Applied & translational genomics最新文献

{"title":"Wheat quality improvement at CIMMYT and the use of genomic selection on it","authors":"Carlos Guzman ,&nbsp;Roberto Javier Peña ,&nbsp;Ravi Singh ,&nbsp;Enrique Autrique ,&nbsp;Susanne Dreisigacker ,&nbsp;Jose Crossa ,&nbsp;Jessica Rutkoski ,&nbsp;Jesse Poland ,&nbsp;Sarah Battenfield","doi":"10.1016/j.atg.2016.10.004","DOIUrl":"10.1016/j.atg.2016.10.004","url":null,"abstract":"<div><p>The International Center for Maize and Wheat Improvement (CIMMYT) leads the Global Wheat Program, whose main objective is to increase the productivity of wheat cropping systems to reduce poverty in developing countries. The priorities of the program are high grain yield, disease resistance, tolerance to abiotic stresses (drought and heat), and desirable quality. The Wheat Chemistry and Quality Laboratory has been continuously evolving to be able to analyze the largest number of samples possible, in the shortest time, at lowest cost, in order to deliver data on diverse quality traits on time to the breeders for making selections for advancement in the breeding pipeline. The participation of wheat quality analysis/selection is carried out in two stages of the breeding process: evaluation of the parental lines for new crosses and advanced lines in preliminary and elite yield trials. Thousands of lines are analyzed which requires a big investment in resources. Genomic selection has been proposed to assist in selecting for quality and other traits in breeding programs. Genomic selection can predict quantitative traits and is applicable to multiple quantitative traits in a breeding pipeline by attaining historical phenotypes and adding high-density genotypic information. Due to advances in sequencing technology, genome-wide single nucleotide polymorphism markers are available through genotyping-by-sequencing at a cost conducive to application for genomic selection. At CIMMYT, genomic selection has been applied to predict all of the processing and end-use quality traits regularly tested in the spring wheat breeding program. These traits have variable levels of prediction accuracy, however, they demonstrated that most expensive traits, dough rheology and baking final product, can be predicted with a high degree of confidence. Currently it is being explored how to combine both phenotypic and genomic selection to make more efficient the genetic improvement for quality traits at CIMMYT spring wheat breeding program.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"11 ","pages":"Pages 3-8"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.10.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76615832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Maximizing the potential of multi-parental crop populations","authors":"Olufunmilayo Ladejobi ,&nbsp;James Elderfield ,&nbsp;Keith A. Gardner ,&nbsp;R. Chris Gaynor ,&nbsp;John Hickey ,&nbsp;Julian M. Hibberd ,&nbsp;Ian J. Mackay ,&nbsp;Alison R. Bentley","doi":"10.1016/j.atg.2016.10.002","DOIUrl":"10.1016/j.atg.2016.10.002","url":null,"abstract":"<div><p>Most agriculturally significant crop traits are quantitatively inherited which limits the ease and efficiency of trait dissection. Multi-parent populations overcome the limitations of traditional trait mapping and offer new potential to accurately define the genetic basis of complex crop traits. The increasing popularity and use of nested association mapping (NAM) and multi-parent advanced generation intercross (MAGIC) populations raises questions about the optimal design and allocation of resources in their creation. In this paper we review strategies for the creation of multi-parent populations and describe two complementary <em>in silico</em> studies addressing the design and construction of NAM and MAGIC populations. The first simulates the selection of diverse founder parents and the second the influence of multi-parent crossing schemes (and number of founders) on haplotype creation and diversity. We present and apply two open software resources to simulate alternate strategies for the development of multi-parent populations.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"11 ","pages":"Pages 9-17"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.10.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89703846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic advancement: Aiming to affirm and improve human life","authors":"Carol Isaacson Barash ,&nbsp;Nigel G. Halford","doi":"10.1016/j.atg.2016.11.002","DOIUrl":"https://doi.org/10.1016/j.atg.2016.11.002","url":null,"abstract":"","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"11 ","pages":"Pages 1-2"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.11.