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PubMed | Diploid Genomics, Complutense University of Madrid, InSilico Genomics S.A., DNAdigest and 11 more.
Type: | Journal: BMC genomics | Year: 2015

We describe the pioneering experience of a Spanish family pursuing the goal of understanding their own personal genetic data to the fullest possible extent using Direct to Consumer (DTC) tests. With full informed consent from the Corpas family, all genotype, exome and metagenome data from members of this family, are publicly available under a public domain Creative Commons 0 (CC0) license waiver. All scientists or companies analysing these data (the Corpasome) were invited to return results to the family.We released 5 genotypes, 4 exomes, 1 metagenome from the Corpas family via a blog and figshare under a public domain license, inviting scientists to join the crowdsourcing efforts to analyse the genomes in return for coauthorship or acknowldgement in derived papers. Resulting analysis data were compiled via social media and direct email.Here we present the results of our investigations, combining the crowdsourced contributions and our own efforts. Four companies offering annotations for genomic variants were applied to four family exomes: BIOBASE, Ingenuity, Diploid, and GeneTalk. Starting from a common VCF file and after selecting for significant results from company reports, we find no overlap among described annotations. We additionally report on a gut microbiome analysis of a member of the Corpas family.This study presents an analysis of a diverse set of tools and methods offered by four DTC companies. The striking discordance of the results mirrors previous findings with respect to DTC analysis of SNP chip data, and highlights the difficulties of using DTC data for preventive medical care. To our knowledge, the data and analysis results from our crowdsourced study represent the most comprehensive exome and analysis for a family quartet using solely DTC data generation to date.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: Health | Award Amount: 2.04M | Year: 2014

IF-EBOLa has been strategically designed to efficiently respond to critical needs required to control the current EBOV outbreak from spreading. The work will involve two of the main EVD outbreak sites, Sierra Leone and Guinea. MDs, public health authorities and virus experts working on site, under ethical regulatory rules, will extend their collaboration to companies and institution to form a consortium of outstanding complementary partners, sharing their innovative technological approaches for a common goal. Our project aim is to contribute to provide an innovative early and accurate diagnostic for an early treatment and includes 2 phases: (I) a phase of preparation including, ethical authorizations, antibody production, technical and field organization as well as the beginning a follow-up of the homeostatic profile of contacts early-EBOV diagnosed and self-cured convalescent individuals in the absence of existing treatment, (with an ultrasensitive detection method of pernicious microorganisms, from the EC USDEP project qualified as a European success story USDEP project in 2010 by the EC-Project Officer) and (II) using a wide validated approach revisited with an innovative concept (strongly supported EC/EMA-WHO), we propose to carry out an experimental passive-immune therapy based on neutralizing capacity of horse anti-EBOV polyclonal F(ab)2 on early-diagnosed patients (n>300 that will be adapted in function of the epidemic situation) to impact and reduce their pre-existing viremia, their mortality, the evolution of their homeostasis profile, during and after this treatment (once patients become convalescents). The homeostasis status evolution will help to generate high quality scientific data to understand the EVD, the effect of this therapy and cure parameters characterized at 3 different levels: immune (transcriptomes, NGS, metagenomics); infectious (other than EBOV, DNA arrays), and EBOV diversity (sequencing and metagenomics).


Bruder C.E.,Southern Research Institute | Yao S.,Southern Research Institute | Larson F.,Orion Integrated Biosciences Inc | Camp J.V.,Southern Research Institute | And 6 more authors.
BMC Genomics | Year: 2010

Background: The ferret (Mustela putorius furo) represents an attractive animal model for the study of respiratory diseases, including influenza. Despite its importance for biomedical research, the number of reagents for molecular and immunological analysis is restricted. We present here a parallel sequencing effort to produce an extensive EST (expressed sequence tags) dataset derived from a normalized ferret cDNA library made from mRNA from ferret blood, liver, lung, spleen and brain.Results: We produced more than 500000 sequence reads that were assembled into 16000 partial ferret genes. These genes were combined with the available ferret sequences in the GenBank to develop a ferret specific microarray platform. Using this array, we detected tissue specific expression patterns which were confirmed by quantitative real time PCR assays. We also present a set of 41 ferret genes with even transcription profiles across the tested tissues, indicating their usefulness as housekeeping genes.Conclusion: The tools developed in this study allow for functional genomic analysis and make further development of reagents for the ferret model possible. © 2010 Bruder et al; licensee BioMed Central Ltd.


