Showing papers in "Expert Review of Molecular Diagnostics in 2015"
TL;DR: A wide overview over applications for the detection of atherosclerosis, cancer, inflammatory diseases and pharmacology, with a focus on developments over the past 5 years is given.
Abstract: Over the last decade, Raman spectroscopy has gained more and more interest in research as well as in clinical laboratories. As a vibrational spectroscopy technique, it is complementary to the also well-established infrared spectroscopy. Through specific spectral patterns, substances can be identified and molecular changes can be observed with high specificity. Because of a high spatial resolution due to an excitation wavelength in the visible and near-infrared range, Raman spectroscopy combined with microscopy is very powerful for imaging biological samples. Individual cells can be imaged on the subcellular level. In vivo tissue examinations are becoming increasingly important for clinical applications. In this review, we present currently ongoing research in different fields of medical diagnostics involving linear Raman spectroscopy and imaging. We give a wide overview over applications for the detection of atherosclerosis, cancer, inflammatory diseases and pharmacology, with a focus on developments over the past 5 years. Conclusions drawn from Raman spectroscopy are often validated by standard methods, for example, histopathology or PCR. The future potential of Raman spectroscopy and its limitations are discussed in consideration of other non-linear Raman techniques.
168 citations
TL;DR: Implementation of RPA technology in developing countries is critically required to assess limitations and potentials of the diagnosis of infectious disease, and may help identify impediments that prevent adoption of new molecular technologies in low resource- and low skill settings.
Abstract: Isothermal molecular diagnostics are bridging the technology gap between traditional diagnostics and polymerase chain reaction-based methods. These new techniques enable timely and accurate testing, especially in settings where there is a lack of infrastructure to support polymerase chain reaction facilities. Despite this, there is a significant lack of uptake of these technologies in developing countries where they are highly needed. Among these novel isothermal technologies, recombinase polymerase amplification (RPA) holds particular potential for use in developing countries. This rapid nucleic acid amplification approach is fast, highly sensitive and specific, and amenable to countries with a high burden of infectious diseases. Implementation of RPA technology in developing countries is critically required to assess limitations and potentials of the diagnosis of infectious disease, and may help identify impediments that prevent adoption of new molecular technologies in low resource- and low skill settings. This review focuses on approaching diagnosis of infectious disease with RPA.
128 citations
TL;DR: Preliminary proteomic, genetic and functional profiling of tumor cell-derived or cancer plasma-derived exosome confirms their unique characteristics and Alterations in protein or nucleic acid profiles of exosomes in plasma of cancer patients responding to therapies appear to correlate with clinical endpoints.
Abstract: Tumor-derived exosomes (TEX) are emerging as a new type of cancer biomarker. TEX are membrane-bound, virus-size vesicles of endocytic origin present in all body fluids of cancer patients. Based on the expanding albeit incomplete knowledge of their biogenesis, secretion by tumor cells and cancer cell-specific molecular and genetic contents, TEX are viewed as promising, clinically-relevant surrogates of cancer progression and response to therapy. Preliminary proteomic, genetic and functional profiling of tumor cell-derived or cancer plasma-derived exosomes confirms their unique characteristics. Alterations in protein or nucleic acid profiles of exosomes in plasma of cancer patients responding to therapies appear to correlate with clinical endpoints. However, methods for TEX isolation and separation from the bulk of human plasma-derived exosomes are not yet established and their role as biomarkers remains to be confirmed. Further development and validation of TEX as noninvasive, liquid equivalents of tumor biopsies are necessary to move this effort forward.
105 citations
TL;DR: Current multiplex IHC methods, which permit identification of at least 3 and up to 30 discrete antigens, have been divided into whole-section staining and spatially-patterned staining categories.
Abstract: Methods to detect immunolabeled molecules at increasingly higher resolutions, even when present at low levels, are revolutionizing immunohistochemistry (IHC). These technologies can be valuable for the management and examination of rare patient tissue specimens, and for improved accuracy of early disease detection. The purpose of this article is to highlight recent multiplexing methods that are candidates for more prevalent use in clinical research and potential translation to the clinic. Multiplex IHC methods, which permit identification of at least 3 and up to 30 discrete antigens, have been divided into whole-section staining and spatially-patterned staining categories. Associated signal enhancement technologies that can enhance performance and throughput of multiplex IHC assays are also discussed. Each multiplex IHC technique, detailed herein, is associated with several advantages as well as tradeoffs that must be taken into consideration for proper evaluation and use of the methods.
95 citations
TL;DR: Recent molecular, therapeutic and clinical advances in choline metabolism in cancer are highlighted, including the development of radiolabeled choline analogs as PET imaging tracers and the increased tCho signal detected by 1H magnetic resonance spectroscopy.
