddcnjlce

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment

Jason Li, Maria A. Doyle, Isaam Saeed, Stephen Q. Wong, Victoria Mar, David L. Goode, Franco Caramia, Ken Doig, Georgina L. Ryland, Ella R. Thompson, Sally M. Hunter, Saman K. Halgamuge (+7 others)
2014 PLoS ONE  
Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging  ...  Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation.  ...  Acknowledgments NeCTAR (Australia's National eResearch Collaboration Tools and Resources) and Yourgene Bioscience, Taiwan, supported the project with cloud expertise, storage and bandwidth.  ... 
doi:10.1371/journal.pone.0095217 pmid:24752294 pmcid:PMC3994043 fatcat:frixxq25jjdjlcfz6ji6wfvn6e

EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics

Sophie Coutant, Chlo� Cabot, Arnaud Lefebvre, Martine L�onard, Elise Prieur-Gaston, Dominique Campion, Thierry Lecroq, H�l�ne Dauchel
2012 BMC Bioinformatics  
Whole exome sequencing (WES) has become the strategy of choice to identify a coding allelic variant for a rare human monogenic disorder.  ...  , molecular types, inheritance mode and multiple samples, (iii) offers the browsing of annotated data and filtered results in various interactive tables, graphical visualizations and statistical charts  ...  The authors thank the LITIS for the host of EVA on one of its server.  ... 
doi:10.1186/1471-2105-13-s14-s9 pmid:23095660 pmcid:PMC3439720 fatcat:b4zgh4j5nrcwvmwbhvgbyh7tra

Informatics for cancer immunotherapy

J Hammerbacher, A Snyder
2017 Annals of Oncology  
Attempts to integrate these data are in early stages of development and are discussed next.  ...  In this review, the use of tumors to gather genetic and expression data will first be explored.  ...  Disclosures Jeff Hammerbacher is the principal investigator on a sponsored research agreement with Neon Therapeutics. Alexandra Snyder is a consultant for Neon Therapeutics.  ... 
doi:10.1093/annonc/mdx682 pmid:29253114 fatcat:l4qhnfixofdsdm7wxeffdhhpga

Reanalysis of Genomic Sequencing Results in a Clinical Laboratory: Advantages and Limitations

Dongju Won, Se Hee Kim, Borahm Kim, Seung-Tae Lee, Hoon-Chul Kang, Jong Rak Choi
2020 Frontiers in Neurology  
Considering the continuous accumulation of data on disease-causing variants, reanalysis of previously established sequencing data is important.  ...  We suggest that reanalysis of genetic variants, mainly using changes in databases and updated interpretations, should be implemented as a routine practice in clinical laboratories.  ...  It may also be attributed to the fact that we performed panel sequencing, not exome sequencing, without changing the previously used bioinformatic tools and without in-depth phenotyping.  ... 
doi:10.3389/fneur.2020.00612 pmid:32695065 pmcid:PMC7338758 fatcat:w5gym5ccvfgzffkwebfcbipd5i

Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing

Riyue Bao, Lei Huang, Jorge Andrade, Wei Tan, Warren A. Kibbe, Hongmei Jiang, Gang Feng
2014 Cancer Informatics  
Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets.  ...  In addition, we briefly discuss the current status and solutions for big data management, analysis, and summarization in the field of bioinformatics. keywords: big data, InDel, next generation sequencing  ...  In this review, we examined bioinformatics software available for whole exome data analysis, including data preprocessing, alignment, post-alignment processing, variant calling, annotation, and prioritization  ... 
doi:10.4137/cin.s13779 pmid:25288881 pmcid:PMC4179624 fatcat:wrlfacy7hzfu7pllgdyifnjphy

A survey of tools for variant analysis of next-generation genome sequencing data

S. Pabinger, A. Dander, M. Fischer, R. Snajder, M. Sperk, M. Efremova, B. Krabichler, M. R. Speicher, J. Zschocke, Z. Trajanoski
2013 Briefings in Bioinformatics  
Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and  ...  We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients  ...  Acknowledgements We thank the reviewers for their numerous constructive suggestions, which helped us to considerably improve the article.  ... 
doi:10.1093/bib/bbs086 pmid:23341494 pmcid:PMC3956068 fatcat:zcunpg3i7bfrvhm5dixp6r6ofq

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment

Khader Shameer, Lokesh P. Tripathi, Krishna R. Kalari, Joel T. Dudley, Ramanathan Sowdhamini
2015 Briefings in Bioinformatics  
In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants.  ...  Accurate assessment of genetic variation in human DNA sequencing studies remains a nontrivial challenge in clinical genomics and genome informatics.  ...  Zimmermann and Jean-Pierre Kocher (Mayo Clinic, Rochester) for useful discussions. The Mayo Clinic Bioinformatics Core provided infrastructure and analytical support to K.R.K.  ... 
doi:10.1093/bib/bbv084 pmid:26494363 pmcid:PMC6078163 fatcat:xeldhpluhjajnnatu44secmb3u

