13,694 research outputs found
The Global Cancer Genomics Consortium: interfacing genomics and cancer medicine.
No full textThe Global Cancer Genomics Consortium (GCGC) is an international collaborative platform that amalgamates cancer biologists, cutting-edge genomics, and high-throughput expertise with medical oncologists and surgical oncologists; they address the most important translational questions that are central to cancer research and treatment. The annual GCGC symposium was held at the Advanced Centre for Treatment Research and Education in Cancer, Mumbai, India, from November 9 to 11, 2011. The symposium showcased international next-generation sequencing efforts that explore cancer-specific transcriptomic changes, single-nucleotide polymorphism, and copy number variations in various types of cancers, as well as the structural genomics approach to develop new therapeutic targets and chemical probes. From the spectrum of studies presented at the symposium, it is evident that the translation of emerging cancer genomics knowledge into clinical applications can only be achieved through the integration of multidisciplinary expertise. In summary, the GCGC symposium provided practical knowledge on structural and cancer genomics approaches, as well as an exclusive platform for focused cancer genomics endeavors
Consortium_Members
No full textList of Mint Evolutionary Genomics Consortium members and institutional affiliations
Consortium_Members
No full textList of Mint Evolutionary Genomics Consortium members and institutional affiliations
Computational pan-genomics: Status, promises and challenges
No full textMany disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different Computational methods and paradigms are needed.We will witness the rapid extension of Computational pan-genomics, a new sub-area of research in Computational biology. In this article, we generalize existing definitions and understand a pangenome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a Computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common Computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to Computational pangenomics can help address many of the problems currently faced in various domains
The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation
No full textT.A.K. was supported by Australian Research Council grants (FT190100462 and LP200301370). M.T.-S. was supported by María Zambrano fellowship from Complutense University of Madrid and NextGenerationEU. The Xenopus laevis Research Resource for Immunobiology is supported by the National Institute of Health (R24-AI-05983). A.A.S. is supported by the NSF Postdoctoral Research Fellowships in Biology Program under Grant No. 2305939.Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.Australian Research CouncilUniversidad Complutense de MadridEuropean CommissionNational Institutes of Health (U.S.)National Science Foundation (U.S.)Depto. de Biodiversidad, Ecología y EvoluciónDepto. de Genética, Fisiología y MicrobiologíaFac. de Ciencias BiológicasTRUEpu
Genomics and the changing profile of human disease
No full textWithin the last decade, much has been written on the impending impact of the Human Genome Project on human health. A typical perspective was offered in 1995 as part of the submission of the Royal College of Physicians to the Science and Technology Committee of the U.K. House of Commons. In describing the future contribution of genetics to medical practice it was stated that, ‘The process has scarcely begun and may not have a major clinical impact for many years; however it represents the change from empirical to rational management of disease and hence its significance can hardly be exaggerated’. Clearly, any body of knowledge that could effect such a change would be of global importance, and if this and similar predictions prove to be correct, they would match in significance the revolution in medical practice provoked by the anatomical discoveries of the Renaissance period.
The Human Genome Project was initiated in 1991, and by 2001, the first consensus sequence of the human genome was simultaneously published by publicly supported researchers (International Human Genome Sequencing Consortium 2001) and the privately financed Celera Genomics (Venter et al. 2001). Access to the growing database on genome structure and function made available through the Human Genome Project has greatly assisted medical researchers, and as a result, by March 2003 over 14,000 single gene disorders affecting both the human nuclear and mitochondrial genomes had been identified (OMIM 2003).