Abstract: Abnormal choline metabolism continues to be identified in multiple cancers. Molecular causes of abnormal choline metabolism are changes in choline kinase-α, ethanolamine kinase-α, phosphatidylcholi...
91 citations
TL;DR: The present article discusses the potential clinical use of exosomal miRNAs as diagnostic and prognostic tumor markers and the emerging role ofExosomes as a mediator of cell-to-cell signaling, to transfer miRNas between cells, is discussed.
Abstract: In cancer, deregulated expression levels of miRNAs are associated with tumorigenesis, tumor progression, metastasis and drug resistance. Apart from their release by apoptotic and necrotic cells, miRNAs can also be actively secreted into the blood circulation by exosomes. Exosomal miRNAs are thought to play an important role in cell-to-cell communication. Based on their biological functions and the possibility of quantifying miRNAs in patient blood in real time, these small non-coding RNA molecules may be a new promising class of potential non-invasive biomarkers. Screening of these liquid biopsies may provide information on target molecules of miRNAs and aberrant signaling pathways that can be blocked by a chosen targeted therapy. Consequently, therapy-associated modulations may facilitate treatment decisions. The present article discusses the potential clinical use of exosomal miRNAs as diagnostic and prognostic tumor markers. The emerging role of exosomes as a mediator of cell-to-cell signaling, to transfer miRNAs between cells, is also discussed.
77 citations
TL;DR: The potential clinical utility of ctDNA analysis using CAncer Personalized Profiling by deep Sequencing (CAPP-Seq), a novel next-generation sequencing-based approach for ultrasensitive ct DNA detection, is focused on.
Abstract: Tumors continually shed DNA into the circulation, where it can be noninvasively accessed. The ability to accurately detect circulating tumor DNA (ctDNA) could significantly impact the management of patients with nearly every cancer type. Quantitation of ctDNA could allow objective response assessment, detection of minimal residual disease and noninvasive tumor genotyping. The latter application overcomes the barriers currently limiting repeated tumor tissue sampling during therapy. Recent technical advancements have improved upon the sensitivity, specificity and feasibility of ctDNA detection and promise to enable innovative clinical applications. Here, we focus on the potential clinical utility of ctDNA analysis using CAncer Personalized Profiling by deep Sequencing (CAPP-Seq), a novel next-generation sequencing-based approach for ultrasensitive ctDNA detection. Applications of CAPP-Seq for the personalization of cancer detection and therapy are discussed.
76 citations
TL;DR: BAP1- or SETD2-mutated ccRCCs have been associated with poor overall survival, while PBRM1 mutations seem to identify a favorable group ofccRCC tumors.
Abstract: Several novel recurrent mutations of histone modifying and chromatin remodeling genes have been identified in renal cell carcinoma. These mutations cause loss of function of several genes located in close proximity to VHL and include PBRM1, BAP1 and SETD2. PBRM1 encodes for BAF180, a component of the SWI/SNF chromatin remodeling complex, and is inactivated in, on average, 36% of clear cell renal cell carcinoma (ccRCC). Mutations of BAP1 encode for the histone deubiquitinase BRCA1 associated protein-1, and are present in 10% of ccRCCs. They are largely mutually exclusive with PBRM1 mutations. Mutations to SETD2, a histone methyltransferase, occur in 10% of ccRCC. BAP1- or SETD2-mutated ccRCCs have been associated with poor overall survival, while PBRM1 mutations seem to identify a favorable group of ccRCC tumors. This review describes the roles of PBRM1, BAP1 and SETD2 in the development and progression of ccRCC and their potential for future personalized approaches.
76 citations
TL;DR: The clinical potential of CNV identification in whole exome sequencing and whole genome sequencing data is discussed and the implications this has on diagnostic laboratories are discussed.
Abstract: Many laboratories now use genomic microarrays as their first-tier diagnostic test for copy number variation (CNV) detection. In addition, whole exome sequencing is increasingly being offered as a diagnostic test for heterogeneous disorders. Although mostly used for the detection of point mutations and small insertion-deletions, exome sequencing can also be used to call CNVs, allowing combined small and large variant analysis. Whole genome sequencing in addition to these advantages also offers the potential to characterize CNVs to unprecedented levels of accuracy, providing position and orientation information. In this review, we discuss the clinical potential of CNV identification in whole exome sequencing and whole genome sequencing data and the implications this has on diagnostic laboratories.
70 citations
TL;DR: An overview of how next generation sequencing has advanced the understanding of epilepsy genetics is provided and some of the recently discovered genes in monogenic epilepsies are discussed.