Valdivia-Granda W.,Orion Integrated Biosciences Inc. | Larson F.,Orion Integrated Biosciences Inc.
Database | Year: 2014

Viruses, viroids and prions are the smallest infectious biological entities that depend on their host for replication. The number of pathogenic viruses is considerably large and their impact in human global health is well documented. Currently, the International Committee on the Taxonomy of Viruses (ICTV) has classified ~4379 virus species while the National Center for Biotechnology Information Viral Genomes Resource (NCBI-VGR) database has mapped 617 705 proteins to eight large taxonomic groups. Despite these efforts, an automated approach for mapping the ICTV master list and its officially accepted virus naming to the NCBI-VGR's taxonomical classification is not available. Due to metagenomic sequencing, it is likely that the discovery and naming of new viral species will increase by at least ten fold. Unfortunately, existing viral databases are not adequately prepared to scale, maintain and annotate automatically ultra-high throughput sequences and place this information into specific taxonomic categories. ORION-VIRCAT is a scalable and interoperable object-relational database designed to serve as a resource for the integration and verification of taxonomical classifications generated by the ICTV and NCBI-VGR. The current release (v1.0) of ORION-VIRCAT is implemented in PostgreSQL and it has been extended to ORACLE, MySQL and SyBase. ORION-VIRCAT automatically mapped and joined 617 705 entries from the NCBI-VGR to the viral naming of the ICTV. This detailed analysis revealed that 399 095 entries from the NCBI-VGR can be mapped to the ICTV classification and that one Order, 10 families, 35 genera and 503 species listed in the ICTV disagree with the the NCBI-VGR classification schema. Nevertheless, we were eable to correct several discrepancies mapping 234 000 additional entries. © 2009 The Author(s).


Mahardika G.N.K.,Udayana University | Dibia N.,Disease Investigation Center | Budayanti N.S.,Udayana University | Susilawathi N.M.,Udayana University | And 6 more authors.
Epidemiology and Infection | Year: 2014

The emergence of human and animal rabies in Bali since November 2008 has attracted local, national and international interest. The potential origin and time of introduction of rabies virus to Bali is described. The nucleoprotein (N) gene of rabies virus from dog brain and human clinical specimens was sequenced using an automated DNA sequencer. Phylogenetic inference with Bayesian Markov Chain Monte Carlo (MCMC) analysis using the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) v. 1.7.5 software confirmed that the outbreak of rabies in Bali was caused by an Indonesian lineage virus following a single introduction. The ancestor of Bali viruses was the descendant of a virus from Kalimantan. Contact tracing showed that the event most likely occurred in early 2008. The introduction of rabies into a large unvaccinated dog population in Bali clearly demonstrates the risk of disease transmission for government agencies and should lead to an increased preparedness and efforts for sustained risk reduction to prevent such events from occurring in future. Copyright © Cambridge University Press 2013 The online version of this article is published within an Open Access environment subject to the conditions of the Creative Commons Attribution licence . © 2013 Cambridge University Press.


Valdivia-Granda W.A.,Orion Integrated Biosciences Inc.
Biosecurity and Bioterrorism | Year: 2010

The intentional release of traditional or combinatorial bioweapons remains one of the most important challenges that will continue to shape homeland security. The misuse of dual-use and how-to methods and techniques in the fields of molecular, synthetic, and computational biology can lessen the technical barriers for launching attacks, even for small groups or individuals. Bioinformatics is guiding the implementation of several biodefense countermeasures. However, existing algorithms have not effectively translated available pathogen genomic data into standardized diagnostics, rational vaccine development, or broad spectrum therapeutics. Despite its potential, bioinformatics has a limited impact on forensic and intelligence operations. More than 12 biodefense databases and information exchange architectures lack interoperability and a common layer that restricts scalability and the development of biodefense enterprises. Therefore, in order to use next-generation genome sequencing for medical intelligence, forensic operations, biothreat awareness, and mitigation, the attention has to be redirected toward the development of computational biology applications. This article debates some of the challenges that the bioinformatics field confronts in terms of biodefense problems and proposes potential opportunities to use pathogen genomic data. Issues related to the analysis of pathogen genomes and emerging methods including genomic barcoding, active curation, and knowledge management and their impact on intelligence, forensics, and policymaking are discussed. © 2010 Mary Ann Liebert, Inc.


Valdivia-Granda W.A.,Orion Integrated Biosciences Inc.
Virulence | Year: 2013

To protect our civilians and warfighters against both known and unknown pathogens, biodefense stakeholders must be able to foresee possible technological trends that could affect their threat risk assessment. However, significant flaws in how we prioritize our countermeasure-needs continue to limit their development. As recombinant biotechnology becomes increasingly simplified and inexpensive, small groups, and even individuals, can now achieve the design, synthesis, and production of pathogenic organisms for offensive purposes. Under these daunting circumstances, a reliable biosurveillance approach that supports a diversity of users could better provide early warnings about the emergence of new pathogens (both natural and manmade), reverse engineer pathogens carrying traits to avoid available countermeasures, and suggest the most appropriate detection, prophylactic, and therapeutic solutions. While impressive in data mining capabilities, real-time content analysis of social media data misses much of the complexity in the factual reality. Quality issues within freeform user-provided hashtags and biased referencing can significantly undermine our confidence in the information obtained to make critical decisions about the natural vs. intentional emergence of a pathogen. At the same time, errors in pathogen genomic records, the narrow scope of most databases, and the lack of standards and interoperability across different detection and diagnostic devices, continue to restrict the multidimensional biothreat assessment. The fragmentation of our biosurveillance efforts into different approaches has stultified attempts to implement any new foundational enterprise that is more reliable, more realistic and that avoids the scenario of the warning that comes too late. This discussion focus on the development of genomic-based decentralized medical intelligence and laboratory system to track emerging and novel microbial health threats in both military and civilian settings and the use of virulence factors for risk assessment. Examples of the use of motif fingerprints for pathogen discrimination are provided.


