Database update Ensembl variation resources

The major goal of sequencing humans and many other species is to understand the link between genomic variation, phenotype and disease. There are numerous valuable and well-established variation resources, but collating and making sense of non-homogeneous, often large-scale data sets from disparate sources remains a challenge. Without a systematic catalogue of these data and appropriate query and annotation tools, understanding the genome sequence of an individual and assessing their disease risk is impossible. In Ensembl, we substantially solve this problem: we develop methods to facilitate data integration and broad access; aggregate information in a

[1]  Paul Flicek,et al.  Haplosaurus computes protein haplotypes for use in precision drug design , 2018, Nature Communications.

[2]  P. Taberlet,et al.  Convergent genomic signatures of domestication in sheep and goats , 2018, Nature Communications.

[3]  Bo Wang,et al.  Gramene 2018: unifying comparative genomics and pathway resources for plant research , 2017, Nucleic Acids Res..

[4]  Robert D. Finn,et al.  Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species , 2017, Nucleic Acids Res..

[5]  Clive D. L. Wynne,et al.  Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs , 2017, Science Advances.

[6]  R. Durbin,et al.  Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly , 2016, bioRxiv.

[7]  P. Stenson,et al.  The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies , 2017, Human Genetics.

[8]  J. Batley,et al.  Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application , 2017, Plant biotechnology journal.

[9]  D. Karolchik,et al.  The UCSC Genome Browser database: 2017 update , 2016, Nucleic Acids Res..

[10]  Helen E. Parkinson,et al.  The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) , 2016, Nucleic Acids Res..

[11]  Karsten M. Borgwardt,et al.  1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana , 2016, Cell.

[12]  Sarah C. Ayling,et al.  The Ensembl gene annotation system , 2016, Database J. Biol. Databases Curation.

[13]  Rachel G Liao,et al.  A federated ecosystem for sharing genomic, clinical data , 2016, Science.

[14]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, Genome Biology.

[15]  Raymond Dalgleish,et al.  HGVS Recommendations for the Description of Sequence Variants: 2016 Update , 2016, Human mutation.

[16]  Albert J. Vilella,et al.  Ensembl comparative genomics resources , 2016, Database J. Biol. Databases Curation.

[17]  Daniel R. Zerbino,et al.  Ensembl regulation resources , 2016, Database J. Biol. Databases Curation.

[18]  James M. Reecy,et al.  Developmental progress and current status of the Animal QTLdb , 2015, Nucleic Acids Res..

[19]  Ricardo Villamarín-Salomón,et al.  ClinVar: public archive of interpretations of clinically relevant variants , 2015, Nucleic Acids Res..

[20]  James Y. Zou Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[21]  Munir Pirmohamed,et al.  A multi-factorial analysis of response to warfarin in a UK prospective cohort , 2016, Genome Medicine.

[22]  M. Gut,et al.  Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses , 2015, BMC Genomics.

[23]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[24]  Karen Eilbeck,et al.  Improving the Sequence Ontology terminology for genomic variant annotation , 2015, Journal of Biomedical Semantics.

[25]  Thomas M. Keane,et al.  The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes , 2015, Mammalian Genome.

[26]  Bale,et al.  Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology , 2015, Genetics in Medicine.

[27]  François Schiettecatte,et al.  OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders , 2014, Nucleic Acids Res..

[28]  Sophia Ananiadou,et al.  Europe PMC: a full-text literature database for the life sciences and platform for innovation , 2014, Nucleic Acids Res..

[29]  Mingming Jia,et al.  COSMIC: exploring the world's knowledge of somatic mutations in human cancer , 2014, Nucleic Acids Res..

[30]  Weisong Liu,et al.  The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease , 2014, Nucleic Acids Res..

[31]  Alessandro Vullo,et al.  The Ensembl REST API: Ensembl Data for Any Language , 2014, Bioinform..

[32]  Tom R. Gaunt,et al.  The UK10K project identifies rare variants in health and disease , 2015, Nature.

[33]  J. Shendure,et al.  A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.

[34]  Jacqueline A. L. MacArthur,et al.  Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants , 2013, Nucleic Acids Res..

[35]  Damian Smedley,et al.  The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data , 2014, Nucleic Acids Res..

[36]  Weisong Liu,et al.  The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications , 2013, J. Biomed. Semant..

[37]  Miles Parkes,et al.  Genetic insights into common pathways and complex relationships among immune-mediated diseases , 2013, Nature Reviews Genetics.

[38]  Jürgen Kleffe,et al.  Equivalent Indels – Ambiguous Functional Classes and Redundancy in Databases , 2013, PloS one.

[39]  Chao Chen,et al.  dbVar and DGVa: public archives for genomic structural variation , 2012, Nucleic Acids Res..

[40]  Monte Westerfield,et al.  ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics , 2012, Nucleic Acids Res..

[41]  J. Woolliams,et al.  Edinburgh Research Explorer Development of a high density 600K SNP genotyping array for chicken , 2022 .

[42]  R. Altman,et al.  Pharmacogenomics Knowledge for Personalized Medicine , 2012, Clinical pharmacology and therapeutics.

[43]  Steve D. M. Brown,et al.  The International Mouse Phenotyping Consortium: past and future perspectives on mouse phenotyping , 2012, Mammalian Genome.

[44]  Sarah Edkins,et al.  Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease , 2011, Nature Genetics.

[45]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[46]  Jeroen F. J. Laros,et al.  LOVD v.2.0: the next generation in gene variant databases , 2011, Human mutation.

[47]  Heng Li,et al.  Tabix: fast retrieval of sequence features from generic TAB-delimited files , 2011, Bioinform..

[48]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[49]  Anna Zhukova,et al.  Modeling sample variables with an Experimental Factor Ontology , 2010, Bioinform..

[50]  Laurent Gil,et al.  Ensembl variation resources , 2010, BMC Genomics.

[51]  Paul Flicek,et al.  eHive: An Artificial Intelligence workflow system for genomic analysis , 2010, BMC Bioinformatics.

[52]  Manuel Corpas,et al.  DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. , 2009, American journal of human genetics.

[53]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[54]  Matthew D. Mailman,et al.  OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI , 2005, Nucleic Acids Res..

[55]  Cynthia L. Smith,et al.  The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information , 2004, Genome Biology.

[56]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[57]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..