Abstract: During the last decade, next generation sequencing technologies such as targeted gene panels, whole exome sequencing and whole genome sequencing have led to an explosion of gene identifications in monogenic epilepsies including both familial epilepsies and severe epilepsies, often referred to as epileptic encephalopathies. The increased knowledge about causative genetic variants has had a major impact on diagnosis of genetic epilepsies and has already been translated into treatment recommendations for a few genes. This article provides an overview of how next generation sequencing has advanced our understanding of epilepsy genetics and discusses some of the recently discovered genes in monogenic epilepsies.
66 citations
TL;DR: A brief overview of Lyme disease testing is provided, emphasizing current usage and limitations and the use of nonvalidated procedures and the prospects for a reduction in such testing practices in the future are discussed.
Abstract: The diagnosis of Lyme disease is a controversial topic. Most practitioners and scientists recognize that Lyme disease is associated with certain objective clinical manifestations supported by laboratory evidence of infection with Borrelia burgdorferi sensu lato (the etiologic agent). There are others, however, who believe that patients with Lyme disease may have a wide variety of entirely nonspecific symptoms without any objective clinical manifestation and that laboratory evidence of infection by B. burgdorferi is not required to support the diagnosis. In reality, this perspective is not evidence based and would inevitably lead to innumerable misdiagnoses, given the high frequency of medically unexplained symptoms, such as fatigue and musculoskeletal pains, in the general population. Although those espousing this viewpoint do not believe that a positive laboratory test is required, nevertheless, they often seek out and promote alternative, unapproved testing methods that frequently provide false-positive...
TL;DR: In resource-poor countries, POCT may be the only means of delivering advanced testing for epidemiologically important diseases, such as tuberculosis of HIV infection, and in advanced healthcare systems, it may be beneficial if health or cost–benefits can be established.
Abstract: In the past half-century, routine central laboratory testing has become increasingly automated and efficient. The majority of clinical chemistry, immunochemistry and hematology testing are performed using high throughput instrumentation, with sophisticated automation. Microbiology, immunohematology and molecular diagnostic testing are also becoming increasingly automated. Recent challenges in healthcare demand new diagnostic solutions worldwide. Point-of-care testing (POCT) offers considerable advantages over central laboratory testing, such as fast and simple specimen handling, and simpler sample requirement (no additives and mostly blood from finger stick; and urine). No transportation is required, and POCT delivers short turnaround time of approximately 5-15 min. In recent years, POCT has gained ground worldwide. In advanced healthcare systems, POCT may be beneficial if health or cost-benefits can be established. In resource-poor countries, POCT may be the only means of delivering advanced testing for epidemiologically important diseases, such as tuberculosis of HIV infection.
TL;DR: There is a critical need to implement minimally invasive clinical tests enabling molecular stratification and prognosis assessment, as well as the prediction and monitoring of treatment response.
Abstract: Glioblastoma (GBM) is the most common and devastating primary malignant brain tumor in adults. The past few years have seen major progress in our understanding of the molecular basis of GBM. These advances, which have contributed to the development of novel targeted therapies, will change the paradigms in GBM therapy from disease-based to individually tailored molecular target-based treatment. No validated circulating biomarkers have yet been integrated into clinical practice for GBM. There is thus a critical need to implement minimally invasive clinical tests enabling molecular stratification and prognosis assessment, as well as the prediction and monitoring of treatment response. After examination of data from recent studies exploring several categories of tumor-associated biomarkers (circulating tumor cells, extracellular vesicles, nucleic acids and oncometabolites) identified in the blood, cerebrospinal fluid and urine, this article discusses the challenges and prospects for the development of circulating biomarkers in GBM.
TL;DR: This review presents a technical overview of WES analysis, variants annotation and interpretation in a clinical setting, and evaluates the usefulness of clinical WES in different clinical indications, such as rare diseases, cancer and complex diseases.
Abstract: Whole-exome sequencing (WES) represents a significant breakthrough in the field of human genetics. This technology has largely contributed to the identification of new disease-causing genes and is now entering clinical laboratories. WES represents a powerful tool for diagnosis and could reduce the 'diagnostic odyssey' for many patients. In this review, we present a technical overview of WES analysis, variants annotation and interpretation in a clinical setting. We evaluate the usefulness of clinical WES in different clinical indications, such as rare diseases, cancer and complex diseases. Finally, we discuss the efficacy of WES as a diagnostic tool and the impact on patient management.
TL;DR: The challenges ahead include: better understanding of the mutation mechanisms of syndromic genes in apparent non-syndromic patients; finding mutations in patients who have tested negative or inconclusive; better variant calling, especially for intronic and synonymous variants; more precise genotype–phenotype correlations and making genetic testing more broadly accessible.