Valdivia-Granda W.A.,Orion Integrated Biosciences Inc
Virulence | Year: 2013

To protect our civilians and warfighters against both known and unknown pathogens, biodefense stakeholders must be able to foresee possible technological trends that could affect their threat risk assessment. However, significant flaws in how we prioritize our countermeasure-needs continue to limit their development. As recombinant biotechnology becomes increasingly simplified and inexpensive, small groups, and even individuals, can now achieve the design, synthesis, and production of pathogenic organisms for offensive purposes. Under these daunting circumstances, a reliable biosurveillance approach that supports a diversity of users could better provide early warnings about the emergence of new pathogens (both natural and manmade), reverse engineer pathogens carrying traits to avoid available countermeasures, and suggest the most appropriate detection, prophylactic, and therapeutic solutions. While impressive in data mining capabilities, real-time content analysis of social media data misses much of the complexity in the factual reality. Quality issues within free-form user-provided hashtags and biased referencing can significantly undermine our confidence in the information obtained to make critical decisions about the natural vs. intentional emergence of a pathogen. At the same time, errors in pathogen genomic records, the narrow scope of most databases, and the lack of standards and interoperability across different detection and diagnostic devices, continue to restrict the multidimensional biothreat assessment. The fragmentation of our biosurveillance efforts into different approaches has stultified attempts to implement any new foundational enterprise that is more reliable, more realistic and that avoids the scenario of the warning that comes too late. This discussion focus on the development of genomic-based decentralized medical intelligence and laboratory system to track emerging and novel microbial health threats in both military and civilian settings and the use of virulence factors for risk assessment. Examples of the use of motif fingerprints for pathogen discrimination are provided. © 2013 Landes Bioscience.


PubMed | Orion Integrated Biosciences Inc.
Type: Journal Article | Journal: Biosecurity and bioterrorism : biodefense strategy, practice, and science | Year: 2010

The intentional release of traditional or combinatorial bioweapons remains one of the most important challenges that will continue to shape homeland security. The misuse of dual-use and how-to methods and techniques in the fields of molecular, synthetic, and computational biology can lessen the technical barriers for launching attacks, even for small groups or individuals. Bioinformatics is guiding the implementation of several biodefense countermeasures. However, existing algorithms have not effectively translated available pathogen genomic data into standardized diagnostics, rational vaccine development, or broad spectrum therapeutics. Despite its potential, bioinformatics has a limited impact on forensic and intelligence operations. More than 12 biodefense databases and information exchange architectures lack interoperability and a common layer that restricts scalability and the development of biodefense enterprises. Therefore, in order to use next-generation genome sequencing for medical intelligence, forensic operations, biothreat awareness, and mitigation, the attention has to be redirected toward the development of computational biology applications. This article debates some of the challenges that the bioinformatics field confronts in terms of biodefense problems and proposes potential opportunities to use pathogen genomic data. Issues related to the analysis of pathogen genomes and emerging methods including genomic barcoding, active curation, and knowledge management and their impact on intelligence, forensics, and policymaking are discussed.


PubMed | University of Georgia, Lawrence Livermore National Laboratory, Orion Integrated Biosciences Inc., U.S. Department of Agriculture and Manhattan College
Type: Journal Article | Journal: Virus genes | Year: 2016

Epizootic hemorrhagic disease virus (EHDV) is an orbivirus of the Reoviridae family that has significant impact on wild and captive white-tailed deer. Although closely related to bluetongue virus that can cause disease in sheep and cattle, North American EHDV historically has not been associated with disease in cattle or sheep. Severe disease in cattle has been reported with other EHDV strains from East Asia and the Middle East. To understand the potential role of viral genetics in the epidemiology of epizootic hemorrhagic disease, a molecular characterization of North American EHDV strains from 1955 to 2012 was conducted via conventional phylogenetic analysis and a new classification approach using motif fingerprint patterns. Overall, this study indicates that the genetic make-up of EHDV populations in North America have slowly evolved over time. The data also suggested limited reassortment events between serotypes 1 and 2 and introduces a new analysis tool for more detailed sequence pattern analysis.

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