From genomic medicine to precision medicine: highlights of 2015

Auffray, Charles; Caulfield, Timothy; Griffin, Julian L.; Khoury, Muin J.; Lupski, James R.; Schwab, Matthias

doi:10.1186/s13073-016-0265-4

Cited by 34 publications

(24 citation statements)

References 28 publications

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“…Another alternative is a hybrid model with complimentary central and local services to balance the need for speed with the advanced expertise and resources [54]. Two prominent examples of the hybrid models in the United States are the Food and Drug Administration (FDA) GenomeTrakr network for the tracking of food-borne pathogens, and the CDC Advanced Molecular Detection (AMD) initiative for the improved surveillance of infectious diseases [55, 56]. The AMD and GenomeTrakr frameworks rely on a participatory model with enhanced analysis, curation and data storage at a central site.…”

Section: Discussionmentioning

confidence: 99%

Validation and Implementation of CLIA-Compliant Whole Genome Sequencing (WGS) in Public Health Laboratory

Truong²,

Greninger³

et al. 2017

Preprint

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BackgroundPublic health microbiology laboratories (PHL) are at the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards.Objectives1) Establish the performance specifications of WGS applications used in PHL to conform with CLIA (Clinical Laboratory Improvements Act) guidelines for laboratory developed tests (LDT), 2) Develop quality assurance (QA) and quality control (QC) measures, 3) Establish reporting language for end users with or without WGS expertise, 4) Create a validation set of microorganisms to be used for future validations of WGS platforms and multi-laboratory comparisons and, 5) Create modular templates for the validation of different sequencing platforms.MethodsMiSeq Sequencer and Illumina chemistry (Illumina, Inc.) were used to generate genomes for 34 bacterial isolates with genome sizes from 1.8 to 4.7 Mb and wide range of GC content (32.1%-66.1%). A customized CLCbio Genomics Workbench - shell script bioinformatics pipeline was used for the data analysis.ResultsWe developed a validation panel comprising ten Enterobacteriaceae isolates, five gram-positive cocci, five gram-negative non-fermenting species, nine Mycobacterium tuberculosis, and five miscellaneous bacteria; the set represented typical workflow in the PHL. The accuracy of MiSeq platform for individual base calling was >99.9% with similar results shown for reproducibility/repeatability of genome-wide base calling. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from MLST and genotyping tests were 100%. A test report format was developed for the end users with and without WGS knowledge.ConclusionWGS was validated for routine use in PHL according to CLIA guidelines for LDTs. The validation panel, sequencing analytics, and raw sequences will be available for future multi-laboratory comparisons of WGS in PHL. Additionally, the WGS performance specifications and modular validation template are likely to be adaptable for the validation of other platforms and reagents kits.

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Section: Discussionmentioning

confidence: 99%

Validation and Implementation of CLIA-Compliant Whole Genome Sequencing (WGS) in Public Health Laboratory

Truong²,

Greninger³

et al. 2017

Preprint

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“…• Completion of the Human Genome Project 14,15 • Launch of the International HapMap Project 16 • Availability of next-generation sequencing 17 • Reports of the importance of proteomics 18 , metabolomics 19 , transcriptomics, and epigenetics 20 that spurred interest in studying 'omics' to understand human disease 21 • Systems biology and network medicine 23,24 • Cloud computing and new techniques in computational biology were developed, making the handling of large datasets possible ('big data') 22 • Widespread emergence of electronic medical records • Blossoming of biomedical informatics • Development of networks of sites for enrolling participants in clinical studies 26 • Increase in data sharing in the research and clinical communities 27 • The Quantified Self movement 28,29 , which aims to increase the use of implanted medical devices • Growth in the use of smartphones and mobile health (mHealth) devices and apps for acquiring continuous physiological data on a real-time basis 30 biological phenomena. The main elements required to achieve this goal include the big data pool of 'omic' information in healthy and diseased states; advanced computational and analytical techniques for explor ing the complex inter actions within the molecular networks that govern pheno types; and nuanced, quantitative, deep pheno typing in health and disease (FIGS 1,2).…”

