Genomatix Software GmbH

Munchen, Germany

Genomatix Software GmbH

Munchen, Germany
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Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: HEALTH.2012.2.1.1-1-B | Award Amount: 15.82M | Year: 2012

EURenOmics will integrate several established consortia devoted to rare kidney diseases with eminent need and potential for diagnostic and therapeutic progress (i.e. steroid resistant nephrotic syndrome, membranous nephropathy, tubulopathies, complement disorders such a haemolytic uraemic syndrome, and congenital kidney malformations). The Consortium has access to the largest clinical cohorts assembled to date (collectively >10,000 patients) with detailed phenotypic information and comprehensive biorepositories containing DNA, blood, urine, amniotic fluid and kidney tissue. The project aims to (1) identify the genetic and epigenetic causes and modifiers of disease and their molecular pathways; (2) define a novel mechanistic disease ontology beyond phenotypical or morphological description; (3) develop innovative technologies allowing rapid diagnostic testing; (4) discover and validate biomarkers of disease activity, prognosis and treatment responses; and (5) develop in vitro and in vivo disease models and apply high-throughput compound library screening. For these purposes we will integrate comprehensive data sets from next generation exome and whole-genome sequencing, ChiP-sequencing, tissue transcriptome and antigen/epitope profiling, and miRNome, proteome/peptidome, and metabolome screening in different body fluids within and across conventional diagnostic categories. These data will be combined in a systems biology approach with high-resolution clinical phenotyping and findings obtained with a large array of established and novel in vitro, ex vivo and in vivo disease models (functiomics) to identify disease-associated genetic variants involved in monogenic or complex genetic transmission, disease-defining molecular signatures, and potential targets for therapeutic intervention. These efforts will converge in the development of innovative diagnostic tools and biomarkers and efficient screening strategies for novel therapeutic agents.

Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: HEALTH.2011.2.1.1-1 | Award Amount: 39.64M | Year: 2011