Of itself, the recognition of specific and often very rare mutations is unlikely to change medical practice or to impinge on the everyday lives of the vast majority of the world’s population. Data on the contribution of predisposing genes to common diseases is still rudimentary, and there is limited information on non-biological factors that influence the genetic structure of human populations and thereby govern the distribution and transmission of disease mutations. An appreciation of the importance of these topics has, however, gradually been emerging, accompanied by the establishment of two new academic disciplines, Community Genetics and Public Health Genetics. The aim of this article is to briefly review the potential influence and effects of these changes on the future profile of genetic disease in industrialized and developing countries
LaGomiCs—Lagomorph Genomics Consortium: an international collaborative effort for sequencing the genomes of an entire mammalian order
No full textThe order Lagomorpha comprises about 90 living species, divided in 2 families: the pikas (Family
Ochotonidae), and the rabbits, hares, and jackrabbits (Family Leporidae). Lagomorphs are important
economically and scientifically as major human food resources, valued game species, pests of
agricultural significance, model laboratory animals, and key elements in food webs. A quarter of
the lagomorph species are listed as threatened. They are native to all continents except Antarctica,
and occur up to 5000 m above sea level, from the equator to the Arctic, spanning a wide range
of environmental conditions. The order has notable taxonomic problems presenting significant
difficulties for defining a species due to broad phenotypic variation, overlap of morphological
characteristics, and relatively recent speciation events. At present, only the genomes of 2 species,
the European rabbit (Oryctolagus cuniculus) and American pika (Ochotona princeps) have been
sequenced and assembled. Starting from a paucity of genome information, the main scientific
aim of the Lagomorph Genomics Consortium (LaGomiCs), born from a cooperative initiative of
the European COST Action “A Collaborative European Network on Rabbit Genome Biology—RGBNet”
and the World Lagomorph Society (WLS), is to provide an international framework for the
sequencing of the genome of all extant and selected extinct lagomorphs. Sequencing the genomes
of an entire order will provide a large amount of information to address biological problems not only related to lagomorphs but also to all mammals. We present current and planned sequencing programs and outline the final objective of LaGomiCs possible through broad international collaboration
Defining suicidality phenotypes for genetic studies: perspectives of the Psychiatric Genomics Consortium Suicide Working Group
No full textSuicidality phenotypes, consisting of suicidal ideation (SI), suicide attempt (SA), and suicide death (SD), are all heritable but present unique challenges in genome-wide association studies (GWAS) due to their individual complexity, overlap with each other and with related self-harm phenotypes, and varying associations with psychiatric disorders. GWAS have uncovered several loci associated with suicidality phenotypes by meta-analyzing data from multiple cohorts. However, combining datasets from many research groups, where each group may use different study designs, phenotyping instruments, and definitions of suicidality phenotypes, presents challenges. Heterogeneity resulting from these differences can limit genetic discovery; harmonizing phenotype definitions to ensure consistency will greatly improve results. Here, we describe a standardized phenotyping protocol that draws on the expertise of a subgroup of clinicians, researchers, and experts from the Psychiatric Genomics Consortium Suicide Working Group to propose consensus definitions for SI, SA, and SD for genetic studies
LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order
No full textThe order Lagomorpha comprises about 90 living species, divided in 2 families: the pikas (Family Ochotonidae), and the rabbits, hares, and jackrabbits (Family Leporidae). Lagomorphs are important economically and scientifically as major human food resources, valued game species, pests of agricultural significance, model laboratory animals, and key elements in food webs. A quarter of the lagomorph species are listed as threatened. They are native to all continents except Antarctica, and occur up to 5000 m above sea level, from the equator to the Arctic, spanning a wide range of environmental conditions. The order has notable taxonomic problems presenting significant difficulties for defining a species due to broad phenotypic variation, overlap of morphological characteristics, and relatively recent speciation events. At present, only the genomes of 2 species, the European rabbit (Oryctolagus cuniculus) and American pika (Ochotona princeps) have been sequenced and assembled. Starting from a paucity of genome information, the main scientific aim of the Lagomorph Genomics Consortium (LaGomiCs), born from a cooperative initiative of the European COST Action "A Collaborative European Network on Rabbit Genome Biology-RGB-Net" and the World Lagomorph Society (WLS), is to provide an international framework for the sequencing of the genome of all extant and selected extinct lagomorphs. Sequencing the genomes of an entire order will provide a large amount of information to address biological problems not only related to lagomorphs but also to all mammals. We present current and planned sequencing programs and outline the final objective of LaGomiCs possible through broad international collaboration
Bovine Pangenome Consortium
No full textThe Bovine Pangenome Consortium is an international research consortium dedicated to the sequencing and assembly of bovid species for research applications. We are comprised of experts in the field of Genetics, Genomics, Bioinformatics and Animal Science from countries throughout the world
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