Abstract
The tremendous increase in DNA sequencing capacity arising from the commercialization of “next generation” instruments has opened the door to innumerable routes of investigation in basic and translational medical science. It enables very large data sets to be gathered, whose interpretation and conversion into useful knowledge is only beginning. A challenge for modern healthcare systems and academic medical centers is to apply these new methods for the diagnosis of disease and the management of patient care without unnecessary delay, but also with appropriate evaluation of the quality of data and interpretation, as well as the clinical value of the insights gained. Most critically, the standards applied for evaluating these new laboratory data and ensuring that the results and their significance are clearly communicated to patients and their caregivers should be at least as rigorous as those applied to other kinds of medical tests. Here, we present an overview of conceptual and practical issues to be considered in planning for the integration of genomic methods or, in principle, any other type of “omics” testing into clinical care.
Highlights
Improvements in DNA sequencing technology in the past decade represent one of the most significant technological achievements in recent history, with far-reaching implications for medicine and society
Standards of evidence for concluding that gene variants are associated with diseases have been proposed, taking into account the large amount of data gathered in genome or exome studies and the potential for false discoveries associated with such large numbers of observations of a sample; for example, in exome studies, p = 5 × 107 has been suggested as one threshold for claiming significance [25,26]
Efforts to integrate genomic approaches, or approaches to analyze transcriptomes, proteomes, metabolomes, microbiomes, etc., into clinical care need to be paralleled by the education of our medical students, residents, clinical fellows and faculty to provide a fund of knowledge and an understanding of the possibilities, strengths and limitations of these approaches when they are translated from research to the bedside
Summary
Improvements in DNA sequencing technology in the past decade represent one of the most significant technological achievements in recent history, with far-reaching implications for medicine and society. Societal expectations and ethical considerations require that any correlations between DNA sequences and predictions of disease risk, prognosis or optimal treatment choice should be held to higher standards of evidence than those that are typically applied in the peer review process for publication of a research article In this overview, we initially highlight areas of recent progress and promise in clinical genomic testing (including whole genome sequence analysis, as well as analysis of selected fractions of the genome, such as the protein coding exome, or large panels of genes of clinical interest) and discuss these new approaches in the context of medical laboratory testing and the current regulatory framework governing such tests in the United States. The potential benefits of clinical genomic testing are tremendous, but devising appropriate systems for quality assurance, data sharing and validation, incorporation into clinical trials and cost-benefit analysis of this new diagnostic area will be an ongoing effort in the coming years
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