In response to the call for a high impact initiative on the human epigenome, the BLUEPRINT Consortium has been formed with the aim of generating at least 100 reference epigenomes and studying them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. BLUEPRINT will focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukaemic counterparts. Reference epigenomes will be generated by state-of-the-art technologies from highly purified cells for a comprehensive set of epigenetic marks in accordance with quality standards set by IHEC. This resource-generating activity will be conducted at dedicated centres to be complemented by confederated hypothesis-driven research into blood-based diseases, including common leukaemias and autoimmune disease (T1D), by epigenetic targets and compound identification, and by discovery and validation of epigenetic markers for diagnostic use. By focussing on 100 samples of known genetic variation BLUEPRINT will complete an epigenome-wide association study, maximizing the biomedical relevance of the reference epigenomes. Key to the success of BLUEPRINT will be the integration with other data sources (i.e. ICGC, 1000 genomes and ENCODE), comprehensive bioinformatic analysis, and user-friendly dissemination to the wider scientific community. The involvement of innovative companies will energize epigenomic research in the private sector by creating new targets for compounds and the development of smart technologies for better diagnostic tests. BLUEPRINT will outreach through a network of associated members and form critical alliances with leading networks in genomics and epigenomics within Europe and worldwide. Through its interdisciplinarity and scientific excellence combined with its strong commitment to networking, training and communication BLUEPRINT strives to become the cornerstone of the EU contribution to IHEC. offer Next Generation Sequencing (NGS) Market Research Report. This Report covers the complete Industry Outlook, Growth, Size, Share and Forecast Till 2022. Get Free Sample Copy of this Report @ The report on global next generation sequencing (NGS) market evaluates the growth trends of the industry through historical study and estimates future prospects based on comprehensive research. The report extensively provides the market share, growth, trends and forecasts for the period 2015-2022. The market size in terms of revenue (USD MN) is calculated for the study period along with the details of the factors affecting the market growth (drivers and restraints). A glimpse of the major drivers and restraints affecting this market is mentioned below: Furthermore, the report quantifies the market share held by the major players of the industry and provides an in-depth view of the competitive landscape. This market is classified into different segments with detailed analysis of each with respect to geography for the study period 2015-2022. The comprehensive value chain analysis of the market will assist in attaining better product differentiation, along with detailed understanding of the core competency of each activity involved. The market attractiveness analysis provided in the report aptly measures the potential value of the market providing business strategists with the latest growth opportunities. The report classifies the market into different segments based on technology, workflow, application and end-use. These segments are studied in detail incorporating the market estimates and forecasts at regional and country level. The segment analysis is useful in understanding the growth areas and probable opportunities of the market. Leading Segment in this market: By Technology - Targeted Sequencing And Resequencing By Application – HLA Testing By End –Use - Academic Research By Geography – North America The report also covers the complete competitive landscape of the worldwide market with company profiles of key players such as Illumina Incorporated, 454 Life Sciences, Agilent Technologies, Knome Inc., Genomatix Software GmbH, GATC Biotech Ag, Oxford Nanopore Technologies Ltd., Macrogen Inc., Life Technologies Corp., DNASTAR Inc., Biomatters Ltd., Life CLC Bio, BGI, Qiagen NV, Perkin Elmer, Inc., Pacific Bioscience, Inc. and Partek, Inc.. A detailed description of each has been included, with information in terms of H.Q, future capacities, key mergers & acquisitions, financial overview, partnerships, collaborations, new product launches, new product developments and other latest industrial developments. For More Information about this Report: 1. INTRODUCTION 2. EXECUTIVE SUMMARY 3. MARKET ANALYSIS 4. NEXT GENERATION SEQUENCING (NSG) MARKET ANALYSIS BY TECHNOLOGY 5. NEXT GENERATION SEQUENCING (NSG) MARKET ANALYSIS BY WORkFlOW 6. NEXT GENERATION SEQUENCING (NSG) MARKET ANALYSIS BY APPLICATION 7. NEXT GENERATION SEQUENCING (NSG) MARKET ANALYSIS BY END-USE 8. NEXT GENERATION SEQUENCING (NSG) MARKET ANALYSIS BY GEOGRAPHY 9. COMPETITIVE LANDSCAPE OF THE NEXT GENERATION SEQUENCING (NSG) COMPANIES 10. COMPANY PROFILES OF THE NEXT GENERATION SEQUENCING (NSG) INDUSTRY is a global business research reports provider, enriching decision makers and strategists with qualitative statistics. is proficient in providing syndicated research report, customized research reports, company profiles and industry databases across multiple domains. Our expert research analysts have been trained to map client’s research requirements to the correct research resource leading to a distinctive edge over its competitors. We provide intellectual, precise and meaningful data at a lightning speed.