Section: Box 1 | Major Medical Advances Enabling Precision Medicinementioning

confidence: 99%

“…First, the completion of the Human Genome Project 14,15 , the launch of the International HapMap Project 16 , the avail ability of nextgeneration sequencing 17 , and reports of the importance of proteomics 18 , metabolomics 19 , tran scriptomics, and epigenetics 20 spurred interest in study ing 'omics' to understand human disease 21 . Second, cloud computing and new techniques in computational biology were developed, making the handling of large datasets possible ('big data') 22 , as we learn to think more in terms of systems biology and network med icine 23,24 .…”

mentioning

confidence: 99%

Precision medicine in cardiology

2016

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The cardiovascular research and clinical communities are ideally positioned to address the epidemic of noncommunicable causes of death, as well as advance our understanding of human health and disease, through the development and implementation of precision medicine. New tools will be needed for describing the cardiovascular health status of individuals and populations, including 'omic' data, exposome and social determinants of health, the microbiome, behaviours and motivations, patient-generated data, and the array of data in electronic medical records. Cardiovascular specialists can build on their experience and use precision medicine to facilitate discovery science and improve the efficiency of clinical research, with the goal of providing more precise information to improve the health of individuals and populations. Overcoming the barriers to implementing precision medicine will require addressing a range of technical and sociopolitical issues. Health care under precision medicine will become a more integrated, dynamic system, in which patients are no longer a passive entity on whom measurements are made, but instead are central stakeholders who contribute data and participate actively in shared decision-making. Many traditionally defined diseases have common mechanisms; therefore, elimination of a siloed approach to medicine will ultimately pave the path to the creation of a universal precision medicine environment.

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“…The global impact of personalized medicine is constantly growing in the last years. Charles Auffray et al (2016) showed the increasing applications of human genetics into public health programs and that numerous initiatives are Fig. (2).…”

Section: Personalized Medicine Issues and Healthcare Implicationsmentioning

confidence: 99%

“…Workflow in psychiatry illustrating strategy of safe and appropriate use of genomic data, strictly guided by the "precaution principle". made around the world to implement clinical genomic, such as the Welcome Trust Deciphering Developmental Disorders (WTDDD) in Europe and the National Human Genome Research Institute Centers for Mendelian Genomics (NHGRI CMG) or The Centers for Disease Control and Prevention (CDC), Advanced Molecular Detection Initiative in USA [57]. As a matter of fact, however, its usage is restricted to a small portion of patients, primarily for the diagnosis of Mendelian conditions and for cancer treatments.…”

Section: Personalized Medicine Issues and Healthcare Implicationsmentioning

confidence: 99%

Clinical Applications of Personalized Medicine: A New Paradigm and Challenge

Sanzo

Cipolloni

Borro

et al. 2017

CPB

108

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The personalized medicine is an emergent and rapidly developing method of clinical practice that uses new technologies to provide decisions in regard to the prediction, prevention, diagnosis and treatment of disease. A continuous evolution of technology and the developments in molecular diagnostics and genomic analysis increased the possibility of an even more understanding and interpretation of the human genome and exome, allowing a "personalized" approach to clinical care, so that the concepts of "Systems Medicine" and "System Biology" are actually increasing. The purpose of this study is to evaluate the personalized medicine about its indications and benefits, actual clinical applications and future perspectives as well as its issues and health care implications. A careful review of the scientific literature on this field that highlighted the applicability and usefulness of this new medical approach as well as the fact that personalized medicine strategy is even more increasing in numerous fields of applications.

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From genomic medicine to precision medicine: highlights of 2015

Cited by 34 publications

References 28 publications

Validation and Implementation of CLIA-Compliant Whole Genome Sequencing (WGS) in Public Health Laboratory

Validation and Implementation of CLIA-Compliant Whole Genome Sequencing (WGS) in Public Health Laboratory

Precision medicine in cardiology

Clinical Applications of Personalized Medicine: A New Paradigm and Challenge

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