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SCA-LSVD: A Repeat-Oriented Locus-Specific variation database for Genotype to Phenotype Correlations in Spinocerebellar Ataxias

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HUMAN MUTATION 2009年第7期30卷 1037-1042页

作者： Faruq, Mohammed Scaria, Vinod Singh, Inder Tyagi, Shivani Srivastava, Achal K. Mukerji, Mitali CSIR IGIB GN Ramachandran Knowledge Ctr Genome Informat Delhi 110007 India All India Inst Med Sci Ctr Neurosci New Delhi India

Repeat expansion has been implicated in 10 out of 17 candidate genes identified for autosomal dominant cerebellar ataxias (ADCAs)-commonly referred as spinocerebellar ataxias (SCAs). Though genetically distinct, the SCAs share a large number of features that confound their clinical classification. In addition, there is a difference in the prevalence and phenotypic expression of ataxias between different ethnic groups. We have created a new SCA-locus-specific variation database (LSVD) that aims to catalog and integrate information on SCAs associated with trinucleotide repeat expansion (SCA 1, SCA 2, SCA 3, SCA 6, SCA 7, SCA 8, SCA 12, SCA 17, Friedreich's ataxia [FRDA], and dentatorubral-pallidoluysian atrophy [DRPLA]) from all over the world. The database has been developed using the Leiden Open (source) variation database (LOVD) software (Leiden University Medical Center, Leiden, the Netherlands). The database houses detailed information on clinical features, such as age and symptom at onset, mode of inheritance, and genotype information, pertaining to the SCA patients from more than 400 families across India. All the compiled genotype data conforms to the HGVS Nomenclature guidelines. This would be a very useful starting point for understanding the molecular correlates of phenotypes in ataxia-a multilocus disease in which related molecular mechanisms converge to overlapping phenotypes. The database is accessible online at http://***/ataxia. Hum Mutat 30:1037-1042, 2009. (C) 2009 Wiley-Liss, Inc.

关键词： SCA-LSVD variation database trinucleotide repeats ataxia

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A database and API for variation, dense genotyping and resequencing data

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BMC BIOINFORMATICS 2010年第1期11卷 1-10页

作者： Rios, Daniel McLaren, William M. Chen, Yuan Birney, Ewan Stabenau, Arne Flicek, Paul Cunningham, Fiona European Bioinformat Inst Cambridge CB10 1SD England

Background: Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and manipulation of such data necessitating the redesign of existing genome-wide bioinformatics resources. Results: Ensembl has created a database and software library to support data storage, analysis and access to the existing and emerging variation data from large mammalian and vertebrate genomes. These tools scale to thousands of individual genome sequences and are integrated into the Ensembl infrastructure for genome annotation and visualisation. The database and software system is easily expanded to integrate both public and non-public data sources in the context of an Ensembl software installation and is already being used outside of the Ensembl project in a number of database and application environments. Conclusions: Ensembl's powerful, flexible and open source infrastructure for the management of variation, genotyping and resequencing data is freely available at http://***.

关键词： variation Data Application Program Interface UCSC Genome Browser variation Object variation database

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VariVis: a visualisation toolkit for variation databases

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BMC BIOINFORMATICS 2008年第1期9卷 1-5页

作者： Smith, Timothy D. Cotton, Richard G. H. Genom Disorders Res Ctr Carlton Vic 3053 Australia Univ Melbourne Dept Med Melbourne Vic 3010 Australia

Background: With the completion of the Human Genome Project and recent advancements in mutation detection technologies, the volume of data available on genetic variations has risen considerably. These data are stored in online variation databases and provide important clues to the cause of diseases and potential side effects or resistance to drugs. However, the data presentation techniques employed by most of these databases make them difficult to use and understand. Results: Here we present a visualisation toolkit that can be employed by online variation databases to generate graphical models of gene sequence with corresponding variations and their consequences. The VariVis software package can run on any web server capable of executing Perl CGI scripts and can interface with numerous database Management Systems and "flat-file" data files. VariVis produces two easily understandable graphical depictions of any gene sequence and matches these with variant data. While developed with the goal of improving the utility of human variation databases, the VariVis package can be used in any variation database to enhance utilisation of, and access to, critical information.

关键词： Visualisation Tool database Curator variation database Human Genome variation Society Visualisation Toolkit

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A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders

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BMC GENOMICS 2014年第3-Sup期15卷 1-7页

作者： Mutarelli, Margherita Marwah, Veer Singh Rispoli, Rossella Carrella, Diego Dharmalingam, Gopuraja Oliva, Gennaro di Bernardo, Diego Telethon Inst Genet & Med I-80131 Naples Italy Fdn Biol Med I-80131 Naples Italy CNR Inst High Performance Comp & Networking I-80131 Naples Italy Univ Naples Federico II Dept Elect Engn & Informat Technol I-80125 Naples Italy