News Article | November 7, 2016

The Global market for Next Generation Sequencing is poised to reach $10 billion by the end of 2020 growing at a CAGR of approximately 20%. The instruments and consumables is the largest segment with a share of around half of the market in 2013. The fastest growing segment is the services with a highest CAGR during the forecast period. The major players are interested in services segment as it provides additional revenue for the company at the same time, increases the sales of instruments and reagents. The major players operating in the NGS market are Illumina Inc (U.S.), Thermo Fisher Scientific (U.S.), Hoffmann-La Roche Ltd (Switzerland), Pacific Bioscieces (U.S.) Agilent Technologies (U.S.), BGI (Beijing Genomics Institute) (China), Qiagen (Netherlands), Biomatters Ltd (New Zealand), and Genomatix Software GmbH (Germany). Currently, North America is the largest market for NGS. This is due to the increased awareness about the quick return of investments and accuracy. Asia Pacific is the fastest growing segment. The Next Generation Sequencing market can be segmented on the basis of Technology (Whole Genome Sequencing, Targeted Resequencing, Whole Exome Sequencing, RNA Sequencing, Chip Sequencing, De Novo Sequencing and Methyl Sequencing), Products (Instruments, Reagents & Consumables, and Services), End user (Hospitals & Healthcare Institutions, Academics, Biotech & Pharma Firms, and Others), Applications (Drug Discovery, Genetic Screening, Diagnostics, Personalized Medicine, Agriculture And Animal Research, Infectious Diseases, and Others) and Geography (North America, Europe, APAC & RoW). Increasing applications in clinical diagnosis boosting the market growth, Speed, cost and accuracy to spur the market growth, Efficient replacement for traditional technologies (Microarrays), and Drug discovery applications demanding NGS technology are the major factors driving the growth of the market. Legal & ethical issues to hamper the market growth, Interpretation of complex data, and Lack of skilled professionals are the major restraints that are hampering the NGS market growth. Market Definition for the specified topic along with identification of key drivers and restraints for the market.  Market analysis for the Global Next Generation Sequencing Market, with region specific assessments and competition analysis on a global and regional scale.  Identification of factors instrumental in changing the market scenarios, rising prospective opportunities and identification of key companies which can influence the market on a global and regional scale.  Extensively researched competitive landscape section with profiles of major companies along with their strategic initiatives and market shares.�  Identification and analysis of the Macro and Micro factors that affect the Global Next Generation Sequencing market on both global and regional scale.  A comprehensive list of key market players along with the analysis of their current strategic interests and key financial information. INTRODUCTION  Study Deliverables  Market Definition  Sizing Units  Base Currency  Review and forecast period years  General Study Assumptions  RESEARCH METHODOLOGY  Introduction  Analysis Methodology  Econometric forecast models  Research Assumptions  EXECUTIVE SUMMARY  KEY INFERENCES  MARKET OVERVIEW AND INDUSTRY TRENDS  Current market scenario  Technology Overview  New developments in therapeutics  Investment analysis  Porters Five Force Analysis  Bargaining Power of suppliers  Bargaining power of buyers  Degree of competition  Threat of substitution  Threat of new entrants  DRIVERS, RESTRAINTS, OPPORTUNITIES AND CHALLENGES ANALYSIS (DROC)  Market Drivers  Increasing applications in clinical diagnosis boosting the market growth  Speed, cost and accuracy to spur the market growth  Efficient replacement for traditional technologies (Microarrays)  Drug discovery applications demanding NGS technology  Market Restraints  Legal & ethical issues to hamper the market growth  Interpretation of complex data  Lack of skilled professionals  Market Opportunities  In NGS Technology, Personalized Medicine & Biomarker  Pre-Sequencing  Cloud Computing  Key Challenges  Interpretation Of Complex Data From NGS Platforms  Clinical Translation of Genomic Discoveries By Technology  Whole Genome Sequencing  Targeted Resequencing  Whole Exome Sequencing  Rna Sequencing  Chip Sequencing  De Novo Sequencing  Methyl Sequencing  By Products  Instruments  Reagents & Consumables  By End Users  Services  Hospitals & Healthcare Institutions  Academics  Biotech & Pharma Firms  Others  By Application  Drug Discovery  Genetic Screening  Diagnostics  Personalized Medicine  Agriculture And Animal Research  Infectious Diseases  Others  GLOBAL NEXT GENERATION SEQUENCING (NGS) MARKET SEGMENTATION BY GEOGRAPHY - REGIONAL SHARES AND FORECAST  North America  USA  Canada  Mexico  Europe  France  UK  Germany  Spain and Portugal  Scandinavia  Italy  BENELUX  Asia-Pacific  India  China  Japan  South Korea  Australia and New Zealand  Rest of Asia Pacific  Middle East and Africa  GCC  Egypt  Morocco  Algeria  South Africa  Rest of Middle East and Africa  Latin America  Brazil  Argentina  Rest of Latin America  COMPETITIVE LANDSCAPE  Merger and Acquisition Analysis  Patent Analysis  The Challengers  KEY VENDORS  Roche Holding Ag  Agilent Technologies, Inc  BGI (Beijing Genomics Institute)  Biomatters, Ltd  Qiagen  Dnastar, Inc  Gatc Biotech Ag  Genomatix Software Gmbh  Illumina, Inc  Knome, Inc  Thermo Fisher Scientific  Macrogen, Inc  Oxford Nanopore Technologies, Ltd  Pacific Biosciences  Partek Incorporated  Perkin Elmer, Inc  ANALYST OUTLOOK FOR INVESTMENT OPPORTUNITIES  FUTURE OUTLOOK OF THE MARKET  APPENDIX  Abbreviations  Bibliography  Disclaimer

