Journal articles on the topic 'Genomics study'
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Parks, M., S. Subramanian, C. Baroni, M. C. Salvatore, G. Zhang, C. D. Millar, and D. M. Lambert. "Ancient population genomics and the study of evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1660 (January 19, 2015): 20130381. http://dx.doi.org/10.1098/rstb.2013.0381.
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Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin ( Pygoscelis adeliae ). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.
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Hien, Le Thi Thu, Nguyen Tuong Van, Kim Thi Phuong Oanh, Nguyen Dang Ton, Huynh Thi Thu Hue, Nguyen Thuy Duong, Pham Le Bich Hang, and Nguyen Hai Ha. "Genomics and big data: Research, development and applications." Vietnam Journal of Biotechnology 19, no. 3 (October 13, 2021): 393–410. http://dx.doi.org/10.15625/1811-4989/16158.
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Recent years, genomics and big data analytics have been widely applied and have significant impacts in various important areas of social life worldwide. The development of the next-generation sequencing (NGS) technologies, such as whole-genome sequencing (WGS), whole-exome sequencing (WES), transcriptome, and/or targeted sequencing, has enabled quickly generating the genomes of interested living organisms. Around the world many nations have invested in and promoted the development of genomics and big data analytics. A number of well-established projects on sequencing of human, animal, plant, and microorganism genomes to generate vast amounts of genomic data have been conducted independently or as collaborative efforts by national or international research networks of scientists specializing in different technical fields of genomics, bioinformatics, computational and statistical biology, automation, artificial intelligence, etc. Complicated and large genomic datasets have been effectively established, storage, managed, and used. Vietnam supports this new field of study through setting up governmental authorized institutions and conducting genomic research projects of human and other endemic organisms. In this paper, the research, development, and applications of genomic big data are reviewed with focusing on: (i) Available sequencing technologies for generating genomic datasets; (ii) Genomics and big data initiatives worldwide; (iii) Genomics and big data analytics in selected countries and Vietnam; (iv) Genomic data applications in key areas including medicine for human health care, agriculture - forestry, food safety, and environment.
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Taylor, Natalie, Stephanie Best, Melissa Martyn, Janet C. Long, Kathryn N. North, Jeffrey Braithwaite, and Clara Gaff. "A transformative translational change programme to introduce genomics into healthcare: a complexity and implementation science study protocol." BMJ Open 9, no. 3 (March 2019): e024681. http://dx.doi.org/10.1136/bmjopen-2018-024681.
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IntroductionTranslating scientific advances in genomic medicine into evidence-based clinical practice is challenging. Studying the natural translation of genomics into ‘early-adopting’ health system sectors is essential. We will (a) examine 29 health systems (Australian and Melbourne Genomics Health Alliance flagships) integrating genomics into practice and (b) combine this learning to co-design and test an evidence-based generalisable toolkit for translating genomics into healthcare.Methods and analysisTwenty-nine flagships integrating genomics into clinical settings are studied as complex adaptive systems to understand emergent and self-organising behaviours among inter-related actors and processes. The Effectiveness–Implementation Hybrid approach is applied to gather information on the delivery and potential for real-world implementation. Stages ‘1’ and ‘2a’ (representing hybrid model 1) are the focus of this protocol. The Translation Science to Population Impact (TSci Impact) framework is used to study policy decisions and service provision, and the Theoretical Domains Framework (TDF) is used to understand individual level behavioural change; both frameworks are applied across stages 1 and 2a. Stage 1 synthesises interview data from 32 participants involved in developing the genomics clinical practice systems and approaches across five ‘demonstration-phase’ (early adopter) flagships. In stage 2a, stakeholders are providing quantitative and qualitative data on process mapping, clinical audits, uptake and sustainability (TSci Impact), and psychosocial and environmental determinants of change (TDF). Findings will be synthesised before codesigning an intervention toolkit to facilitate implementation of genomic testing. Study methods to simultaneously test the comparative effectiveness of genomic testing and the implementation toolkit (stage 2b), and the refined implementation toolkit while simply observing the genomics intervention (stage 3) are summarised.Ethics and disseminationEthical approval has been granted. The results will be disseminated in academic forums and used to refine interventions to translate genomics evidence into healthcare. Non-traditional academic dissemination methods (eg, change in guidelines or government policy) will also be employed.
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Howard Sharp, Katianne M., Niki Jurbergs, Annastasia Ouma, Lynn Harrison, Elsie Gerhardt, Leslie Taylor, Kayla Hamilton, et al. "Factors Associated With Declining to Participate in a Pediatric Oncology Next-Generation Sequencing Study." JCO Precision Oncology, no. 4 (September 2020): 202–11. http://dx.doi.org/10.1200/po.19.00213.
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PURPOSE For the advances of pediatric oncology next-generation sequencing (NGS) research to equitably benefit all children, a diverse and representative sample of participants is needed. However, little is known about demographic and clinical characteristics that differentiate families who decline enrollment in pediatric oncology NGS research. METHODS Demographic and clinical data were retrospectively extracted for 363 pediatric patients (0-21 years) with cancer approached for enrollment in Genomes for Kids (G4K), a study examining the feasibility of comprehensive clinical genomic analysis of tumors and paired normal samples. Demographic and clinical factors that significantly differentiated which families declined were subsequently compared, for 348 families, with enrollment in Clinical Implementation of Pharmacogenetics (PG4KDS), a pharmacogenomics study with more explicit therapeutic benefit examining genes affecting drug responses and metabolism. RESULTS Fifty-three families (14.6%) declined enrollment in G4K. Race/ethnicity was the only variable that significantly differentiated study refusal according to multivariable logistic regression, with families of black children more likely to decline enrollment compared with families of non-Hispanic or Hispanic white children. Reasons for declining G4K were generally consistent with other pediatric genomics research: feeling overwhelmed and insurance discrimination fears were most frequently cited. Families of black children were also more likely to decline enrollment in PG4KDS. Thirteen (3.7%) of the 348 families approached for both studies declined PG4KDS. CONCLUSION Race/ethnicity differentiated study declination across two different pediatric oncology genomics studies, suggesting enrollment disparities in the context of pediatric oncology genomics research. Genomics research participant samples that do not fully represent racial and ethnic minorities risk further exacerbating health disparities. Additional work is needed to understand the nuances of parental decision making in genomic research and facilitate enrollment of diverse patient populations.
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Lamichhaney, Sangeet, Daren C. Card, Phil Grayson, João F. R. Tonini, Gustavo A. Bravo, Kathrin Näpflin, Flavia Termignoni-Garcia, et al. "Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1777 (June 3, 2019): 20180248. http://dx.doi.org/10.1098/rstb.2018.0248.
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Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
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Alam, Intikhab, Mike Cornell, Darren M. Soanes, Cornelia Hedeler, Han Min Wong, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver, and Norman W. Paton. "A Methodology for Comparative Functional Genomics." Journal of Integrative Bioinformatics 4, no. 3 (December 1, 2007): 112–22. http://dx.doi.org/10.1515/jib-2007-69.
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Abstract The continuing and rapid increase in the number of fully sequenced genomes is creating new opportunities for comparative studies. However, although many genomic databases store data from multiple organisms, for the most part they provide limited support for comparative genomics. We argue that refocusing genomic data management to provide more direct support for comparative studies enables systematic identification of important relationships between species, thereby increasing the value that can be obtained from sequenced genomes. The principal result of the paper is a methodology, in which comparative analyses are constructed over a foundation based on sequence clusters and evolutionary relationships. This methodology has been applied in a systematic study of the fungi, and we describe how comparative analyses have been implemented as an analysis library over the e-Fungi data warehouse.
