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GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

Umadevi Paila, Brad A. Chapman, Rory Kirchner, Aaron R. Quinlan, Paul P. Gardner
2013 PLoS Computational Biology  
Unlike existing tools, GEMINI integrates genetic variation with a diverse and flexible set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation  ...  We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation.  ...  Acknowledgments We are grateful for insightful comments and suggestions from Oliver Hofmann and Ryan Layer. Author Contributions Conceived and designed the experiments: ARQ.  ... 
doi:10.1371/journal.pcbi.1003153 pmid:23874191 pmcid:PMC3715403 fatcat:lae4evkav5c4ren6y7cttlekye

VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants

Eric Ho, Qin Cao, Sau Lee, Kevin Y Yip
2014 BMC Genomics  
To help explore the potential biological implications of these genetic variants, software tools have been previously developed for integrating various types of information about these genomic regions from  ...  Results: To make exploration of whole lists of genetic variants simple and accessible, we have developed a new Web-based system called VAS (Variant Annotation System, available at https://yiplab.cse.cuhk.edu.hk  ...  [4], GC content Annotation Gencode [17] Variations dbSNP [30] Table 2 2 Data integration time of different methods.  ... 
doi:10.1186/1471-2164-15-886 pmid:25306238 pmcid:PMC4210471 fatcat:wflio4bi6nhdpnfwu7aqxeycle

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]  
Additionally, methods for detecting structural variations are overviewed. Finally, approaches and current guidelines for clinical interpretation of genomic variants are discussed.  ...  Next-generation sequencing (NGS) techniques allow high-throughput detection of a vast amount of variations in a cost-efficient manner.  ...  GEMINI: Integrative detecting biologically important single exploration of genetic variation and nucleotide mutations in cancer. genome annotations.  ... 
doi:10.5772/intechopen.85524 fatcat:yaasb4tk3rgebhmmu26qkd5d4u

Seave: a comprehensive web platform for storing and interrogating human genomic variation

Velimir Gayevskiy, Tony Roscioli, Marcel E Dinger, Mark J Cowley, Jonathan Wren
2018 Bioinformatics  
Genome sequencing has had a remarkable impact on our ability to study the effects of human genetic variation, however, variant interpretation remains the major bottleneck.  ...  Understanding the potential impact of variants, including structural variants, requires extensive annotation from disparate sources of knowledge, and in silico prediction algorithms.  ...  genetic variation.  ... 
doi:10.1093/bioinformatics/bty540 pmid:30561546 pmcid:PMC6298057 fatcat:3morrngacrhlpl3ql2h4n3n7am

OncoGEMINI: Software for Investigating Tumor Variants From Multiple Biopsies With Integrated Cancer Annotations [article]

Thomas J. Nicholas, Michael J. Cormier, Xiaomeng Huang, Yi Qiao, Gabor T. Marth, Aaron R. Quinlan
2020 bioRxiv   pre-print
Here we describe OncoGEMINI, a new tool designed for exploring the complex patterns and trajectory of somatic and inherited variation observed in heterogeneous tumors biopsied over the course of treatment  ...  Additionally, by incorporating existing annotations and resources that facilitate the interpretation of cancer mutations (e.g., CIViC, DGIdb), OncoGEMINI enables rapid searches for, and potential identification  ...  Recognizing this need, we introduce OncoGEMINI as new software to explore genetic variation observed across multiple tumor biopsies and facilitate the identification of both inherited and somatic mutations  ... 
doi:10.1101/2020.03.10.979591 fatcat:y33cv4gdmjagbnm5hx4l5jszs4

Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale

Alex V. Kotlar, Cristina E. Trevino, Michael E. Zwick, David J. Cutler, Thomas S. Wingo
2018 Genome Biology  
It is the first program capable of handling 58 sequencing experiments on the scale of thousands of whole-genome samples and tens of 59 millions of variants online in a web browser, and integrates the first  ...  Genetic disease studies require thousands of samples to obtain 40 adequate power, and the resulting WGS datasets are hundreds of gigabytes in size and contain 41 tens of millions of variants.  ...  Acknowledgements 550 We thank Kelly Shaw and Katherine Squires for beta testing and design suggestions. We thank 551 Viren Patel and the Emory Integrated Genomics Core (EIGC) for technical support.  ... 
doi:10.1186/s13059-018-1387-3 pmid:29409527 pmcid:PMC5801807 fatcat:qv2f4sassrfknohlavfp5g4tyi

Seave: a comprehensive web platform for storing and interrogating human genomic variation [article]

Velimir Gayevskiy, Tony Roscioli, Marcel E Dinger, Mark J Cowley
2018 bioRxiv   pre-print
Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists.  ...  Capability for genome sequencing and variant calling has increased dramatically, enabling large scale genomic interrogation of human disease.  ...  between diseases and genetic variation.  ... 
doi:10.1101/258061 fatcat:tdh6hdykwfgyngvwst3cpzwmy4

Cutevariant: a GUI-based desktop application to explore genetics variations [article]

Sacha Schutz, Tristan Montier, Emmanuelle Genin
2021 bioRxiv   pre-print
Cutevariant is a user-friendly GUI based desktop application for genomic research designed to search for variations in DNA samples collected in annotated files and encoded in the Variant Calling Format  ...  Cutevariant is distributed as a multiplatform client-side software under an opensource licence and is available at https://github.com/labsquare/Cutevariant.  ...  Conflict of Interest: none declared  ... 
doi:10.1101/2021.02.10.430619 fatcat:z34k6ssvk5hbzby7naovif6pk4

Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale [article]

Alex V. Kotlar, Cristina E. Trevino, Michael E. Zwick, David J. Cutler, Thomas S. Wingo
2017 bioRxiv   pre-print
Critically, Bystro's annotation and filtering capabilities are orders of magnitude faster than previous solutions, saving weeks of processing time for large experiments.  ...  Bystro (https://bystro.io/) is the first online, cloud-based application that makes variant annotation and filtering accessible to all researchers for terabyte-sized whole-genome experiments containing  ...  Acknowledgements We thank Kelly Shaw and Katherine Squires for beta testing and design suggestions. We thank Viren Patel and the Emory Integrated Genomics Core (EIGC) for technical support.  ... 
doi:10.1101/146514 fatcat:p7buiiogtzexlefkjpbstxfqya

OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations

Thomas J. Nicholas, Michael J. Cormier, Xiaomeng Huang, Yi Qiao, Gabor T. Marth, Aaron R. Quinlan
2021 Genome Medicine  
Results Here, we describe OncoGEMINI, a new tool designed for exploring the complex patterns and trajectory of somatic and inherited variation observed in heterogeneous tumors biopsied over the course  ...  Conclusions By combining relevant genomic annotations alongside specific filtering tools, OncoGEMINI provides powerful and customizable approaches that enable the quick identification of individual tumor  ...  The authors also acknowledge all those that contributed to the GEMINI tool and other accompanying tools from which OncoGEMINI was developed.  ... 
doi:10.1186/s13073-021-00854-6 pmid:33771218 pmcid:PMC7995589 fatcat:hqqdxgpqlncv7mrsodrdc7aynq

Diverse Monogenic Subforms of Human Spermatogenic Failure [article]

Liina Nagirnaja, Alexandra Lopes, Wu-Lin Charng, Brian Miller, Rytis Stakaitis, Ieva Golubickaite, Alexandra Stendahl, Tianpengcheng Luan, Corinna Friedrich, Eisa Mahyari, Eloise Faidal, Laura Kasak (+37 others)
2022 medRxiv   pre-print
Due to the biological complexity of sperm production, defining the genetic basis of NOA has proven challenging, and to date, the most advanced classification of NOA subforms is based on simple description  ...  Our findings highlight NOA as an understudied Mendelian disorder and provide a conceptual structure for organizing the complex genetics of male infertility, which may serve as a basis for disease classification  ...  Acknowledgements We thank all of the study participants and the numerous medical staff that enabled this study.  ... 
doi:10.1101/2022.07.19.22271581 fatcat:ayxbnf7kcbf33muscwlkdfq62i

Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities [article]

Caitlin A. Nichols, William J. Gibson, Meredith S. Brown, Jack A. Kosmicki, John P. Busanovich, Hope Wei, Laura M. Urbanski, Naomi Curimjee, Ashton C. Berger, Galen F. Gao, Andrew D. Cherniack, Sirano Dhe-Paganon (+2 others)
2019 bioRxiv   pre-print
Hundreds to thousands of non-driver genes undergo loss of heterozygosity (LOH) events per tumor, generating discrete differences between tumor and normal cells.  ...  We further show that allele-specific inactivation of either of two essential genes (PRIM1 and EXOSC8) reduces growth of cells harboring that allele, while cells harboring the non-targeted allele remain  ...  While individual GEMINI genes have been described previously 4 , our work integrated genome-wide assessments of gene essentiality, genetic variation, and LOH to generate the first systematic analysis of  ... 
doi:10.1101/534529 fatcat:7ic3y7ocsfgw3gc2jutiov5qze

Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering

Mehul Jani, Kalai Mathee, Rajeev K. Azad
2016 Frontiers in Microbiology  
Zisland Explorer This new tool scans a genome for "leaps" in cumulative GC profile; these atypical regions are annotated GIs (Wei et al., 2016) .  ...  Compositional atypicality, genetic instability, presence of integration host factor beta subunit and a flanking tRNA-Asn gene indicate the likely horizontal acquisition of this island.  ...  Copyright © 2016 Jani, Mathee and Azad. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).  ... 
doi:10.3389/fmicb.2016.01210 pmid:27536294 pmcid:PMC4971588 fatcat:jvn3xgloynb2tepeit3hbrrg3u

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

Girum Fitihamlak Ejigu, Jaehee Jung
2020 Biology  
This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders.  ...  Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation.  ...  GEMINI [104] is a framework that allows exploring all forms of human genetic variation. GEMINI integrates genetic variation with diverse genome annotation from databases such as dbSNP and KEGG.  ... 
doi:10.3390/biology9090295 pmid:32962098 pmcid:PMC7565776 fatcat:gdaxbwygqnaapiqisyf56ajpea

Integrating Evolutionary Genetics to Medical Genomics: Evolutionary Approaches to Investigate Disease-Causing Variants [chapter]

Ugur Sezerman, Tugce Bozkurt, Fatma Sadife Isleyen
2020 Molecular Medicine [Working Title]  
Finally, we present an example of a real-life case where the use of evolutionary genetics information facilitated the discovery of disease-causing variants in medical genomics.  ...  In recent years, next-generation sequencing (NGS) platforms that facilitate generation of a vast amount of genomic variation data have become widely used for diagnostic purposes in medicine.  ...  This chapter aims to contribute to the integration of evolutionary genetics to medical genomics.  ... 
doi:10.5772/intechopen.92738 fatcat:gy7xau3ulvcvvg3uvhvg6yc2we
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