Fiesel F.C.,Hertie Institute for Clinical Brain Research | Weber S.S.,Hertie Institute for Clinical Brain Research | Supper J.,University of Tübingen | Supper J.,Genomatix Software GmbH | And 2 more authors.
Nucleic Acids Research | Year: 2012

TDP-43 is linked to neurodegenerative diseases including frontotemporal dementia and amyotrophic lateral sclerosis. Mostly localized in the nucleus, TDP-43 acts in conjunction with other ribonucleoproteins as a splicing co-factor. Several RNA targets of TDP-43 have been identified so far, but its role(s) in pathogenesis remains unclear. Using Affymetrix exon arrays, we have screened for the first time for splicing events upon TDP-43 knockdown. We found alternative splicing of the ribosomal S6 kinase 1 (S6K1) Aly/REF-like target (SKAR) upon TDP-43 knockdown in non-neuronal and neuronal cell lines. Alternative SKAR splicing depended on the first RNA recognition motif (RRM1) of TDP-43 and on 5′-GA-3' and 5′-UG-3′ repeats within the SKAR pre-mRNA. SKAR is a component of the exon junction complex, which recruits S6K1, thereby facilitating the pioneer round of translation and promoting cell growth. Indeed, we found that expression of the alternatively spliced SKAR enhanced S6K1-dependent signaling pathways and the translational yield of a splice-dependent reporter. Consistent with this, TDP-43 knockdown also increased translational yield and significantly increased cell size. This indicates a novel mechanism of deregulated translational control upon TDP-43 deficiency, which might contribute to pathogenesis of the protein aggregation diseases frontotemporal dementia and amyotrophic lateral sclerosis. © 2011 The Author(s).

Werner T.,Genomatix Software GmbH
Briefings in Bioinformatics | Year: 2010

Genome-wide sequencing has enabled modern biomedical research to relate more and more events in healthy as well as disease-affected cells and tissues to the genomic sequence. Now next generation sequencing (NGS) extends that reach into multiple almost complete genomes of the same species, revealing more and more details about how individual genomes as well as individual aspects of their regulation differ from each other. The inclusion of NGS-based transcriptome sequencing, chromatin-immunoprecipitation (ChIP) of transcription factor binding and epigenetic analyses (usually based on DNA methylation or histone modification ChIP) completes the picture with unprecedented resolution enabling the detection of even subtle differences such as alternative splicing of individual exons. Functional genomics aims at the elucidation of the molecular basis of biological functions and requires analyses that go far beyond the primary analysis of the reads such as mapping to a genome template sequence. The various and complex interactions between the genome, gene products and metabolites define biological function, which necessitates inclusion of results other than sequence tags in quite elaborative approaches. However, the extra efforts pay off in revealing mechanisms as well as providing the foundation for new strategies in systems biology and personalized medicine. This review emphasizes the particular contribution NGS-based technologies make to functional genomics research with a special focus on gene regulation by transcription factor binding sites. © The Author 2010. Published by Oxford University Press.