Background: Mendelian disorders are mostly caused by single mutations in the DNA sequence of a gene, leading to a phenotype with pathologic consequences. Whole Exome Sequencing of patients can be a cost-effective alternative to standard genetic screenings to find causative mutations of genetic diseases, especially when the number of cases is limited. Analyzing exome sequencing data requires specific expertise, high computational resources and a reference variant database to identify pathogenic variants. Results: We developed a database of variations collected from patients with Mendelian disorders, which is automatically populated thanks to an associated exome-sequencing pipeline. The pipeline is able to automatically identify, annotate and store insertions, deletions and mutations in the database. The resource is freely available online http://***. The exome sequencing pipeline automates the analysis workflow (quality control and read trimming, mapping on reference genome, post-alignment processing, variation calling and annotation) using state-of-the-art software tools. The exome-sequencing pipeline has been designed to run on a computing cluster in order to analyse several samples simultaneously. The detected variants are annotated by the pipeline not only with the standard variant annotations (e. g. allele frequency in the general population, the predicted effect on gene product activity, etc.) but, more importantly, with allele frequencies across samples progressively collected in the database itself, stratified by Mendelian disorder. Conclusions: We aim at providing a resource for the genetic disease community to automatically analyse whole exome-sequencing samples with a standard and uniform analysis pipeline, thus collecting variant allele frequencies by disorder. This resource may become a valuable tool to help dissecting the genotype underlying the disease phenotype through an improved selection of putative patient-specific causative or phenotyp

关键词： Exome Sequencing Causative Mutation Analysis Pipeline Whole Exome Sequencing variation database

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HUMA: A platform for the analysis of genetic variation in humans

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HUMAN MUTATION 2018年第1期39卷 40-51页

作者： Brown, David K. Bishop, Ozlem Tastan Rhodes Univ Res Unit Bioinformat RUBi Dept Biochem & Microbiol ZA-6140 Grahamstown South Africa

The completion of the human genome project at the beginning of the 21st century, along with the rapid advancement of sequencing technologies thereafter, has resulted in exponential growth of biological data. In genetics, this has given rise to numerous variation databases, created to store and annotate the ever-expanding dataset of known mutations. Usually, these databases focus on variation at the sequence level. Few databases focus on the analysis of variation at the 3D level, that is, mapping, visualizing, and determining the effects of variation in protein structures. Additionally, these Web servers seldom incorporate tools to help analyze these data. Here, we present the Human Mutation Analysis (HUMA) Web server and database. HUMA integrates sequence, structure, variation, and disease data into a single, connected database. A user-friendly interface provides click-based data access and visualization, whereas a RESTful Web API provides programmatic access to the data. Tools have been integrated into HUMA to allow initial analyses to be carried out on the server. Furthermore, users can upload their private variation datasets, which are automatically mapped to public data and can be analyzed using the integrated tools. HUMA is freely accessible at .

关键词： downstream variant analysis HUMA protein variants structural bioinformatics SNP variation database

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Establishment of an international database for genetic variants in esophageal cancer

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13TH OESO WORLD CONFERENCE: THE ESOPHAGIOME II 2016年第1期1381卷 45-49页

作者： Vihinen, Mauno Lund Univ Dept Expt Med Sci Prot Struct & Bioinformat Grp BMC B13 SE-22184 Lund Sweden

The establishment of a database has been suggested in order to collect, organize, and distribute genetic information about esophageal cancer. The World Organization for Specialized Studies on Diseases of the Esophagus and the Human Variome Project will be in charge of a central database of information about esophageal cancer-related variations from publications, databases, and laboratories;in addition to genetic details, clinical parameters will also be included. The aim will be to get all the central players in research, clinical, and commercial laboratories to contribute. The database will follow established recommendations and guidelines. The database will require a team of dedicated curators with different backgrounds. Numerous layers of systematics will be applied to facilitate computational analyses. The data items will be extensively integrated with other information sources. The database will be distributed as open access to ensure exchange of the data with other databases. variations will be reported in relation to reference sequences on three levels-DNA, RNA, and protein-whenever applicable. In the first phase, the database will concentrate on genetic variations including both somatic and germline variations for susceptibility genes. Additional types of information can be integrated at a later stage.

关键词： esophageal cancer variation database mutation database disease-causing variations mutation data integration OESO the Human Variome Project

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Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline

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BMC BIOINFORMATICS 2013年第1期14卷 1-6页

作者： Khodabakhshi, Alireza Hadj Fejes, Anthony P. Birol, Inanc Jones, Steven J. M. BC Canc Agcy Genome Sci Ctr Vancouver BC V5Z 4S6 Canada

Background: In the past decade, bioinformatics tools have matured enough to reliably perform sophisticated primary data analysis on Next Generation Sequencing (NGS) data, such as mapping, assemblies and variant calling, however, there is still a dire need for improvements in the higher level analysis such as NGS data organization, analysis of mutation patterns and Genome Wide Association Studies (GWAS). Results: We present a high throughput pipeline for identifying cancer mutation targets, capable of processing billions of variations across thousands of samples. This pipeline is coupled with our Human variation database to provide more complex down stream analysis on the variations hosted in the database. Most notably, these analysis include finding significantly mutated regions across multiple genomes and regions with mutational preferences within certain types of cancers. The results of the analysis is presented in HTML summary reports that incorporate gene annotations from various resources for the reported regions. Conclusion: MuteProc is available for download through the Vancouver Short Read Analysis Package on Sourceforge: http://***. Instructions for use and a tutorial are provided on the accompanying wiki pages at https://***/apps/mediawiki/vancouvershortr/***?title=Pipeli ne_introduction.

关键词： Next Generation Sequencing Application Programming Interface Annotation database Next Generation Sequencing Data variation database

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Human variome project - current overview

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Molecular cytogenetics 2014年第Suppl 1 Proceedings of the International Conference on Human期7卷 I1页

作者： Richard Cotton Human Variome Project International Limited Melbourne Australia Department of Pathology The University of Melbourne Australia.

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