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Open Targets Platform: new developments and updates two years on

Denise Carvalho-Silva, Andrea Pierleoni, Miguel Pignatelli, ChuangKee Ong, Luca Fumis, Nikiforos Karamanis, Miguel Carmona, Adam Faulconbridge, Andrew Hercules, Elaine McAuley, Alfredo Miranda, Gareth Peat (+6 others)
2018 Nucleic Acids Research  
The Open Targets Platform integrates evidence from genetics, genomics, transcriptomics, drugs, animal models and scientific literature to score and rank target-disease associations for drug target identification  ...  Here, we present the latest developments of the Open Targets Platform, expanding the evidence and target-disease associations with new and improved data sources, refining data quality, enhancing website  ...  our target-disease associations and the databases that provide us with annotations for our targets and diseases.  ... 
doi:10.1093/nar/gky1133 pmid:30462303 fatcat:2elh777ogbhknky33z5xfvaxfa

Mouse genetic and phenotypic resources for human genetics

Paul N. Schofield, Robert Hoehndorf, Georgios V. Gkoutos
2012 Human Mutation  
We discuss the nature and availability of data, mice and ES cells from these large-scale programmes, the use of these resources to help prioritise and validate candidate genes in human genetic association  ...  Large-scale community projects using mice, based on forward and reverse genetics, and now the pan-genomic phenotyping efforts of the International Mouse Phenotyping Consortium (IMPC), are generating resources  ...  Related work in the authors' laboratories is funded by the National Institutes of Health (R01 HG004838-02), the Commission of the European Union (EUMODIC contract number LSHG- CT-2006-037188) and the  ... 
doi:10.1002/humu.22077 pmid:22422677 pmcid:PMC3473354 fatcat:izb7ubfajjcmzjteprtcmnlw24

Systems genetics, bioinformatics and eQTL mapping

Hong Li, Hongwen Deng
2010 Genetica  
The expected strength of association between expression-level traits and a clinical trait is a function of the underlying genetic model in natural populations, and the gene differential expression between  ...  Some examples are DNA-capturing techniques to facilitate gene hunting efforts in highly repetitive genomes, motif-directed profiling to specifically target genetic variation in functional parts of the  ... 
doi:10.1007/s10709-010-9480-x pmid:20811929 fatcat:x6rxzagxd5amrocmnawylvzcmi

Enhancing the Promise of Drug Repositioning through Genetics

Jayne-Louise E. Pritchard, Tracy A. O'Mara, Dylan M. Glubb
2017 Frontiers in Pharmacology  
The multitude of genome-wide association studies (GWASs) conducted in recent years represents a large potential pool of novel targets for drug repositioning.  ...  Although traitassociated variants identified from GWAS still need to be causally linked to a target gene, recently developed functional genomic techniques, databases, and workflows are helping to remove  ...  Open Targets Open Targets collates publicly available data to enable www.targetvalidation.org/ Koscielny et al., 2017 the identification of genes associated with disease through genetic variants and gene  ... 
doi:10.3389/fphar.2017.00896 pmid:29270124 pmcid:PMC5724196 fatcat:jx3xsglei5dqhgpok43ggxbzfm

Genetics of human metabolism: an update

Gabi Kastenmüller, Johannes Raffler, Christian Gieger, Karsten Suhre
2015 Human Molecular Genetics  
Furthermore, it has been shown that GIMs provide testable hypotheses for functional genomics and metabolomics and for the identification of novel gene functions and metabolite identities. mGWAS with growing  ...  Knowledge of genetic variation in metabolism has many applications of biomedical and pharmaceutical interests, including the functional understanding of genetic associations with clinical end points, design  ...  Conflict of Interest statement. None declared.  ... 
doi:10.1093/hmg/ddv263 pmid:26160913 pmcid:PMC4572003 fatcat:ndmq3hj52vf6bfozrf4zttk6m4