Supper J.,Genomatix Software GmbH
Methods (San Diego, Calif.) | Year: 2013

In recent years, gene fusions have gained significant recognition as biomarkers. They can assist treatment decisions, are seldom found in normal tissue and are detectable through Next-generation sequencing (NGS) of the transcriptome (RNA-seq). To transform the data provided by the sequencer into robust gene fusion detection several analysis steps are needed. Usually the first step is to map the sequenced transcript fragments (RNA-seq) to a reference genome. One standard application of this approach is to estimate expression and detect variants within known genes, e.g. SNPs and indels. In case of gene fusions, however, completely novel gene structures have to be detected. Here, we describe the detection of such gene fusion events based on our comprehensive transcript annotation (ElDorado). To demonstrate the utility of our approach, we extract gene fusion candidates from eight breast cancer cell lines, which we compare to experimentally verified gene fusions. We discuss several gene fusion events, like BCAS3-BCAS4 that was only detected in the breast cancer cell line MCF7. As supporting evidence we show that gene fusions occur more frequently in copy number enriched regions (CNV analysis). In addition, we present the Transcriptome Viewer (TViewer) a tool that allows to interactively visualize gene fusions. Finally, we support detected gene fusions through literature mining based annotations and network analyses. In conclusion, we present a platform that allows detecting gene fusions and supporting them through literature knowledge as well as rich visualization capabilities. This enables scientists to better understand molecular processes, biological functions and disease associations, which will ultimately lead to better biomedical knowledge for the development of biomarkers for diagnostics and therapies. Copyright © 2012 Elsevier Inc. All rights reserved.

Werner T.,Genomatix Software GmbH | Werner T.,University of Michigan
Reproduction, Fertility and Development | Year: 2011

Reproduction and fertility are controlled by specific events naturally linked to oocytes, testes and early embryonal tissues. A significant part of these events involves gene expression, especially transcriptional control and alternative transcription (alternative promoters and alternative splicing). While methods to analyse such events for carefully predetermined target genes are well established, until recently no methodology existed to extend such analyses into a genome-wide de novo discovery process. With the arrival of next generation sequencing (NGS) it becomes possible to attempt genome-wide discovery in genomic sequences as well as whole transcriptomes at a single nucleotide level. This does not only allow identification of the primary changes (e.g. alternative transcripts) but also helps to elucidate the regulatory context that leads to the induction of transcriptional changes. This review discusses the basics of the new technological and scientific concepts arising from NGS, prominent differences from microarray-based approaches and several aspects of its application to reproduction and fertility research. These concepts will then be illustrated in an application example of NGS sequencing data analysis involving postimplantation endometrium tissue from cows. © 2011 IETS.

Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2012.2.1.1-3 | Award Amount: 4.68M | Year: 2012

High-throughput sequencing (HTS) is a powerful and rapidly evolving family of technologies with a multitude of applications. They include genetics of rare and common diseases, understanding of disease mechanism and progression through transcriptome and epigenome profiling, cancer stratification, personalised medicine and molecular systems biology of gene regulation. The genome, epigenome, transcriptome and interactome are all intricately connected, and modern HTS technology can probe all of these -omic levels. Statistical analysis is a crucial component of many experiments and studies, and the quality and efficiency of the analysis often determines the success of a project. In this collaborative project we will develop a range of new statistical analysis tools to solve open problems in HTS data analysis, ranging from low-level processing of sequence reads up to systems-level modelling of disease associated and cellular processes. We will provide to a wide audience an integrated computational framework for HTS data analysis and interpretation that is robust, efficient and user-friendly. We will establish improved procedures for the publishing of statistical software as an integral part of the scientific publication process, within the framework of the Bioconductor project. We will provide tools to benchmark experimental protocols and statistical methods, and we will provide training materials and a extensive training programme to rapidly disseminate these new tools to the broader biomedical community. SME partners will integrate these new tools within their analysis pipelines with associated user-friendly commercial software providing access to their additional proprietary tools. SMEs will benefit from basic methodology development done in a public, pre-competitive arena and will be able to use these technologies to enhance their products and services.

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