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Blaškovičová, Jana, and Ján Labuda. "Analytical methods in herpesvirus genomics." Acta Chimica Slovaca 7, no. 2 (October 1, 2014): 109–18. http://dx.doi.org/10.2478/acs-2014-0019.
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Abstract Genomics is a branch of bioanalytical chemistry characterized as the study of the genome structure and function. Genome represents the complete set of chromosomal and extrachromosomal genes of an organism, a cell, an organelle or a virus. There are at least five from eight species of herpesviruses commonly widespread among humans, Herpes simplex virus type 1 and 2, Varicella zoster virus, Epstein-Barr virus and Cytomegalovirus. Human gammaherpesviruses can cause serious diseases including B-cell lymphoma and Kaposi’s sarcoma. Diagnostics and study of the herpesviruses is directly dependent on the development of modern analytical methods able to detect and determine the presence and evolution of herpesviral particles/ genomes. Diagnostics and genomic characterization of human herpesvirus species is based on bioanalytical methods such as polymerase chain reaction (PCR), DNA sequencing, gel electrophoresis, blotting and others. The progress in analytical approaches in the herpesvirus genomics is reviewed in this article.
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Lucas, Joseph E., Carlos M. Carvalho, Julia Ling-Yu Chen, Jen-Tsan Chi, and Mike West. "Cross-Study Projections of Genomic Biomarkers: An Evaluation in Cancer Genomics." PLoS ONE 4, no. 2 (February 19, 2009): e4523. http://dx.doi.org/10.1371/journal.pone.0004523.
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Vadlamudi, Lata, Carmen Maree Bennett, Melanie Tom, Ghusoon Abdulrasool, Kristian Brion, Ben Lundie, Hnin Aung, et al. "A Multi-Disciplinary Team Approach to Genomic Testing for Drug-Resistant Epilepsy Patients—The GENIE Study." Journal of Clinical Medicine 11, no. 14 (July 21, 2022): 4238. http://dx.doi.org/10.3390/jcm11144238.
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Background. The genomic era has led to enormous progress in clinical care and a multi-disciplinary team (MDT) approach is imperative for integration of genomics into epilepsy patient care. Methods. The MDT approach involved patient selection, genomic testing choice, variant discussions and return of results. Genomics analysis included cytogenomic testing and whole exome sequencing (WES). Neurologist surveys were undertaken at baseline and after genomic testing to determine if genomic diagnoses would alter their management, and if there was a change in confidence in genomic testing and neurologist perceptions of the MDT approach. Results. The total diagnostic yield from all genomic testing was 17% (11/66), with four diagnoses from cytogenomic analyses. All chromosomal microarray (CMA) diagnoses were in patients seen by adult neurologists. Diagnostic yield for WES was 11% (7/62). The most common gene with pathogenic variants was DCX, reported in three patients, of which two were mosaic. The genomic diagnosis impacted management in 82% (9/11). There was increased confidence with integrating genomics into clinical care (Pearson chi square = 83, p = 0.004) and qualitative comments were highly supportive of the MDT approach. Conclusions. We demonstrated diagnostic yield from genomic testing, and the impact on management in a cohort with drug-resistant epilepsy. The MDT approach increased confidence in genomic testing and neurologists valued the input from this approach. The utility of CMA was demonstrated in epilepsy patients seen by adult neurologists as was the importance of considering mosaicism for previously undiagnosed patients.
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Goldenberg, Aaron J., Roselle Ponsaran, Amy Gaviglio, Dalton Simancek, and Beth A. Tarini. "Genomics and Newborn Screening: Perspectives of Public Health Programs." International Journal of Neonatal Screening 8, no. 1 (January 28, 2022): 11. http://dx.doi.org/10.3390/ijns8010011.
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This study assesses the benefits and challenges of using genomics in Newborn Screening Programs (NBS) from the perspectives of State program officials. This project aims to help programs develop policies that will aid in the integration of genomic technology. Discussion groups were conducted with the NBS Program and Laboratory Directors in the seven HRSA Regional Genomics Collaboratives (August 2014–March 2016). The discussion groups addressed expected uses of genomics, potential benefits, and challenges of integrating genomic technology, and educational needs for parents and other NBS stakeholders: Twelve focus groups were conducted, which included participants from over 40 state programs. Benefits of incorporating genomics included improving screening modalities, supporting diagnostic procedures, and screening for a wider spectrum of disorders. Challenges included the costs of genomics, the ability to educate parents and health care providers about results, and the potential negative psychosocial impact of genomic information. Attempts to address the challenges of integrating genomics must focus on preserving the child welfare goals of NBS programs. Health departments will need to explore how genomics could be used to enhance programs while maintaining universal access to screening.
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Skoglund, Pontus, and Iain Mathieson. "Ancient Genomics of Modern Humans: The First Decade." Annual Review of Genomics and Human Genetics 19, no. 1 (August 31, 2018): 381–404. http://dx.doi.org/10.1146/annurev-genom-083117-021749.
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The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric modern human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa expansion, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document population transformations on every inhabited continent—in particular the effect of agricultural expansions in Africa, Europe, and Oceania—and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field.
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Khan, Nida Tabassum, Namra Jameel, and Maham Jamil Khan. "Functional Genomics–Linking Genotype with Phenotype on Genome-wide Scale." INTERNATIONAL JOURNAL OF APPLIED PHARMACEUTICAL SCIENCES AND RESEARCH 4, no. 01 (January 1, 2019): 4–12. http://dx.doi.org/10.21477/ijapsr.4.1.2.
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Functional genomics manipulates genomic data to study genes and its expression on a genome wide scale involving high-throughput methods. The keyobjective of Functional genomics is to exploit the data acquired from transcriptomic and genomic studies to explain the functions and interfaces of a genome and its corresponding phenotype.
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Jayanthi, K., and C. Mahesh. "A Study on machine learning methods and applications in genetics and genomics." International Journal of Engineering & Technology 7, no. 1.7 (February 5, 2018): 201. http://dx.doi.org/10.14419/ijet.v7i1.7.10653.
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Machine learning enables computers to help humans in analysing knowledge from large, complex data sets. One of the complex data is genetics and genomic data which needs to analyse various set of functions automatically by the computers. Hope this machine learning methods can provide more useful for making these data for further usage like gene prediction, gene expression, gene ontology, gene finding, gene editing and etc. The purpose of this study is to explore some machine learning applications and algorithms to genetic and genomic data. At the end of this study we conclude the following topics classifications of machine learning problems: supervised, unsupervised and semi supervised, which type of method is suitable for various problems in genomics, applications of machine learning and future views of machine learning in genomics.
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Passamonti, Matilde Maria, Elisa Somenzi, Mario Barbato, Giovanni Chillemi, Licia Colli, Stéphane Joost, Marco Milanesi, et al. "The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock." Animals 11, no. 10 (September 28, 2021): 2833. http://dx.doi.org/10.3390/ani11102833.
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Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Sabba, Sara, Meroua Smara, Mehdi Benhacine, Loubna Terra, and Zine Eddine Terra. "Residual Neural Network in Genomics." Computer Science Journal of Moldova 30, no. 3(90) (December 2022): 308–34. http://dx.doi.org/10.56415/csjm.v30.17.
