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CRAVAT: cancer-related analysis of variants toolkit

Christopher Douville, Hannah Carter, Rick Kim, Noushin Niknafs, Mark Diekhans, Peter D. Stenson, David N. Cooper, Michael Ryan, Rachel Karchin
2013 Computer applications in the biosciences : CABIOS  
Here, we provide a web-based application, Cancer-Related Analysis of Variants Toolkit, designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and  ...  Cancer-Related Analysis of Variants Toolkit provides predictive scores for germline variants, somatic mutations and relative gene importance, as well as annotations from published literature and databases  ...  Funding: National Institutes of Health CA 152432, National Science Foundation DBI 0845275. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btt017 pmid:23325621 pmcid:PMC3582272 fatcat:y4ap346htfcofjlh6k7ghbczfi

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit [article]

David Masica, Christopher Douville, Collin Tokheim, Rohit Bhattacharya, RyangGuk Kim, Kyle Moad, Michael C. Ryan, Rachel Karchin
2017 bioRxiv   pre-print
The Cancer-Related Analysis of Variants Toolkit (CRAVAT) is an evolving suite of informatics tools for mutation interpretation that includes mutation projecting and quality control, impact prediction and  ...  CRAVAT can be run on a public web-portal, in the cloud, or downloaded for local use, and is easily integrated with other methods for cancer omics analysis.  ...  Figure 1B shows selected displays from the CRAVAT Gene and Variant tabs.  ... 
doi:10.1101/162859 fatcat:5byjwmonhzg4llx4zbd6m4tvym

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit

David L. Masica, Christopher Douville, Collin Tokheim, Rohit Bhattacharya, RyangGuk Kim, Kyle Moad, Michael C. Ryan, Rachel Karchin
2017 Cancer Research  
The Cancer-Related Analysis of Variants Toolkit (CRA-VAT) is an evolving suite of informatics tools for mutation interpretation that includes mutation mapping and quality control, impact prediction and  ...  CRAVAT can be run on a public web portal, in the cloud, or downloaded for local use, and is easily integrated with other methods for cancer omics analysis. Cancer Res; 77(21); e35-38. Ó2017 AACR.  ...  The Cancer-Related Analysis of Variants Toolkit (CRAVAT; ref. 1) is designed to streamline the many steps outlined above, quickly returning mutation interpretations in an interactive and user-friendly  ... 
doi:10.1158/0008-5472.can-17-0338 pmid:29092935 fatcat:swpkwe2ywrbwzhpqa3r6zt4osa

Integrated Informatics Analysis of Cancer-Related Variants

Kymberleigh A. Pagel, Rick Kim, Kyle Moad, Ben Busby, Lily Zheng, Collin Tokheim, Michael Ryan, Rachel Karchin
2020 JCO Clinical Cancer Informatics  
METHODS We present the Open Custom Ranked Analysis of Variants Toolkit 1 (OpenCRAVAT) a new open-source, scalable decision support system for variant and gene prioritization.  ...  Resources made available via the store are well suited for analysis of cancer, as well as Mendelian and complex diseases.  ...  [5] [6] [7] One such Web-based DSF is the Cancer-Related Analysis of Variants Toolkit 8 (CRAVAT), which prioritizes somatic mutations. 9 In this work, we present OpenCRAVAT, an extension of CRAVAT  ... 
doi:10.1200/cci.19.00132 pmid:32228266 pmcid:PMC7113103 fatcat:ry3vfrlmxjhshavakixtrwbrfm

Identification of Somatic Genetic Alterations Using Whole-Exome Sequencing of Uterine Leiomyosarcoma Tumors

Lihua Chen, Jiajia Li, Xiaohua Wu, Zhong Zheng
2021 Frontiers in Oncology  
Analysis of somatic copy number variants (CNVs) showed regions of chromosomal gain at 1q21-23, 19p13, 17q21, and 17q25, whereas regions of chromosomal loss were observed at 2q35, 2q37, 1p36, 10q26, 6p22  ...  Amplification of the SHARPIN gene was associated with shorter PFS and OS in soft tissue sarcoma, as shown by TCGA database analysis.  ...  by using the Cancer-Related Analysis of Variants Toolkit (CRAVAT) for genomic variant interpretation.  ... 
doi:10.3389/fonc.2021.687899 pmid:34178683 pmcid:PMC8226214 fatcat:knnph6jhz5apfjja6o2i2qrx3y

