Making the leap from research laboratory to clinic: Challenges and opportunities for next-generation sequencing in infectious disease diagnostics

Posted on September 20, 2016 By John Jones Journal articles

In this late 2015 review and background article, Goldberg et al. provide the details of discussions held during meetings leading up to a February 2016 colloquium hosted by the American Academy of Microbiology on the Applications of Clinical Microbial Next-Generation Sequencing. The details of these meetings reveal the state of next-generation sequencing, its clinical applications, and the regulatory, financial, and research barriers that exist in NGS' further expansion in clinical settings. They conclude that "[t]he rapid evolution of NGS challenges both the regulatory framework and the development of laboratory standards and will require additional funding and incentives to drive tangible improvements and progress" to realize "the potential benefit that NGS has for patients and their families."

Information technology support for clinical genetic testing within an academic medical center

Posted on September 12, 2016 By John Jones Journal articles

Aronson et al. of Partners HealthCare and their Laboratory for Molecular Medicine (LMM) experienced first-hand the process of developing infrastructure for the germline genetic testing process. In this 2016 paper published in Journal of Personalized Medicine, the group shares its experiences of that process, from designating necessary support infrastructure (including a self-developed tool called GeneInsight Clinic) to its integration with other systems such as electronic health records, case management system, and laboratory information systems. They close by stating "a need for an application that interfaces with the range of systems" in the genetic testing environment and that "[s]uch a system could provide the basis for enhanced clinical decision support infrastructure."

Principles of metadata organization at the ENCODE data coordination center

Posted on September 6, 2016 By John Jones Journal articles

"Defining and organizing the set of metadata that is relevant, informative and applicable to diverse experimental techniques is challenging," the team of Hong et al. state in the introduction of this 2016 paper published in Database. But the team, motivated by the Encyclopedia of DNA Elements (ENCODE) project and its offshoots, explain and demonstrate their metadata standard and its viability across many types of genomic assays and projects. The group believes that the standard's flexibility and ability to allow for transparent and reproducible experimental data offer much potential. "[A]long with its organizing principles and key features for implementation," they conclude, "[it] could be widely adopted as an open LIMS system."

Integrated systems for NGS data management and analysis: Open issues and available solutions

Posted on August 30, 2016 By John Jones Journal articles

This 2016 paper by Bianchi et al., published in Frontiers in Genetics, takes a closer look at the major issues concerning next-generations sequencing (NGS) technology. The group raises five main concerns than an NGS research group should be aware of before approaching NGS technologies and briefly states positives and negatives to the most current popular tools. The group concludes "[a]lthough larger groups with enough computational members may prefer to develop and maintain their own tailored frameworks, smaller laboratories would save resources and improve their results by adopting solutions developed by third parties," including open-source and cloud-based tools.

Practical approaches for mining frequent patterns in molecular datasets

Posted on August 24, 2016 By John Jones Journal articles

Most researchers in the life sciences know now of the concept of "big data" and the push to better organize and mine the data that comes out of biological research. However, the techniques used to mine promising and interesting information from accumulating biological datasets are still developing. In this 2016 paper published in Bioinformatics and Biology Insights, Naulaerts et al. look at three specific software tools for mining and presenting useful biological data from complex datasets. They conclude that while the Apriori and arules software tools have their benefits and drawbacks, "MIME showed its value when subsequent mining steps were required" and is inherently easy-to-use.