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90015230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncertainty and innovation: Understanding the role of cell-based manufacturing facilities in shaping regulatory and commercialization environments","authors":"Rosario Isasi ,&nbsp;Vasiliki Rahimzadeh ,&nbsp;Kathleen Charlebois","doi":"10.1016/j.atg.2016.11.001","DOIUrl":"https://doi.org/10.1016/j.atg.2016.11.001","url":null,"abstract":"<div><p>The purpose of this qualitative study is to elucidate stakeholder perceptions of, and institutional practices related to cell-based therapies and products (CTP) regulation and commercialization in Canada. The development of reproducible, safe and effective CTPs is predicated on regulatory and commercialization environments that enable innovation. Manufacturing processes constitute a critical step for CTP development in this regard. The road from CTP manufacturing to translation in the clinic, however, has yet to be paved. This study aims to fill an empirical gap in the literature by exploring how CTP manufacturing facilities navigate Canadian regulatory and commercialization environments, which together drive the translation of novel CTPs from bench to bedside. Using the multi-level model of practice-driven institutional change proposed by Smets et al., we demonstrate how CTP manufacturing practices are governed by established standards, yet meaningfully shape higher-order regulatory and commercial norms in CTP research and development. We identify four key themes that undergird such processes of innovation: 1) managing regulatory uncertainty, which stems from an inability to classify CTPs within existing regulatory categories for approval and commercialization purposes; 2) building a ‘business case’ whereby a CTP's market potential is determined in large part by proving its safety and effectiveness; 3) standardizing manufacturing procedures that mobilize CTPs from a research and development phase to a commercialization one; and 4) networking between researchers and regulators to develop responsible commercialization processes that reflect the uniqueness of CTPs as distinct from other biologics and medical devices.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"11 ","pages":"Pages 27-39"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.11.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90015232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Developing integrated crop knowledge networks to advance candidate gene discovery","authors":"Keywan Hassani-Pak ,&nbsp;Martin Castellote ,&nbsp;Maria Esch ,&nbsp;Matthew Hindle ,&nbsp;Artem Lysenko ,&nbsp;Jan Taubert ,&nbsp;Christopher Rawlings","doi":"10.1016/j.atg.2016.10.003","DOIUrl":"10.1016/j.atg.2016.10.003","url":null,"abstract":"<div><p>The chances of raising crop productivity to enhance global food security would be greatly improved if we had a complete understanding of all the biological mechanisms that underpinned traits such as crop yield, disease resistance or nutrient and water use efficiency. With more crop genomes emerging all the time, we are nearer having the basic information, at the gene-level, to begin assembling crop gene catalogues and using data from other plant species to understand how the genes function and how their interactions govern crop development and physiology. Unfortunately, the task of creating such a complete knowledge base of gene functions, interaction networks and trait biology is technically challenging because the relevant data are dispersed in myriad databases in a variety of data formats with variable quality and coverage. In this paper we present a general approach for building genome-scale knowledge networks that provide a unified representation of heterogeneous but interconnected datasets to enable effective knowledge mining and gene discovery. We describe the datasets and outline the methods, workflows and tools that we have developed for creating and visualising these networks for the major crop species, wheat and barley. We present the global characteristics of such knowledge networks and with an example linking a seed size phenotype to a barley WRKY transcription factor orthologous to TTG2 from Arabidopsis, we illustrate the value of integrated data in biological knowledge discovery. The software we have developed (<span>www.ondex.org</span><svg><path></path></svg>) and the knowledge resources (<span>http://knetminer.rothamsted.ac.uk)</span><svg><path></path></svg> we have created are all open-source and provide a first step towards systematic and evidence-based gene discovery in order to facilitate crop improvement.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"11 ","pages":"Pages 18-26"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.10.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82595771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial transfer: Implications for assisted reproductive technologies","authors":"AS Reznichenko ,&nbsp;C Huyser ,&nbsp;MS Pepper","doi":"10.1016/j.atg.2016.10.001","DOIUrl":"https://doi.org/10.1016/j.atg.2016.10.001","url":null,"abstract":"<div><p>The use of mitochondrial transfer as a clinic procedure is drawing closer to reality. Here we provide a detailed overview of mitochondrial transfer techniques – both established and recent – including pronuclear, spindle, ooplasmic and blastomere transfer. Reasons as to why some techniques are more suitable for the prevention of mitochondrial DNA disease than others, as well as the advantages and disadvantages of each methodology, are discussed. The possible clinical introduction of these techniques has raised concerns about the adverse effects they may have on resultant embryos and offspring. Success rates of each technique, embryo viability and developmental consequences post mitochondrial transfer are addressed through analysis of evidence obtained from both animal and human studies. Counterarguments against potential mitochondrial-nuclear genome incompatibility are also provided. Additional clinical applications of mitochondrial transfer techniques are discussed. These include the rescue or enhancement of fertility in women of advanced maternal age or those suffering from diabetes. An alternative to using mitochondrial DNA transfer for germ line therapies is the therapeutic use of somatic cell nuclear transfer for the generation of personalised stem cells. Although ethically challenging, this method could offer patients already suffering from mitochondrial DNA diseases a novel treatment option.