Comprehensive Analysis of MEN1 Mutations and Their Role in Cancer

Devi D. Nelakurti, Amrit L. Pappula, Swetha Rajasekaran, Wayne O. Miles, Ruben C. Petreaca
2020 Cancers  
In this study, we cataloged the reported germline mutations from the ClinVar database and compared them with the somatic mutations detected in cancers from the Catalogue of Somatic Mutations in Cancer  ...  Many of these inherited mutations are associated with a number of pathogenic syndromes of the parathyroid and pancreas, and some also predispose patients to hyperplasia.  ...  Conflicts of Interest: All authors declare no conflict of interest.  ... 
doi:10.3390/cancers12092616 pmid:32937789 fatcat:xylcu5qmnbbjtful373nbfehxm

A Genome-Wide Profiling of Glioma Patients with an IDH1 Mutation Using the Catalogue of Somatic Mutations in Cancer Database

Amrit L. Pappula, Shayaan Rasheed, Golrokh Mirzaei, Ruben C. Petreaca, Renee A. Bouley
2021 Cancers  
The majority of the mutations observed in these genes were further confirmed to be either drivers or pathogenic by the Cancer-Related Analysis of Variants Toolkit (CRAVAT).  ...  Gene expression analysis showed down-regulation of DRG2 and MSN expression, both of which promote cell proliferation and invasion.  ...  Acknowledgments: The authors thank James and Ellen Bazzoli and Nucor Steel, Marion Inc. for their generous donations to sponsor the laboratories of R.C.P. and R.A.B., respectively.  ... 
doi:10.3390/cancers13174299 pmid:34503108 pmcid:PMC8428353 fatcat:fyjutqy6ljb2zcvrv2vdf7fiiy

Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach

Ioannis Karageorgos, Clint Mizzi, Efstathia Giannopoulou, Cristiana Pavlidis, Brock A. Peters, Zoi Zagoriti, Peter D. Stenson, Konstantinos Mitropoulos, Joseph Borg, Haralabos P. Kalofonos, Radoje Drmanac, Andrew Stubbs (+4 others)
2015 Human Genomics  
Subsequent analysis, focused on the latter variant class most likely to be involved in cancer predisposition, revealed two variants of prime interest, namely MSH2 c.2732T>A (p.L911R) and BRCA1 c.2955delC  ...  A considerable number of genomic variants have been previously reported to be causative of, or associated with, an increased risk for various types of cancer.  ...  Acknowledgements This study was funded by the European Commission (RD-CONNECT; FP7-304555) research grant to GPP and endorsed by the Genomic Medicine Alliance Cancer Genomics Working Group.  ... 
doi:10.1186/s40246-015-0034-2 pmid:26092435 pmcid:PMC4499216 fatcat:ubiz5qsq55b6jgtk5uj56fumrm

OpenCRAVAT, an open source collaborative platform for the annotation of human genetic variation [article]

Kymberleigh A Pagel, Rick Kim, Kyle Moad, Ben Busby, Lily Zheng, Matthew Hynes-Grace, Collin Tokheim, Michael Ryan, Rachel Karchin
2019 bioRxiv   pre-print
Resources made available via the store are well-suited for analysis of cancer, as well as Mendelian and complex diseases.  ...  There are databases of genes and variants, phenotype-genotype relationships, algorithms that score and rank genes, and in silico variant effect prediction tools.  ...  The Open Custom Ranked Analysis of Variants Toolkit (OpenCRAVAT) is a freely available open source framework for the annotation and visualization of human genetic variation and genomic elements.  ... 
doi:10.1101/794297 fatcat:yfnu3jvmxvd3rjeren5esolt44

Comprehensive Genetic Analysis of DGAT2 Mutations and Gene Expression Patterns in Human Cancers

Meghan Graber, Hayley Barta, Ryan Wood, Amrit Pappula, Martin Vo, Ruben C. Petreaca, Wilber Escorcia
2021 Biology  
Using the Variant Effect Scoring Tool (VEST), we identify multiple mutations with a high likelihood of contributing to cellular transformation.  ...  Using data from the Catalogue of Somatic Mutations in Cancer (COSMIC), we analyzed all cancer genetic DGAT2 alterations, including mutations, copy number variations and gene expression.  ...  The Cancer-Related Analysis of Variants Toolkit (CRAVAT) software was employed to determine the likelihood of mutations being drivers or passengers and was used as previously described [22, 23] .  ... 
doi:10.3390/biology10080714 fatcat:fo7scfktrfds7ez6qcxwdd2hia

Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization [chapter]

Osman Ugur Sezerman, Ege Ulgen, Nogayhan Seymen, Ilknur Melis Durasi
2019 Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations [Working Title]  
Finally, approaches and current guidelines for clinical interpretation of genomic variants are discussed.  ...  Best practices of reads-to-variant discovery workflows for germline and somatic short genomic variants are presented along with the most commonly utilized tools for each step.  ...  Two popular examples are Oncotator [68] and CRAVAT [69] . Oncotator, a widely used cancer-specific annotation tool, is often preferred for the annotation of somatic short variants.  ... 
doi:10.5772/intechopen.85524 fatcat:yaasb4tk3rgebhmmu26qkd5d4u

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

Feixiong Cheng, Junfei Zhao, Zhongming Zhao
2015 Briefings in Bioinformatics  
Cancer is often driven by the accumulation of genetic alterations, including single nucleotide variants, small insertions or deletions, gene fusions, copy-number variations, and large chromosomal rearrangements  ...  So far, the somatic mutation landscapes and signatures of >10 major cancer types have been reported; however, pinpointing driver mutations and cancer genes from millions of available cancer somatic mutations  ...  We apologize that we cannot include and cite all related studies owing to the limited space of manuscript space.  ... 
doi:10.1093/bib/bbv068 pmid:26307061 pmcid:PMC4945827 fatcat:kjvqingypzertd7gppopjjzb7e

Mutational screening through comprehensive bioinformatics analysis to detect novel germline mutations in the APC gene in patients with familial adenomatous polyposis (FAP)

Faranak Ghadamyari, Mohammad Mehdi Heidari, Sirous Zeinali, Mehri Khatami, Shahin Merat, Hamideh Bagherian, Leili Rejali, Farzaneh Ghasemi
2021 Journal of clinical laboratory analysis (Print)  
Familial adenomatous polyposis (FAP) as a colon cancer predisposition syndrome is an autosomal-dominant inherited condition and is diagnosed by the progress of hundreds or thousands of adenomatous colonic  ...  Bioinformatics analysis and three-dimensional structural modeling predicted that these missense and nonsense mutations generally are associated with the deleted or truncated domains of APC and have functional  ...  Abbreviations: CRAVAT, Cancer-Related Analysis of Variants Toolkit; VEST, Variant Effect Scoring Tool.  ... 
doi:10.1002/jcla.23768 pmid:33769591 pmcid:PMC8128300 fatcat:7vufosrns5fsxfmqmhb7jiyyk4

Computational approaches to identify functional genetic variants in cancer genomes

2013 Nature Methods  
techniques to annotate somatic variants and predict their impact on cancer phenotype.  ...  Large-scale sequencing of cancer genomes often reveals many thousands of somatic missense (amino acid-changing) mutations in proteins.  ...  For instance the Cancer-Related Analysis of Variants Toolkit (CRAVAT) 57 maps mutations to their consequences on protein-coding genes and it predicts their implication in cancer and disease using Cancer-specific  ... 
doi:10.1038/nmeth.2562 pmid:23900255 pmcid:PMC3919555 fatcat:6v3wgyr36jgibnqc3y2isl4cjq

Multi-Omics Characterization of the Spontaneous Mesenchymal–Epithelial Transition in the PMC42 Breast Cancer Cell Lines

Sugandha Bhatia, James Monkman, Tony Blick, Pascal HG Duijf, Shivashankar H. Nagaraj, Erik W. Thompson
2019 Journal of Clinical Medicine  
Thus, integrative 'omics' characterization established that the PMC42 system is a relevant MET model and provides insights into the regulation of phenotypic plasticity in breast cancer.  ...  We investigated chromosomal heterogeneity and chromosomal instability (CIN) profiles of two sister PMC42 breast cancer (BC) cell lines to assess the relationship between their karyotypes and EMP phenotypic  ...  Conflicts of Interest: The authors declare they have no competing financial interests in relation to the work described.  ... 
doi:10.3390/jcm8081253 pmid:31430931 pmcid:PMC6723942 fatcat:d5fgwlisfbhxbhscq5kbbnbnfm
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