Human genetics in full resolution

Alicia Schiavi, Nicholas Light, Veronique Adoue, Stephan Busche, Tomi Pastinen
2011 Genome Biology  
Large-scale studies: insight into the past and future The steadily dropping price of DNA sequencing is opening up possibilities for large-scale population studies using NGS technology that were previously  ...  Given the rapid advances in disease variant identification and the falling costs of sequencing, the utility of large-scale whole-genome sequencing studies for rare variant discovery, and even as a clinical  ... 
doi:10.1186/gb-2011-12-11-309 pmid:22115312 pmcid:PMC3334593 fatcat:3wu4d6vme5dyjntpij6rpbt3wq

Psoriasis and Genetics

N Dand, S Mahil, F Capon, C Smith, M Simpson, J Barker
2020 Acta Dermato-Venereologica  
This review summarises recent progress in elucidating the genetic basis of psoriasis, particularly through large genome-wide association studies.  ...  Psoriasis is a common inflammatory skin disease caused by the interplay between multiple genetic and environmental risk factors.  ...  While a large GWAS-based investigation found the genetic architectures of psoriasis and cardiometabolic traits to be largely distinct (95) , an epidemiological association with obesity is well established  ... 
doi:10.2340/00015555-3384 pmid:31971603 fatcat:7dwo2mxbevc2nbn7igljopbg7e

Genetics without genes? The centrality of genetic markers in livestock genetics and genomics

James W. E. Lowe, Ann Bruce
2019 History and Philosophy of the Life Sciences  
We define a genetic marker as a (usually material) element existing in different forms in the genome, that can be identified and mapped using a variety (and often combination) of quantitative, classical  ...  that a progressively stronger focus on the identification and mapping of markers rather than genes per se became a hallmark of the community.  ...  We would additionally like to thank all those who have participated in oral history interviews as part of our research into pig genomics, and those who have allowed us to see their personal documents.  ... 
doi:10.1007/s40656-019-0290-x pmid:31659490 fatcat:3sjxc3gwsrfw3mftoyt4pi7e5a

Advances in mouse genetics for the study of human disease

Steve D M Brown
2021 Human Molecular Genetics  
Advances in large-scale mouse mutagenesis programmes allied to high-throughput mouse phenomics are now addressing this challenge and systematically revealing novel gene function and multi-morbidities.  ...  Alongside the development of these pan-genomic mutational resources, mouse genetics is employing a range of diversity resources to delineate genegene and gene–environment interactions and to explore genetic  ...  Advances in large-scale mouse mutagenesis programmes allied to high-throughput mouse phenomics are now addressing this challenge and systematically revealing novel gene function and multimorbidities.  ... 
doi:10.1093/hmg/ddab153 pmid:34089057 pmcid:PMC8490014 fatcat:dwoeuvwoibdf5d6czfg2mejhua

Systems genetics: challenges and developing strategies

Hong Li, Ping Zhang
2012 Biologia (Bratislava)  
Analysis of expression quantitative trait loci (eQTLs) is an emerging technique in which individuals are genotyped across a panel of genetic markers and, simultaneously, phenotyped using DNA microarrays  ...  Systems genetics is leading researchers to understand genetics systems from holism's viewpoint, and will open a wide field of vision for genetics researchers in systems biology era.  ...  Some examples are DNA-capturing techniques to facilitate gene hunting efforts in highly repetitive genomes, motifdirected profiling to specifically target genetic variation in functional parts of the genome  ... 
doi:10.2478/s11756-012-0026-9 fatcat:sl3skc3c4fbmtmo7n3pw2klod4