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"11 ","pages":"Pages 40-47"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.10.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91758870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Translating genetics beyond bench and bedside: A comparative perspective on health care infrastructures for ‘familial’ breast cancer","authors":"Erik Aarden","doi":"10.1016/j.atg.2016.09.001","DOIUrl":"10.1016/j.atg.2016.09.001","url":null,"abstract":"<div><p>Developments in genomics research are considered to have great potential for improving health care – making genomics an urgent site for translational efforts. Yet while much emphasis is put on the technical challenges of translation, there is less scholarly attention for the social infrastructures through which novel medical interventions may be delivered to patient populations. Reflecting the idea that cancer is at the frontier of genomic applications in health care, this paper explores how the assessment of familial breast cancer risks was ‘translated’ into routine health care in Germany, the Netherlands and the United Kingdom. The paper identifies regulation, institutionalization and standardization as key mechanisms of translation that find distinct expression in particular sociocultural contexts and shape both the social and technical making of genomics into routine clinical practice. Translation is therefore an area of social as well as technical concern, and therefore requires collective decision-making.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"11 ","pages":"Pages 48-54"},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.09.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73141932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic advancement: Aiming to affirm and improve human life☆","authors":"C. Barash, Nigel G Halford","doi":"10.1016/j.atg.2016.11.002","DOIUrl":"https://doi.org/10.1016/j.atg.2016.11.002","url":null,"abstract":"","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"37 1","pages":"1 - 2"},"PeriodicalIF":0.0,"publicationDate":"2016-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82863506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial transfer: Implications for assisted reproductive technologies","authors":"A. Reznichenko, C. Huyser, M. Pepper","doi":"10.1016/j.atg.2016.10.001","DOIUrl":"https://doi.org/10.1016/j.atg.2016.10.001","url":null,"abstract":"","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"86 1","pages":"40 - 47"},"PeriodicalIF":0.0,"publicationDate":"2016-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84006273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Barriers to clinical adoption of next generation sequencing: Perspectives of a policy Delphi panel","authors":"Donna A. Messner ,&nbsp;Jennifer Al Naber ,&nbsp;Pei Koay ,&nbsp;Robert Cook-Deegan ,&nbsp;Mary Majumder ,&nbsp;Gail Javitt ,&nbsp;Patricia Deverka ,&nbsp;Rachel Dvoskin ,&nbsp;Juli Bollinger ,&nbsp;Margaret Curnutte ,&nbsp;Subhashini Chandrasekharan ,&nbsp;Amy McGuire","doi":"10.1016/j.atg.2016.05.004","DOIUrl":"10.1016/j.atg.2016.05.004","url":null,"abstract":"<div><p>This research aims to inform policymakers by engaging expert stakeholders to identify, prioritize, and deliberate the most important and tractable policy barriers to the clinical adoption of next generation sequencing (NGS). A 4-round Delphi policy study was done with a multi-stakeholder panel of 48 experts. The first 2 rounds of online questionnaires (reported here) assessed the importance and tractability of 28 potential barriers to clinical adoption of NGS across 3 major policy domains: intellectual property, coverage and reimbursement, and FDA regulation. We found that: 1) proprietary variant databases are seen as a key challenge, and a potentially intractable one; 2) payer policies were seen as a frequent barrier, especially a perceived inconsistency in standards for coverage; 3) relative to other challenges considered, FDA regulation was not strongly perceived as a barrier to clinical use of NGS. Overall the results indicate a perceived need for policies to promote data-sharing, and a desire for consistent payer coverage policies that maintain reasonably high standards of evidence for clinical utility, limit testing to that needed for clinical care decisions, and yet also flexibly allow for clinician discretion to use genomic testing in uncertain circumstances of high medical need.</p></div>","PeriodicalId":90104,"journal":{"name":"Applied & translational genomics","volume":"10 ","pages":"Pages 19-24"},"PeriodicalIF":0.0,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.atg.2016.05.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76534656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}