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Residual neural network (ResNet) is a Deep Learning model introduced by He et al. in 2015 to enhance traditional convolutional neural networks proposed to solve computer vision problems. It uses skip connections over some layer blocks to avoid vanishing gradient problem. Currently, many researches are focused to test and prove the efficiency of the ResNet on different domains such as genomics. In fact, the study of human genomes provides important information on the detection of diseases and their best treatments. Therefore, most of the scientists opted for bioinformatics solutions to get results in a reasonable time. In this paper, our interest is to show the effectiveness of the ResNet model on genomics. For that, we propose two new ResNet models to enhance the results of two genomic problems previously resolved by CNN models. The obtained results are very promising and they proved the performance of our ResNet models compared to the CNN models.
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Maradiegue, Ann H., Quannetta T. Edwards, and Diane Seibert. "5-Years Later – Have Faculty Integrated Medical Genetics into Nurse Practitioner Curriculum?" International Journal of Nursing Education Scholarship 10, no. 1 (October 31, 2013): 245–54. http://dx.doi.org/10.1515/ijnes-2012-0007.
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AbstractMany genetic/genomic educational opportunities are available to assist nursing faculty in their knowledge and understanding of genetic/genomics. This study was conducted to assess advance practice nursing faculty members’ current knowledge of medical genetics/genomics, their integration of genetics/genomics content into advance practice nursing curricula, any prior formal training/education in genetics/genomics, and their comfort level in teaching genetics/genomic content. A secondary aim was to conduct a comparative analysis of the 2010 data to a previous study conducted in 2005, to determine changes that have taken place during that time period. During a national nurse practitioner faculty conference, 85 nurse practitioner faculty voluntarily completed surveys. Approximately 70% of the 2010 faculty felt comfortable teaching basic genetic/genomic concepts compared to 50% in 2005. However, there continue to be education gaps in the genetic/genomic content taught to advance practice nursing students. If nurses are going to be a crucial member of the health-care team, they must achieve the requisite competencies to deliver the increasingly complex care patients require.
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Nakagawa, Hidewaki. "Prostate cancer genomics by high-throughput technologies: genome-wide association study and sequencing analysis." Endocrine-Related Cancer 20, no. 4 (April 26, 2013): R171—R181. http://dx.doi.org/10.1530/erc-13-0113.
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Prostate cancer (PC) is the most common malignancy in males. It is evident that genetic factors at both germline and somatic levels play critical roles in prostate carcinogenesis. Recently, genome-wide association studies (GWAS) by high-throughput genotyping technology have identified more than 70 germline variants of various genes or chromosome loci that are significantly associated with PC susceptibility. They include multiple 8q24 loci, prostate-specific genes, and metabolism-related genes. Somatic alterations in PC genomes have been explored by high-throughput sequencing technologies such as whole-genome sequencing and RNA sequencing, which have identified a variety of androgen-responsive events and fusion transcripts represented by E26 transformation-specific (ETS) gene fusions. Recent innovations in high-throughput genomic technologies have enabled us to analyze PC genomics more comprehensively, more precisely, and on a larger scale in multiple ethnic groups to increase our understanding of PC genomics and biology in germline and somatic studies, which can ultimately lead to personalized medicine for PC diagnosis, prevention, and therapy. However, these data indicate that the PC genome is more complex and heterogeneous than we expected from GWAS and sequencing analyses.
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Ryu, Borim, Soo-Yong Shin, Rong-Min Baek, Jeong-Whun Kim, Eunyoung Heo, Inchul Kang, Joshua SungWoo Yang, and Sooyoung Yoo. "Clinical Genomic Sequencing Reports in Electronic Health Record Systems Based on International Standards: Implementation Study." Journal of Medical Internet Research 22, no. 8 (August 10, 2020): e15040. http://dx.doi.org/10.2196/15040.
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Background To implement standardized machine-processable clinical sequencing reports in an electronic health record (EHR) system, the International Organization for Standardization Technical Specification (ISO/TS) 20428 international standard was proposed for a structured template. However, there are no standard implementation guidelines for data items from the proposed standard at the clinical site and no guidelines or references for implementing gene sequencing data results for clinical use. This is a significant challenge for implementation and application of these standards at individual sites. Objective This study examines the field utilization of genetic test reports by designing the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) for genomic data elements based on the ISO/TS 20428 standard published as the standard for genomic test reports. The goal of this pilot is to facilitate the reporting and viewing of genomic data for clinical applications. FHIR Genomics resources predominantly focus on transmitting or representing sequencing data, which is of less clinical value. Methods In this study, we describe the practical implementation of ISO/TS 20428 using HL7 FHIR Genomics implementation guidance to efficiently deliver the required genomic sequencing results to clinicians through an EHR system. Results We successfully administered a structured genomic sequencing report in a tertiary hospital in Korea based on international standards. In total, 90 FHIR resources were used. Among 41 resources for the required fields, 26 were reused and 15 were extended. For the optional fields, 28 were reused and 21 were extended. Conclusions To share and apply genomic sequencing data in both clinical practice and translational research, it is essential to identify the applicability of the standard-based information system in a practical setting. This prototyping work shows that reporting data from clinical genomics sequencing can be effectively implemented into an EHR system using the existing ISO/TS 20428 standard and FHIR resources.
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Kwon, Ronald Y., Claire J. Watson, and David Karasik. "Using zebrafish to study skeletal genomics." Bone 126 (September 2019): 37–50. http://dx.doi.org/10.1016/j.bone.2019.02.009.
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Oikkonen, Jaana, and Irma Järvelä. "Genomics approaches to study musical aptitude." BioEssays 36, no. 11 (August 25, 2014): 1102–8. http://dx.doi.org/10.1002/bies.201400081.
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Osipowski, Paweł, Magdalena Pawełkowicz, Michał Wojcieszek, Agnieszka Skarzyńska, Zbigniew Przybecki, and Wojciech Pląder. "A high-quality cucumber genome assembly enhances computational comparative genomics." Molecular Genetics and Genomics 295, no. 1 (October 16, 2019): 177–93. http://dx.doi.org/10.1007/s00438-019-01614-3.
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Abstract Genetic variation is expressed by the presence of polymorphisms in compared genomes of individuals that can be transferred to next generations. The aim of this work was to reveal genome dynamics by predicting polymorphisms among the genomes of three individuals of the highly inbred B10 cucumber (Cucumis sativus L.) line. In this study, bioinformatic comparative genomics was used to uncover cucumber genome dynamics (also called real-time evolution). We obtained a new genome draft assembly from long single molecule real-time (SMRT) sequencing reads and used short paired-end read data from three individuals to analyse the polymorphisms. Using this approach, we uncovered differentiation aspects in the genomes of the inbred B10 line. The newly assembled genome sequence (B10v3) has the highest contiguity and quality characteristics among the currently available cucumber genome draft sequences. Standard and newly designed approaches were used to predict single nucleotide and structural variants that were unique among the three individual genomes. Some of the variant predictions spanned protein-coding genes and their promoters, and some were in the neighbourhood of annotated interspersed repetitive elements, indicating that the highly inbred homozygous plants remained genetically dynamic. This is the first bioinformatic comparative genomics study of a single highly inbred plant line. For this project, we developed a polymorphism prediction method with optimized precision parameters, which allowed the effective detection of small nucleotide variants (SNVs). This methodology could significantly improve bioinformatic pipelines for comparative genomics and thus has great practical potential in genomic metadata handling.