Managing Large-Scale Genomic Datasets and Translation into Clinical Practice

T. Lecroq, L. F. Soualmia
2014 IMIA Yearbook of Medical Informatics  
In the first article, the authors present VEST (Variant Effect Scoring Tool) which is a supervised machine learning tool for prioritizing variants found in exome sequencing projects that are more likely  ...  Indeed, there is a need for powerful tools for managing and interpreting complex data, but also a need for user-friendly tools developed for the clinicians in their daily practice.  ...  Acknowledgements We would like to acknowledge the valuable support of Martina Hutter and all the reviewers in the evaluation process of the section Bioinformatics and Translational Informatics of the IMIA  ... 
doi:10.15265/iy-2014-0039 pmid:25123745 pmcid:PMC4287066 fatcat:632h5quyizbntoavtpxk34bgni

High throughput sequencing approaches to mutation discovery in the mouse

Michelle M. Simon, Ann-Marie Mallon, Gareth R. Howell, Laura G. Reinholdt
2012 Mammalian Genome  
However, successful application of HTS for mutation discovery is relies heavily on the sequencing approach employed and strategies for data analysis.  ...  Here, we review current HTS applications and resources for mutation discovery and provide an overview of the practical considerations for HTS implementation and data analysis.  ...  For manual annotation, all of the data required for variant annotation are freely available from public genome browsers like UCSC Genome Bioinformatics and Ensembl in file formats that can be directly  ... 
doi:10.1007/s00335-012-9424-0 pmid:22991087 pmcid:PMC3724459 fatcat:inqn5j3g6bcvhgbwtj7lrmirse

Informatics for Cancer Immunotherapy [article]

Jeff Hammerbacher, Alexandra Snyder Charen
2017 bioRxiv   pre-print
Attempts to integrate these data are in early stages of development and are discussed next.  ...  In this review, the use of tumors to gather genetic and expression data will first be explored.  ...  Disclosures Jeff Hammerbacher is the principal investigator on a sponsored research agreement with Neon Therapeutics. Alexandra Snyder is a consultant for Neon Therapeutics.  ... 
doi:10.1101/152264 fatcat:w2mj5gwlybek7fg22v24j6dcde

VAReporter: variant reporter for cancer research of massive parallel sequencing

Po-Jung Huang, Chi-Ching Lee, Ling-Ya Chiu, Kuo-Yang Huang, Yuan-Ming Yeh, Chia-Yu Yang, Cheng-Hsun Chiu, Petrus Tang
2018 BMC Genomics  
In particular, disease-oriented targeted enrichment sequencing is becoming a widely-accepted application for diagnostic purposes, which can interrogate known diagnostic variants as well as identify novel  ...  Results: We introduce a workflow named VAReporter to facilitate the management of variant assessment in disease-targeted sequencing, the identification of pathogenic variants, the interpretation of biological  ...  Bertrand Tan (Department of Biomedical Sciences, Chang Gung University) for his critical review of this manuscript.  ... 
doi:10.1186/s12864-018-4468-5 pmid:29764369 pmcid:PMC5954270 fatcat:zy37a5ptjffcjjprxrgovbvjja

Treatment strategy for papillary renal cell carcinoma type 2: a case series of seven patients treated based on next generation sequencing data

Ji-Yeon Kim, Hyoung-Oh Jeong, Dae Seog Heo, Bhumsuk Keam, Kyung Chul Moon, Cheol Kwak, Jinho Jang, Seunghoon Kim, Jong-Il Kim, Semin Lee, Se-Hoon Lee
2020 Annals of Translational Medicine  
Genome sequencing could help identify candidates for targeted therapy in PRCC2, a genetically heterogeneous disease.  ...  In this study, we aimed to perform precision treatment of PRCC2 based on genetic information. We performed exome and genome sequencing of tumor tissues and matched normal samples.  ...  Both germline and somatic variants were annotated using Variant Effect Predictor (version 92) (24) , and only the protein-altering variants were used for subsequent analyses (  ... 
doi:10.21037/atm-20-3466 pmid:33313134 pmcid:PMC7723617 fatcat:nzonxq7itfb2xevpwe7eromh7y

Challenges imposed by minor reference alleles on the identification and reporting of clinical variants from exome data

Mahmoud Koko, Mohammed O. E. Abdallah, Mutaz Amin, Muntaser Ibrahim
2018 BMC Genomics  
The conventional variant calling of pathogenic alleles in exome and genome sequencing requires the presence of the non-pathogenic alleles as genome references.  ...  We highlighted how the current variant calling standards miss homozygous reference disease variants in these sites and provided a bioinformatic panel that can be used to screen these variants using commonly  ...  Acknowledgements A preprint of this article was reviewed anonymously in Peerage of Science.  ... 
doi:10.1186/s12864-018-4433-3 pmid:29334895 pmcid:PMC5769444 fatcat:2oa5hhp6tzgijdjmujlbymzjia
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