Detection of low-abundance nucleic acids is a challenging task, which over the last two decades has been solved using enzymatic target amplification. Enzymatic synthesis enhances the signal so that diverse, scientifically and clinically relevant molecules can be identified and studied, including cancer DNA, viral nucleic acids, and regulatory RNAs. However, using enzymes increases the detection time and cost, not to mention the high risk of mistakes with amplification and data alignment. These limitations have stimulated a growing interest in enzyme-free methods within researchers and industry. In this review we discuss recent advances in signal-enhancing approaches aimed at nucleic acid diagnostics that do not require target amplification. Regardless of enzyme usage, signal enhancement is crucial for the reliable detection of nucleic acids at low concentrations. We pay special attention to novel nanomaterials, fluorescence microscopy, and technical advances in detectors for optical assessment. We summarize sensitivity parameters of the currently available assays and devices which makes this review relevant to the broad spectrum of researchers working in fields from biophysics, to engineering, to synthetic biology and bioorganic chemistry.
There is currently an unmet need for reliable tools that allow for direct detection and quantification of modifications in genomic DNA. For example, in cancer research and clinical diagnostics, target DNA has to be amplified and sequenced in order to reveal mutations. For 5-methylcytosine detection, bisulfite treatment of DNA is applied for the analysis, which often leads to poor specificity and reproducibility of the results. Herein we describe a simple approach that specifically detects clinically significant modifications in the human oncogenes BRAF and KRAS. We prove that this can be done using a fast and reliable hybridization assay applying novel internally labelled oligonucleotide probes and optical detection methods.
Background Two main aspects lead the implementation of precision oncology into clinical practice: the adoption of extended genome sequencing technologies and the institution of the Molecular Tumor Boards (MTBs). CIPOMO (Italian Association of Heads of Oncology Department) promoted a national survey across top health care professionals to gain an understanding of the current state of precision oncology in Italy. Methods Nineteen questions were sent via the SurveyMonkey platform to 169 heads of oncology departments. Their answers were collected in February 2022. Results Overall, 129 directors participated; 113 sets of answers were analyzed. Nineteen regions out of 21 participated as a representative sample of the Italian health care system. The use of next-generation sequencing (NGS) is unevenly distributed; informed consent and clinical reports are managed differently, as the integration of medical, biologic, and informatics domains in a patient-centered workflow is inconsistent. A heterogeneous MTB environment emerged. A total of 33.6% of the responding professionals did not have access to MTBs while 76% of those who have did not refer cases. Conclusions NGS technologies and MTBs are not homogeneously implemented in Italy. This fact potentially jeopardizes equal access chances to innovative therapies for patients. This survey was carried out as part of an organizational research project, pursuing a bottom–up approach to identify the needs and possible solutions to optimize the process. These results could be a starting point for clinicians, scientific societies, and health care institutions to outline the best practices and offer shared recommendations for precision oncology implementation in current clinical practice.
Oncology is going through the fastest innovation period in the history of medicine and a growing number of patients improve or experience increased chances of survival. The declining death rate, starting from 1991, resulted in 2.9 million deaths avoided in the United States so far. A growing prevalence of patients is observed in all Western countries. New cancer drug approvals between 2000 and 2016, linked to other diagnostic, surgical, and health care improvements, were significantly associated with death reduction for the most common cancers. Alongside many positive aspects, other effects of innovations in oncology also deserve attention, especially challenges associated with the substantial increase of knowledge volume, the sharp growth of prevalence, and a concomitant or consequent increase in clinical, social, and organizational complexity. We analyse some of the consequences of oncology innovation on healthcare systems and professionals and present some suggestions on how these could be addressed by healthcare systems.
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