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McBride, Colleen M., Kristi D. Graves, Kimberly A. Kaphingst, Caitlin G. Allen, Catharine Wang, Elva Arredondo, and William M. P. Klein. "Behavioral and social scientists’ reflections on genomics: a systematic evaluation within the Society of Behavioral Medicine." Translational Behavioral Medicine 9, no. 6 (April 5, 2019): 1012–19. http://dx.doi.org/10.1093/tbm/ibz044.
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ABSTRACT Clinical and public health translation of genomics could be facilitated by expertise from behavioral medicine, yet genomics has not been a significant focus of the Society of Behavioral Medicine (SBM). SBM convened a working group (WG) to lead a systematic exploration of members’ views on: (a) whether SBM should give a higher priority to genomic translation and (b) what efforts, if any, should be made to support this increased engagement. The WG used a stepped process over 2 years that began by gaining input from SBM leadership regarding key issues and suggestions for approach, engaging a cross section of membership to expand and record these discussions, followed by systematic qualitative analyses to inform priority action steps. Discussions with SBM leaders and members suggested that genomics was relevant to SBM, particularly for junior members. SBM members’ expertise in social and behavioral theory, and implementation study designs, were viewed as highly relevant to genomic translation. Participants expressed that behavioral and social scientists should be engaged in translational genomics work, giving special attention to health disparities. Proposed action steps are aligned with a “push–pull” framework of innovation dissemination. “Push” strategies aim to reach potential adopters and included linking members with genomics expertise to those wanting to become involved and raising awareness of evidence-based genomic applications ready for implementation. “Pull” strategies aim to expand demand and included developing partnerships with genomics societies and advocating for funding, study section modifications, and training programs.
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Ellis, Louise A., Janet C. Long, Chiara Pomare, Zeyad Mahmoud, Rebecca Lake, Genevieve Dammery, and Jeffrey Braithwaite. "Mapping continuous learning using social network research: a social network study of Australian Genomics as a Learning Health System." BMJ Open 12, no. 10 (October 2022): e064663. http://dx.doi.org/10.1136/bmjopen-2022-064663.
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ObjectivesTo explore a macrolevel Learning Health System (LHS) and examine if an intentionally designed network can foster a collaborative learning community over time. The secondary aim was to demonstrate the application of social network research to the field of LHS.DesignTwo longitudinal online questionnaires of the Australian Genomics learning community considering relationships between network members at three time points: 2016, 2018, 2019. The questionnaire included closed Likert response questions on collaborative learning patterns and open-response questions to capture general perceptions of the community. Social network data were analysed and visually constructed using Gephi V.0.9.2 software, Likert questions were analysed using SPSS, and open responses were analysed thematically using NVivo.SettingAustralian Genomic Health Alliance.ParticipantsClinicians, scientists, researchers and community representatives.ResultsAustralian Genomics members highlighted the collaborative benefits of the network as a learning community to foster continuous learning in the ever-evolving field of clinical genomics. The learning community grew from 186 members (2016), to 384 (2018), to 439 (2019). Network density increased (2016=0.023, 2018=0.043), then decreased (2019=0.036). Key players remained consistent with potential for new members to achieve focal positions in the network. Informal learning was identified as the most influential learning method for genomic practice.ConclusionsThis study shows that intentionally building a network provides a platform for continuous learning—a fundamental component for establishing an LHS. The Australian Genomics learning community shows evidence of maturity and sustainability in supporting the continuous learning culture of clinical genomics. The network provides a practical means to spread new knowledge and best practice across the entire field. We show that intentionally designed networks provide the opportunity and means for interdisciplinary learning between diverse agents over time and demonstrate the application of social network research to the LHS field.
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Watt, Stuart, Wei Jiao, Andrew M. K. Brown, Teresa Petrocelli, Ben Tran, Tong Zhang, Janet Dancey, Lillian L. Siu, Lincoln D. Stein, and Vincent Ferretti. "Designing a web application for personalized medicine trials." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): e13107-e13107. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.e13107.
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e13107 Background: Clinical genomics uses information from a patient's genome in clinical decision-making, an example of personalized medicine. The OICR/UHN Genomics Cohort Study is assessing the feasibility and developing standard operating procedures for clinical genomics in late stage cancer patients to enable larger trials. Tumor DNA from consenting patients is sequenced across 19 genes to identify actionable mutations and inform use of targeted therapeutic agents. Informatics systems are critical as the study involves 40 staff in 5 cancer centres, 2 laboratories, 3 genomics technologies, and spans screening, consent, obtaining/processing biopsy samples, genomic analysis, clinical laboratory verification, and reporting for decision-making. Methods: We used a process-centered method to develop a web system to manage study activities. Initially it tracked patients, samples, genomic results, decisions and reports across the cohort, monitored progress and sent reminders, working alongside an electronic data capture (EDC) system for the trial's clinical and genomic results. We later added a system to read, store, and analyze the genomics data, and a knowledge base of mutations’ tumor frequency (from the COSMIC database) annotated with clinical significance and drug sensitivity to generate reports for clinicians. Results: The web tracker proved highly adaptive. The design method allowed procedural refinements mid-study, including changes in sample preparation, sample sources, and differences in nomenclature across technologies. As the study procedures stabilized, the system provided deeper support for clinical decision making, enabling the generation of draft reports for verification by an expert panel prior to forwarding to the treating physician. The web tracker complemented the EDC system with its fixed modules for collection of clinical data and genomic results. Conclusions: The system effectively complemented clinical trial software. An agile development process enabled procedures to be refined as feasibility issues were found and resolved, and enabled flexible analysis of mutation data. Our design approach helped stabilize effective procedures for a clinical genomics service, and establish means to assess its performance.
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Kansal, Arushi, Catherine Quinlan, Zornitza Stark, Peter G. Kerr, Andrew J. Mallett, Chandni Lakshmanan, Stephanie Best, and Kushani Jayasinghe. "Theory Designed Strategies to Support Implementation of Genomics in Nephrology." Genes 13, no. 10 (October 21, 2022): 1919. http://dx.doi.org/10.3390/genes13101919.
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(1) Background: Genomic testing is increasingly utilized as a clinical tool; however, its integration into nephrology remains limited. The purpose of this study was to identify barriers and prioritize interventions for the widespread implementation of genomics in nephrology. (2) Methods: Qualitative, semi-structured interviews were conducted with 25 Australian adult nephrologists to determine their perspectives on interventions and models of care to support implementation of genomics in nephrology. Interviews were guided by a validated theoretical framework for the implementation of genomic medicine—the Consolidated Framework of Implementation Research (CFIR). (3) Results: Nephrologists were from 18 hospitals, with 7 having a dedicated multidisciplinary kidney genetics service. Most practiced in the public healthcare system (n = 24), a large number were early-career (n = 13), and few had genomics experience (n = 4). The top three preferred interventions were increased funding, access to genomics champions, and education and training. Where interventions to barriers were not reported, we used the CFIR/Expert Recommendations for Implementing Change matching tool to generate theory-informed approaches. The preferred model of service delivery was a multidisciplinary kidney genetics clinic. (4) Conclusions: This study identified surmountable barriers and practical interventions for the implementation of genomics in nephrology, with multidisciplinary kidney genetics clinics identified as the preferred model of care. The integration of genomics education into nephrology training, secure funding for testing, and counselling along with the identification of genomics champions should be pursued by health services more broadly.
