9,036 research outputs found

    Opportunities in biotechnology

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    Rapid detection of copy number variations and point mutations in BRCA1/2 genes using a single workflow by ion semiconductor sequencing pipeline

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    Molecular analysis of BRCA1 (MIM# 604370) and BRCA2 (MIM #600185) genes is essential for familial breast and ovarian cancer prevention and treatment. An efficient, rapid, cost-effective accurate strategy for the detection of pathogenic variants is crucial. Mutations detection of BRCA1/2 genes includes screening for single nucleotide variants (SNVs), small insertions or deletions (indels), and Copy Number Variations (CNVs). Sanger sequencing is unable to identify CNVs and therefore Multiplex Ligation Probe amplification (MLPA) or Multiplex Amplicon Quantification (MAQ) is used to complete the BRCA1/2 genes analysis. The rapid evolution of Next Generation Sequencing (NGS) technologies allows the search for point mutations and CNVs with a single platform and workflow. In this study we test the possibilities of NGS technology to simultaneously detect point mutations and CNVs in BRCA1/2 genes, using the OncomineTM BRCA Research Assay on Personal Genome Machine (PGM) Platform with Ion Reporter Software for sequencing data analysis (Thermo Fisher Scientific). Comparison between the NGS-CNVs, MLPA and MAQ results shows how the NGS approach is the most complete and fast method for the simultaneous detection of all BRCA mutations, avoiding the usual time consuming multistep approach in the routine diagnostic testing of hereditary breast and ovarian cancers

    Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

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    Despite the tremendous success, pitfalls have been observed in every step of a clinical metabolomics workflow, which impedes the internal validity of the study. Furthermore, the demand for logistics, instrumentations, and computational resources for metabolic phenotyping studies has far exceeded our expectations. In this conceptual review, we will cover inclusive barriers of a metabolomics-based clinical study and suggest potential solutions in the hope of enhancing study robustness, usability, and transferability. The importance of quality assurance and quality control procedures is discussed, followed by a practical rule containing five phases, including two additional "pre-pre-" and "post-post-" analytical steps. Besides, we will elucidate the potential involvement of machine learning and demonstrate that the need for automated data mining algorithms to improve the quality of future research is undeniable. Consequently, we propose a comprehensive metabolomics framework, along with an appropriate checklist refined from current guidelines and our previously published assessment, in the attempt to accurately translate achievements in metabolomics into clinical and epidemiological research. Furthermore, the integration of multifaceted multi-omics approaches with metabolomics as the pillar member is in urgent need. When combining with other social or nutritional factors, we can gather complete omics profiles for a particular disease. Our discussion reflects the current obstacles and potential solutions toward the progressing trend of utilizing metabolomics in clinical research to create the next-generation healthcare system.11Ysciescopu

    Keynote Address: The Future of Cardiovascular Epidemiology: Current Trends?

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    This is the Research Retreat\u27s Keynote presentation by Vasan S. Ramachandran, MD, who is Principal Investigator and Co-Director, Echocardiography/Vascular Laboratory, Framingham Heart Study. Dr. Ramachandran is also Chief, Section of Preventive Medicine and Epidemiology and Professor of Medicine, Boston University School of Medicine. Dr. Ramachandran discusses the future of cardiovascular epidemiology, including the roles of: cHealth (community), sHealth (social), mHealth (mobile), eHealth (electronic), and gHealth (genomic)

    Building towards precision medicine: empowering medical professionals for the next revolution

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    A new paradigm in disease classification, diagnosis and treatment is rapidly approaching. Known as precision medicine, this new healthcare model incorporates and integrates genetic information, microbiome data, and information on patientsā€™ environment and lifestyle to better identify and classify disease processes, and to provide custom-tailored therapeutic solutions. In spite of its promises, precision medicine faces several challenges that need to be overcome to successfully implement this new healthcare model. In this paper we identify four main areas that require attention: data, tools and systems, regulations, and people. While there are important ongoing efforts for addressing the first three areas, we argue that the human factor needs to be taken into consideration as well. In particular, we discuss several studies that show how primary care physicians and clinicians in general feel underequipped to interpret genetic tests and direct-to-consumer genomic tests. Considering the importance of genetic information for precision medicine applications, this is a pressing issue that needs to be addressed. To increase the number of professionals with the necessary expertise to correctly interpret the genomics profiles of their patients, we propose several strategies that involve medical curriculum reforms, specialist training, and ongoing physician training

    Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine

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    ā€œLetā€™s pull these technologies out of the ivory towerā€: The politics, ethos, and ironies of participant-driven genomic research

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    This paper investigates how groups of ā€˜citizen scientistsā€™ in non-traditional settings and primarily online networks claim to be challenging conventional genomic research processes and norms. Although these groups are highly diverse, they all distinguish their efforts from traditional university- or industry-based genomic research as being ā€˜participant-drivenā€™ in one way or another. Participant-driven genomic research (PDGR) groups often work from ā€˜labsā€™ that consist of servers and computing devices as much as wet lab apparatus, relying on information-processing software for data-driven, discovery-based analysis rather than hypothesis-driven experimentation. We interviewed individuals from a variety of efforts across the expanding ecosystem of PDGR, including academic groups, start-ups, activists, hobbyists, and hackers, in order to compare and contrast how they relate their stated objectives, practices, and political and moral stances to institutions of expert scientific knowledge production. Results reveal that these groups, despite their diversity, share commitments to promoting alternative modes of housing, conducting, and funding genomic research and, ultimately, sharing knowledge. In doing so, PDGR discourses challenge existing approaches to research governance as well, especially the regulation, ethics, and oversight of human genomic information management. Interestingly, the reaction of the traditional genomics research community to this revolutionary challenge has not been negative: in fact, the community seems to be embracing the ethos espoused by PDGR, at the highest levels of science policy. As conventional genomic research assimilates the ethos of PDGR, the movementā€™s ā€˜democratizingā€™ views on research governance are likely to become normalized as well, creating new tensions for science policy and research ethics
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