Genetic-Driven Druggable Target Identification and Validation

Matteo Floris, Stefania Olla, David Schlessinger, Francesco Cucca
2018 Trends in Genetics  
Here, we discuss the increasing benefits for drug discovery gained from recent advances in genomic and large-scale genetic studies of traits and diseases. i www.omim.org ii www.ebi.ac.uk/gwas/ Floris et  ...  Systematic genetic association testing of both human diseases and quantitative traits, along with resultant findings of coincident associations between them, is becoming a powerful approach to infer drug  ...  This strategy requires comprehensive and unbiased ascertainment of genetic variation, through large-scale DNA sequencing and the use of informative imputation panels, to split the genetic contributions  ... 
doi:10.1016/j.tig.2018.04.004 pmid:29803319 pmcid:PMC6088790 fatcat:cpoj2ewtg5botoy6cz3mdbsyoe

Genetics of Atopic Dermatitis: From DNA Sequence to Clinical Relevance

Mari Løset, Sara J. Brown, Marit Saunes, Kristian Hveem
2019 Dermatology  
Assisted by the recent development of large-scale high-throughput genomics, more than 30 genetic loci have been linked to AD across different populations.  ...  Identification of these loci, together with functional studies, has already provided new insights into disease biology and identified novel drug targets.  ...  Brumpton for commenting on the paper and revising the section on Mendelian randomization, and Brooke N. Wolford for insights on genetic sequencing studies and constructive criticism of the paper.  ... 
doi:10.1159/000500402 pmid:31203284 fatcat:tlvt4e7qwja3xhtn23wjz3st34

Genetic Landscape of Open Chromatin in Yeast

Kibaick Lee, Sang Cheol Kim, Inkyung Jung, Kwoneel Kim, Jungmin Seo, Heun-Sik Lee, Gireesh K. Bogu, Dongsup Kim, Sanghyuk Lee, Byungwook Lee, Jung Kyoon Choi, Hunter Fraser
2013 PLoS Genetics  
The OCRs associated with these multi-target trans-loci coincided with recombination hotspots, telomeres, and gene-rich regions according to the function of the associated regulators.  ...  While individual OCRs were associated with a handful of specific genetic markers, gene expression levels were associated with many regulatory loci.  ...  Acknowledgments We thank Jaehwan Jahng and Dae Woong Jung for help with the data analysis, Dr. Leonid Kruglyak and Dr. Rachel Brem for providing the yeast strains, and Dr.  ... 
doi:10.1371/journal.pgen.1003229 pmid:23408895 pmcid:PMC3567132 fatcat:4xhpaubxljgyzm2piterhodgpe

Systematic Mapping of Genetic Interaction Networks

Scott J. Dixon, Michael Costanzo, Anastasia Baryshnikova, Brenda Andrews, Charles Boone
2009 Annual Review of Genetics  
Genetic interactions influencing a phenotype of interest can be identified systematically using libraries of genetic tools that perturb biological systems in a defined manner.  ...  Techniques enabling systematic genetic interaction mapping have been extended to other single-celled organisms, the bacteria Escherichia coli and the yeast Schizosaccharomyces pombe, opening the way to  ...  This work was supported by a postdoctoral fellowship from the Canadian Institutes of Health Research to S.J.D. and grants from Genome Canada (2004-OGI-3-01) and the Canadian Institutes of Health Research  ... 
doi:10.1146/annurev.genet.39.073003.114751 pmid:19712041 fatcat:jqjqhebnivbplgeb2d7y3rg44u

Genetic basis of autoimmunity

Alexander Marson, William J. Housley, David A. Hafler
2015 Journal of Clinical Investigation  
Haliburton, and K.K. Farh for suggestions on the manuscript. The review also benefitted from our conversations with all members of the Marson and Hafler laboratories.  ...  Genetic mapping of quantitative traits including gene expression is a complementary approach to epigenomic annotation of functional genomic elements.  ...  Looking forward, targeted genome editing of disease variants (termed "SNP editing") in primary human cell types associated with specific diseases is likely to open new possibilities in understanding pathogenesis  ... 
doi:10.1172/jci78086 pmid:26030227 pmcid:PMC4497748 fatcat:3pf6jl32hrgdrljqqbh7vr4osy
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