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Ogunrin, Olubunmi, Funmilola Taiwo, and Lucy Frith. "Genomic Literacy and Awareness of Ethical Guidance for Genomic Research in Sub-Saharan Africa: How Prepared Are Biomedical Researchers?" Journal of Empirical Research on Human Research Ethics 14, no. 1 (October 25, 2018): 78–87. http://dx.doi.org/10.1177/1556264618805194.
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Achieving the objectives of rolling out genomic research programs in sub-Saharan Africa depends on how prepared indigenous biomedical researchers are for this type of research. We explored the level of preparedness of biomedical researchers in a sub-Saharan African country using in-depth interviews to obtain data on their understanding of genomics and genomic research and assess their awareness of the scope of the country’s code of health research ethics. Thirty biomedical researchers were interviewed. Only eight were familiar with concepts of genomics, a form of “genomic health literacy.” The majority were not aware of the country’s code of research ethics. This study showed that generally biomedical researchers were not genomic health literate, unaware of the code and its limitations as a source of ethical guidance for the conduct of genomic research. These findings underscore the need for educational training in genomics and creating awareness of ethical oversight for genomic research in sub-Saharan Africa.
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Carpenter, Seren, and R. Steven Conlan. "Clinical Functional Genomics." Cancers 13, no. 18 (September 15, 2021): 4627. http://dx.doi.org/10.3390/cancers13184627.
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Functional genomics is the study of how the genome and its products, including RNA and proteins, function and interact to affect different biological processes. The field of functional genomics includes transcriptomics, proteomics, metabolomics and epigenomics, as these all relate to controlling the genome leading to expression of particular phenotypes. By studying whole genomes—clinical genomics, transcriptomes and epigenomes—functional genomics allows the exploration of the diverse relationship between genotype and phenotype, not only for humans as a species but also in individuals, allowing an understanding and evaluation of how the functional genome ‘contributes’ to different diseases. Functional variation in disease can help us better understand that disease, although it is currently limited in terms of ethnic diversity, and will ultimately give way to more personalized treatment plans.
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Sharoff, Leighsa. "A snapshot of nurses’ understanding, perceptions and comfort level of genomics." Journal of Nursing Education and Practice 11, no. 12 (July 27, 2021): 1. http://dx.doi.org/10.5430/jnep.v11n12p1.
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Objective: The primary aim of this study explored holistic nurses’ self-perceived genomic knowledge, perceptions, attitude and comfort of genomics. A second aim compared results to previous findings of nurse educators and advanced degree practicing registered nurses’ genomic knowledge utilizing the same survey instruments.Methods: Design: Recruitment of participants, through the American Holistic Nurses Association (AHNA), was achieved via an anonymous Survey Monkey link of the Genetic and Genomic Literacy Assessment (GGLA) survey. The GGLA survey comprised three aspects: Self-Perceived Genomic Knowledge Survey; Perceptions and Attitudes about Genomics Integration into Nursing Practice Survey and the Comfort Level of Genomics Survey. Method: The GGLA survey link was made available via the AHNA newsletter.Results: Holistic nurses (n = 41) self-perceived genomic knowledge level demonstrated a knowledge base gap in their comprehension and ability to explain genomic concepts to their patients. Majority of holistic nurses were significantly not comfortable with their genomic knowledge (90% or greater). Comparison with nurse educators (n = 53) and advanced degree practicing registered nurses’ (n = 36) genomic knowledge provided additional insight.Conclusions: A significant majority of nurses are unprepared to adopt genomics into their practice whilst experiencing a lack comfort and confidence. The global success of nursing practice resides with its’ practitioners being fully informed and competent with all required competencies, especially if nursing is to remain prevalent within personalized healthcare.
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Dewell, Sarah, Karen Benzies, and Carla Ginn. "Precision Health and Nursing: Seeing the Familiar in the Foreign." Canadian Journal of Nursing Research 52, no. 3 (September 2020): 199–208. http://dx.doi.org/10.1177/0844562120945159.
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Precision health is the integration of personal genomic data with biological, environmental, behavioral, and other information relevant to the care of a patient. Genetics and genomics are essential components of precision health. Genetics is the study of the effects of individual genes, and genomics is the study of all the components of the genome and interactions between genes, environmental factors, and other psychosocial and cultural factors. Knowledge about the role of genetics and genomics on health outcomes has increased substantially since the completion of the human genome project in 2003. Insights about genetics and genomics obtained from bench science are now having positive clinical implications on patient health outcomes. Nurses have the potential to make distinct contributions to precision health due to their unique role in the health care system. In this article, we discuss gaps in the development of precision health in nursing and how nursing can expand the definition of precision health to actualize its potential. Precision health plays a role in nursing practice. Understanding this connection positions nurses to incorporate genetic and genomic knowledge into their nursing practice.
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Daniels, Rachel F., Stephen F. Schaffner, Edward A. Wenger, Joshua L. Proctor, Hsiao-Han Chang, Wesley Wong, Nicholas Baro, et al. "Modeling malaria genomics reveals transmission decline and rebound in Senegal." Proceedings of the National Academy of Sciences 112, no. 22 (May 4, 2015): 7067–72. http://dx.doi.org/10.1073/pnas.1505691112.
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To study the effects of malaria-control interventions on parasite population genomics, we examined a set of 1,007 samples of the malaria parasite Plasmodium falciparum collected in Thiès, Senegal between 2006 and 2013. The parasite samples were genotyped using a molecular barcode of 24 SNPs. About 35% of the samples grouped into subsets with identical barcodes, varying in size by year and sometimes persisting across years. The barcodes also formed networks of related groups. Analysis of 164 completely sequenced parasites revealed extensive sharing of genomic regions. In at least two cases we found first-generation recombinant offspring of parents whose genomes are similar or identical to genomes also present in the sample. An epidemiological model that tracks parasite genotypes can reproduce the observed pattern of barcode subsets. Quantification of likelihoods in the model strongly suggests a reduction of transmission from 2006–2010 with a significant rebound in 2012–2013. The reduced transmission and rebound were confirmed directly by incidence data from Thiès. These findings imply that intensive intervention to control malaria results in rapid and dramatic changes in parasite population genomics. The results also suggest that genomics combined with epidemiological modeling may afford prompt, continuous, and cost-effective tracking of progress toward malaria elimination.
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Hu, Shiqi, Gaojie Li, Jingjing Yang, and Hongwei Hou. "Aquatic Plant Genomics: Advances, Applications, and Prospects." International Journal of Genomics 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/6347874.
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Genomics is a discipline in genetics that studies the genome composition of organisms and the precise structure of genes and their expression and regulation. Genomics research has resolved many problems where other biological methods have failed. Here, we summarize advances in aquatic plant genomics with a focus on molecular markers, the genes related to photosynthesis and stress tolerance, comparative study of genomes and genome/transcriptome sequencing technology.
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Tahir Ul Qamar, Muhammad, Xitong Zhu, Feng Xing, and Ling-Ling Chen. "ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline." Bioinformatics 35, no. 20 (March 9, 2019): 4156–58. http://dx.doi.org/10.1093/bioinformatics/btz168.
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Abstract Summary Since the idea of pan-genomics emerged several tools and pipelines have been introduced for prokaryotic pan-genomics. However, not a single comprehensive pipeline has been reported which could overcome multiple challenges associated with eukaryotic pan-genomics. To aid the eukaryotic pan-genomic studies, here we present ppsPCP pipeline which is designed for eukaryotes especially for plants. It is capable of scanning presence/absence variants (PAVs) and constructing a fully annotated pan-genome. We believe with these unique features of PAV scanning and building a pan-genome together with its annotation, ppsPCP will be useful for plant pan-genomic studies and aid researchers to study genetic/phenotypic variations and genomic diversity. Availability and implementation The ppsPCP is freely available at github DOI: https://doi.org/10.5281/zenodo.2567390 and webpage http://cbi.hzau.edu.cn/ppsPCP/. Supplementary information Supplementary data are available at Bioinformatics online.
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Feofanova, Elena Valeryevna, Guo-Qiang Zhang, Samden Lhatoo, Ginger A. Metcalf, Eric Boerwinkle, and Eric Venner. "The Implementation Science for Genomic Health Translation (INSIGHT) Study in Epilepsy: Protocol for a Learning Health Care System." JMIR Research Protocols 10, no. 3 (March 26, 2021): e25576. http://dx.doi.org/10.2196/25576.
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Background Genomic medicine is poised to improve care for common complex diseases such as epilepsy, but additional clinical informatics and implementation science research is needed for it to become a part of the standard of care. Epilepsy is an exemplary complex neurological disorder for which DNA diagnostics have shown to be advantageous for patient care. Objective We designed the Implementation Science for Genomic Health Translation (INSIGHT) study to leverage the fact that both the clinic and testing laboratory control the development and customization of their respective electronic health records and clinical reporting platforms. Through INSIGHT, we can rapidly prototype and benchmark novel approaches to incorporating clinical genomics into patient care. Of particular interest are clinical decision support tools that take advantage of domain knowledge from clinical genomics and can be rapidly adjusted based on feedback from clinicians. Methods Building on previously developed evidence and infrastructure components, our model includes the following: establishment of an intervention-ready genomic knowledge base for patient care, creation of a health informatics platform and linking it to a clinical genomics reporting system, and scaling and evaluation of INSIGHT following established implementation science principles. Results INSIGHT was approved by the Institutional Review Board at the University of Texas Health Science Center at Houston on May 15, 2020, and is designed as a 2-year proof-of-concept study beginning in December 2021. By design, 120 patients from the Texas Comprehensive Epilepsy Program are to be enrolled to test the INSIGHT workflow. Initial results are expected in the first half of 2023. Conclusions INSIGHT’s domain-specific, practical but generalizable approach may help catalyze a pathway to accelerate translation of genomic knowledge into impactful interventions in patient care. International Registered Report Identifier (IRRID) PRR1-10.2196/25576
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Grisham, Julie. "Genomics company formed from Framingham heart study." Nature Biotechnology 18, no. 8 (August 2000): 818–19. http://dx.doi.org/10.1038/78414.
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Le, Brandon H., Javier A. Wagmaister, Tomokazu Kawashima, Anhthu Q. Bui, John J. Harada, and Robert B. Goldberg. "Using Genomics to Study Legume Seed Development." Plant Physiology 144, no. 2 (June 2007): 562–74. http://dx.doi.org/10.1104/pp.107.100362.
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Gitlitz, Barbara J., Deborah Morosini, Alicia L. Sable-Hunt, Bonnie J. Addario, Mark Byron Jennings, Stacy L. Mach, and Geoffrey R. Oxnard. "The genomics of Young Lung Cancer Study." Journal of Clinical Oncology 33, no. 15_suppl (May 20, 2015): TPS11110. http://dx.doi.org/10.1200/jco.2015.33.15_suppl.tps11110.
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Kelley, Joanna L., and Yoav Gilad. "Effective study design for comparative functional genomics." Nature Reviews Genetics 21, no. 7 (April 24, 2020): 385–86. http://dx.doi.org/10.1038/s41576-020-0242-z.
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Wang, Linhai, Jingyin Yu, Donghua Li, and Xiurong Zhang. "Sinbase: An Integrated Database to Study Genomics, Genetics and Comparative Genomics in Sesamum indicum." Plant and Cell Physiology 56, no. 1 (December 4, 2014): e2-e2. http://dx.doi.org/10.1093/pcp/pcu175.
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Hatfull, Graham F. "Actinobacteriophages: Genomics, Dynamics, and Applications." Annual Review of Virology 7, no. 1 (September 29, 2020): 37–61. http://dx.doi.org/10.1146/annurev-virology-122019-070009.
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Actinobacteriophages are viruses that infect bacterial hosts in the phylum Actinobacteria. More than 17,000 actinobacteriophages have been described and over 3,000 complete genome sequences reported, resulting from large-scale, high-impact, integrated research-education initiatives such as the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) program. Their genomic diversity is enormous; actinobacteriophages comprise many architecturally mosaic genomes with distinct DNA sequences. Their genome diversity is driven by the highly dynamic interactions between phages and their hosts, and prophages can confer a variety of systems that defend against attack by genetically distinct phages; phages can neutralize these defense systems by coding for counter-defense proteins. These phages not only provide insights into diverse and dynamic phage populations but also have provided numerous tools for mycobacterial genetics. A case study using a three-phage cocktail to treat a patient with a drug-resistant Mycobacterium abscessus suggests that phages may have considerable potential for the therapeutic treatment of mycobacterial infections.
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Best, Stephanie, Janet C. Long, Clara Gaff, Jeffrey Braithwaite, and Natalie Taylor. "Investigating the Adoption of Clinical Genomics in Australia. An Implementation Science Case Study." Genes 12, no. 2 (February 23, 2021): 317. http://dx.doi.org/10.3390/genes12020317.
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Despite the overwhelming interest in clinical genomics, uptake has been slow. Implementation science offers a systematic approach to reveal pathways to adoption and a theory informed approach to addressing barriers presented. Using case study methodology, we undertook 16 in-depth interviews with nongenetic medical specialists to identify barriers and enablers to the uptake of clinical genomics. Data collection and analysis was guided by two evidence-based behaviour change models: the Theoretical Domains Framework (TDF), and the Capability, Opportunity Motivation Behaviour model (COM-B). Our findings revealed the use of implementation science not only provided a theoretical structure to frame the study but also facilitated uncovering of traditionally difficult to access responses from participants, e.g., “safety in feeling vulnerable” (TDF code emotion/COM-B code motivation). The most challenging phase for participants was ensuring appropriate patients were offered genomic testing. There were several consistent TDF codes: professional identity, social influences, and environmental context and resources and COM-B codes opportunity and motivation, with others varying along the patient journey. We conclude that implementation science methods can maximise the value created by the exploration of factors affecting the uptake of clinical genomics to ensure future interventions are designed to meet the needs of novice nongenetic medical specialists.
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Gray, Stacy W., Sarah E. Gollust, Deanna Alexis Carere, Clara A. Chen, Angel Cronin, Sarah S. Kalia, Huma Q. Rana, et al. "Personal Genomic Testing for Cancer Risk: Results From the Impact of Personal Genomics Study." Journal of Clinical Oncology 35, no. 6 (February 20, 2017): 636–44. http://dx.doi.org/10.1200/jco.2016.67.1503.
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Purpose Significant concerns exist regarding the potential for unwarranted behavior changes and the overuse of health care resources in response to direct-to-consumer personal genomic testing (PGT). However, little is known about customers’ behaviors after PGT. Methods Longitudinal surveys were given to new customers of 23andMe (Mountain View, CA) and Pathway Genomics (San Diego, CA). Survey data were linked to individual-level PGT results through a secure data transfer process. Results Of the 1,042 customers who completed baseline and 6-month surveys (response rate, 71.2%), 762 had complete cancer-related data and were analyzed. Most customers reported that learning about their genetic risk of cancers was a motivation for testing (colorectal, 88%; prostate, 95%; breast, 94%). No customers tested positive for pathogenic mutations in highly penetrant cancer susceptibility genes. A minority of individuals received elevated single nucleotide polymorphism-based PGT cancer risk estimates (colorectal, 24%; prostate, 24%; breast, 12%). At 6 months, customers who received elevated PGT cancer risk estimates were not significantly more likely to change their diet, exercise, or advanced planning behaviors or engage in cancer screening, compared with individuals at average or reduced risk. Men who received elevated PGT prostate cancer risk estimates changed their vitamin and supplement use more than those at average or reduced risk (22% v 7.6%, respectively; adjusted odds ratio, 3.41; 95% CI, 1.44 to 8.18). Predictors of 6-month behavior include baseline behavior (exercise, vitamin or supplement use, and screening), worse health status (diet and vitamin or supplement use), and older age (advanced planning, screening). Conclusion Most adults receiving elevated direct-to-consumer PGT single nucleotide polymorphism-based cancer risk estimates did not significantly change their diet, exercise, advanced care planning, or cancer screening behaviors.
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Rahma, Azhar T., Iffat Elbarazi, Bassam R. Ali, George P. Patrinos, Luai A. Ahmed, and Fatma Al Maskari. "Genomics and Pharmacogenomics Knowledge, Attitude and Practice of Pharmacists Working in United Arab Emirates: Findings from Focus Group Discussions—A Qualitative Study." Journal of Personalized Medicine 10, no. 3 (September 18, 2020): 134. http://dx.doi.org/10.3390/jpm10030134.
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(1) Background: Genomics and pharmacogenomics are relatively new fields in medicine in the United Arab Emirates (UAE). Understanding the knowledge, attitudes and current practices among pharmacists is an important pillar to establish the roadmap for implementing genomic medicine and pharmacogenomics; (2) Methods: A qualitative method was used, with focus group discussions (FGDs) being conducted among pharmacists working in public and private hospitals in Abu Dhabi Emirate. Snowball sampling was used. Thematic inductive analysis was performed by two researchers independently. NVIVO software was used to establish the themes; (3) Results: Lack of knowledge of genomics and pharmacogenomics among pharmacists was one of the most prominent findings. Therefore, the role of pharmacist in making the right decisions was highlighted to be a barrier for pharmacogenomics implementation in the UAE. Pharmacists have a positive attitude toward pharmacogenomics, but they are preoccupied with concern of confidentiality. In addition, religion and culture shadowed their attitudes toward genetic testing; (4) Conclusions: It is highly recommended to introduce new courses and training workshops for healthcare providers to improve the opportunities for genomics and pharmacogenomics application in the UAE. Pharmacists agreed that the health authorities should take the lead for improving trust and confidence in the system for a better future in the era of genomics and pharmacogenomics.
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May, Andrew K., Heather Seymour, Harriet Etheredge, Heather Maher, Marta C. Nunes, Shabir A. Madhi, Simiso M. Sokhela, et al. "Coronavirus Host Genomics Study: South Africa (COVIGen-SA)." Global Health 2022 (October 6, 2022): 1–14. http://dx.doi.org/10.1155/2022/7405349.
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Host genetic factors are known to modify the susceptibility, severity, and outcomes of COVID-19 and vary across populations. However, continental Africans are yet to be adequately represented in such studies despite the importance of genetic factors in understanding Africa’s response to the pandemic. We describe the development of a research resource for coronavirus host genomics studies in South Africa known as COVIGen-SA—a multicollaborator strategic partnership designed to provide harmonised demographic, clinical, and genetic information specific to Black South Africans with COVID-19. Over 2,000 participants have been recruited to date. Preliminary results on 1,354 SARS-CoV-2 positive participants from four participating studies showed that 64.7% were female, 333 had severe disease, and 329 were people living with HIV. Through this resource, we aim to provide insights into host genetic factors relevant to African-ancestry populations, using both genome-wide association testing and targeted sequencing of important genomic loci. This project will promote and enhance partnerships, build skills, and develop resources needed to address the COVID-19 burden and associated risk factors in South African communities.
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Zhu, Liucun, Ying Zhang, Wenna Guo, Xin-Jian Xu, and Qiang Wang. "De NovoAssembly and Characterization ofSophora japonicaTranscriptome Using RNA-seq." BioMed Research International 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/750961.
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Sophora japonicaLinn (Chinese Scholar Tree) is a shrub species belonging to the subfamily Faboideae of the pea family Fabaceae. In this study, RNA sequencing ofS. japonicatranscriptome was performed to produce large expression datasets for functional genomic analysis. Approximate 86.1 million high-quality clean reads were generated and assembledde novointo 143010 unique transcripts and 57614 unigenes. The average length of unigenes was 901 bps with an N50 of 545 bps. Four public databases, including the NCBI nonredundant protein (NR), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Cluster of Orthologous Groups (COG), were used to annotate unigenes through NCBI BLAST procedure. A total of 27541 of 57614 unigenes (47.8%) were annotated for gene descriptions, conserved protein domains, or gene ontology. Moreover, an interaction network of unigenes inS. japonicawas predicted based on known protein-protein interactions of putative orthologs of well-studied plant genomes. The transcriptome data ofS. japonicareported here represents first genome-scale investigation of gene expressions in Faboideae plants. We expect that our study will provide a useful resource for further studies on gene expression, genomics, functional genomics, and protein-protein interaction inS. japonica.
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Trent, Jeffrey, John Carpten, Michael Reich, Ted Liefeld, Jonathan Keats, Spyro Mousses, William Hahn, et al. "The Multiple Myeloma Research Consortium Genomics Initiative." Blood 110, no. 11 (November 16, 2007): 2498. http://dx.doi.org/10.1182/blood.v110.11.2498.2498.
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Abstract The Multiple Myeloma Research Consortium (MMRC) Genomics Initiative is a three-year program to analyze tumor tissue from hundreds of multiple myeloma (MM) patients via gene expression profiling (GEP), comparative genomic hybridization (aCGH), and exon re-sequencing. In addition, RNAi knockdown of selected genes in MM tumor cell lines is being evaluated to identify potential new targets. All genomic data generated is scheduled for placement in an open-access Multiple Myeloma Genomics Portal pre-publication and in near real-time (www.broad.mit.edu/mmgp). Additionally, samples are also destined for drug validation and correlative science on clinical protocols as this study moves forward. This comprehensive project is spearheaded by the MMRC and conducted via collaboration with the Eli and Edythe L. Broad Institute of MIT and Harvard, the Translational Genomics Research Institute (TGen), Mayo Clinic Arizona, and The Dana-Farber Cancer Center. The study is supported by the collection from member institutions of the MMRC of bone marrow aspirates and matched peripheral blood samples from over 1000 patients. Specific genomic technologies that are currently being employed across this sample set include GEP using Affymetrix Human Genome U133A 2.0 Plus Arrays, and, in parallel, efforts to identify regions of genomic gain and loss are using Agilent Human Genome CGH arrays. In contrast to other large-scale genomic projects based on exon-sequencing of targeted gene sets, this project will be the first to perform genome-scale single molecule sequencing (SMS) of DNA from patient specimens. Results will be targeted against candidate classes of genes (e.g. kinases, phosphatases, known oncogenes and tumor suppressors), and genes from GEP or within candidate regions of copy gain or loss identified by the aCGH experiments. Mutations will be further validated in an independent set of patient specimens. Finally we will attempt to identify points of vulnerability of MM through systematic loss-of-function screens in myeloma cell lines using high-throughput RNA interference (using both shRNA and siRNA platforms). Importantly, data generated from this genomics initiative will ultimately be made public pre-publication through the established MMRC Multiple Myeloma Genomics Portal. Data from all aspects of this project (sample collection and analyte isolation, GEP, aCGH, SMS, RNAi and bioinformatics) will be described in this presentation. The power of this study is the comprehensive collection of gene expression, CGH, and genome sequencing on a single reference set of clinically annotated samples. The addition of RNAi screens makes this a very important and unique data resource, which we hope will help expedite the discovery of novel targeted agents for MM scientific community.
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Nichols, Heather L., Ning Zhang, and Xuejun Wen. "Proteomics and genomics of microgravity." Physiological Genomics 26, no. 3 (August 2006): 163–71. http://dx.doi.org/10.1152/physiolgenomics.00323.2005.
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Many serious adverse physiological changes occur during spaceflight. In the search for underlying mechanisms and possible new countermeasures, many experimental tools and methods have been developed to study microgravity caused physiological changes, ranging from in vitro bioreactor studies to spaceflight investigations. Recently, genomic and proteomic approaches have gained a lot of attention; after major scientific breakthroughs in the fields of genomics and proteomics, they are now widely accepted and used to understand biological processes. Understanding gene and/or protein expression is the key to unfolding the mechanisms behind microgravity-induced problems and, ultimately, finding effective countermeasures to spaceflight-induced alterations. Significant progress has been made in identifying the genes/proteins responsible for these changes. Although many of these genes and/or proteins were observed to be either upregulated or downregulated, however, no large-scale genomics and proteomics studies have been published so far. This review aims at summarizing the current status of microgravity-related genomics and proteomics studies and stimulating large-scale proteomics and genomics research activities.
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Mahajan, R., and P. Gupta. "Proteomics: taking over where genomics leaves off." Czech Journal of Genetics and Plant Breeding 46, No. 2 (June 29, 2010): 47–53. http://dx.doi.org/10.17221/34/2009-cjgpb.
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The proteomic studies are simultaneously developed in several directions and significantly influence our notions on the capabilities of biological sciences. The need for proteomics research is necessary as there are certain genes in a cell that encode proteins with specific functions. Using a variety of techniques, proteomics can be used to study how proteins interact within a system or how the protein expression changes in different parts of the body, in different stages of its life cycle and in different environmental conditions as every individual has one genome and many proteomes. Besides the qualitative and quantitative description of the expressed proteins, proteomics also deals with the analysis of mutual interactions of proteins. Thereby, candidate proteins can be identified which may be used as starting-points for diagnostic or even therapeutic approaches.
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Chadwick, Jennifer Q., Kenneth C. Copeland, Dannielle E. Branam, Julie A. Erb-Alvarez, Sohail I. Khan, Michael T. Peercy, Mark E. Rogers, Bobby R. Saunkeah, Jeanie B. Tryggestad, and David F. Wharton. "Genomic Research and American Indian Tribal Communities in Oklahoma: Learning From Past Research Misconduct and Building Future Trusting Partnerships." American Journal of Epidemiology 188, no. 7 (April 24, 2019): 1206–12. http://dx.doi.org/10.1093/aje/kwz062.
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Abstract Research misconduct and consequential harms have been inflicted upon American Indian/Alaska Native communities for decades. To protect their people and culture and to retain oversight over research, many Native communities have established tribal health research and institutional review boards. The Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY) Study showcases a successful, trusting research collaboration with tribal nations and academic investigators in Oklahoma. In 2006, the TODAY Study investigators proposed a modification of the study protocol to collect biological specimens from participants for genomic analyses and indefinite storage. Partnering American Indian tribal nations elected not to participate in the genomics collection and repository proposal. Reasons included 1) protection of cultural values, 2) concerns regarding community anonymity, 3) a potential threat to tribal services eligibility, 4) broad informed consent language, and 5) vague definitions of data access and usage. The nations believed the proposed genomics analyses presented a risk of harm to their people and nations without clear benefit. Since the 2006 proposal and the advancement of genomics research, many tribal communities in Oklahoma, appreciating the potential benefits of genomic research, are developing policies regarding oversight of/access to data and biological specimens to mitigate risks and provide members and communities with opportunities to participate in safe and meaningful genomic research.
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Borsatto, Kelly Cristine, Monika Aparecida Coronado, Raghuvir Krishnaswamy Arni, and Chaboli Alevi Kaio Cesar. "Omics Tools Applied to the Study of Chagas Disease Vectors: Cytogenomics and Genomics." American Journal of Tropical Medicine and Hygiene 104, no. 6 (June 2, 2021): 1973–77. http://dx.doi.org/10.4269/ajtmh.20-1047.
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Abstract.Chagas disease is an illness caused by the protozoan Trypanosoma cruzi that is distributed in 21 countries of Latin America. The main way of transmission of T. cruzi is through the feces of triatomines infected with the parasite. With technological advances came new technologies called omics. In the pre-genomic era, the omics science was based on cytogenomic studies of triatomines. With the Rhodnius prolixus genome sequencing project, new omics tools were applied to understand the organism at a systemic level and not just from a genomic point of view. Thus, the present review aims to put together the cytogenomic and genomic information available in the literature for Chagas disease vectors. Here, we review all studies related to cytogenomics and genomics of Chagas disease vectors, contributing to the direction of further research with these insect vectors, because it was evident that most studies focus on cytogenomic knowledge of the species. Given the importance of genomic studies, which contributed to the knowledge of taxonomy, systematics, as well as the vector’s biology, the need to apply these techniques in other genera and species of Triatominae subfamily is emphasized.
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Alghazwi, Mohammed, Fatih Turkmen, Joeri Van Der Velde, and Dimka Karastoyanova. "Blockchain for Genomics: A Systematic Literature Review." Distributed Ledger Technologies: Research and Practice 1, no. 2 (December 2022): 1–28. http://dx.doi.org/10.1145/3563044.
Full textAbstract:
Human genomic data carry unique information about an individual and offer unprecedented opportunities for healthcare. The clinical interpretations derived from large genomic datasets can greatly improve healthcare and pave the way for personalized medicine. Sharing genomic datasets, however, poses major challenges, as genomic data is different from traditional medical data, indirectly revealing information about descendants and relatives of the data owner and carrying valid information even after the owner passes away. Therefore, stringent data ownership and control measures are required when dealing with genomic data. In order to provide a secure and accountable infrastructure, blockchain technologies offer a promising alternative to traditional distributed systems. Indeed, the research on blockchain-based infrastructures tailored to genomics is on the rise. However, there is a lack of a comprehensive literature review that summarizes the current state-of-the-art methods in the applications of blockchain in genomics. In this article, we systematically look at the existing work both commercial and academic, and discuss the major opportunities and challenges. Our study is driven by five research questions that we aim to answer in our review. We also present our projections of future research directions which we hope the researchers interested in the area can benefit from.