Abstract: Next-generation sequencing, also known as massively paralleled sequencing, offers an unprecedented opportunity to study disease mechanisms of inherited retinal dystrophies: a dramatic change from a few years ago. The specific involvement of the retina and the manageable number of genes to sequence make inherited retinal dystrophies an attractive model to study genotype–phenotype correlations. Costs are reducing rapidly and the current overall mutation detection rate of approximately 60% offers real potential for personalized medicine and treatments. This report addresses the challenges ahead, which include: better understanding of the mutation mechanisms of syndromic genes in apparent non-syndromic patients; finding mutations in patients who have tested negative or inconclusive; better variant calling, especially for intronic and synonymous variants; more precise genotype–phenotype correlations and making genetic testing more broadly accessible.
TL;DR: The role of emerging biomarkers is summarized, based on the current understanding of the prostate cancer metabolome, which showed an upregulation of androgen-induced protein synthesis, an increased amino acid metabolism and a perturbation of nitrogen breakdown pathways, along with high total choline-containing compounds and phosphocholine levels.
Abstract: Metabolomic profiling offers a powerful methodology for understanding the perturbations of biochemical systems occurring during a disease process. During neoplastic transformation, prostate cells undergo metabolic reprogramming to satisfy the demands of growth and proliferation. An early event in prostate cell transformation is the loss of capacity to accumulate zinc. This change is associated with a higher energy efficiency and increased lipid biosynthesis for cellular proliferation, membrane formation and cell signaling. Moreover, recent studies have shown that sarcosine, an N-methyl derivative of glycine, was significantly increased during disease progression from normal to localized to metastatic prostate cancer. Mapping the metabolomic profiles to their respective biochemical pathways showed an upregulation of androgen-induced protein synthesis, an increased amino acid metabolism and a perturbation of nitrogen breakdown pathways, along with high total choline-containing compounds and phosphocholine l...
TL;DR: The current state of research on circulating epigenetic alterations (DNA methylation, miRNA and long non-coding RNA) in serum and plasma of patients with bladder cancer, prostate cancer, renal cell carcinoma and testicular germ cell cancer is discussed.
Abstract: In the era of personalized medicine, there is an urgent need for non-invasive biomarkers to optimize the individual treatment of cancer patients. Epigenetic alterations, including DNA methylation and non-coding RNAs, are a hallmark of malignant tumors. The detection of many of these epigenetic conditions is feasible in bodily fluids, that is, blood plasma and serum, and may therefore be used for liquid biopsy. In this review, we summarize and discuss the current state of research on circulating epigenetic alterations (DNA methylation, miRNA and long non-coding RNA) in serum and plasma of patients with bladder cancer, prostate cancer, renal cell carcinoma and testicular germ cell cancer.
TL;DR: The challenges and opportunities of when using genomic information for the diagnosis and prognosis of AD are summarized.
Abstract: Alzheimer’s disease (AD), the most common form of dementia in western societies, is a pathologically and clinically heterogeneous disease with a strong genetic component. The recent advances in high-throughput genome technologies allowing for the rapid analysis of millions of polymorphisms in thousands of subjects has significantly advanced our understanding of the genomic underpinnings of AD susceptibility. During the last 5 years, genome-wide association and whole-exome- and whole-genome sequencing studies have mapped more than 20 disease-associated loci, providing insights into the molecular pathways involved in AD pathogenesis and hinting at potential novel therapeutic targets. This review article summarizes the challenges and opportunities of when using genomic information for the diagnosis and prognosis of AD.
TL;DR: Current possibilities to enrich and, in particular, detect viable CTCs with emphasis on the EPithelial ImmunoSPOT technology are discussed, which will contribute to identifying the biological properties of metastatic cells and reveal new therapeutic targets against disseminating cancer cells.
Abstract: Circulating tumor cells (CTCs) in the blood of cancer patients have received increasing attention as new diagnostic tool enabling 'liquid biopsies'. In contrast to the wealth of descriptive studies demonstrating the clinical relevance of CTCs as biomarkers, the extremely low concentration of CTCs in the peripheral blood of most cancer patients challenges further functional studies. This article discusses the current possibilities to enrich and, in particular, detect viable CTCs with emphasis on the EPithelial ImmunoSPOT technology. This functional assay detects viable CTCs at the single-cell level and has been used on hundreds of patients with different tumor types including epithelial tumors (breast, prostate and colon cancer) and melanomas. Moreover, the article summarizes recent advances in the in vitro and in vivo expansion of CTCs from cancer patients. These functional analyses will contribute to identifying the biological properties of metastatic cells and reveal new therapeutic targets against disseminating cancer cells.
TL;DR: The opportunities, known limitations and future perspectives of the recently introduced Epi proColon® 2.0 test, which is based on the detection of aberrantly methylated DNA of the v2 region of the septin 9 gene in plasma, are evaluated.
Abstract: Colorectal cancer (CRC) is a slow-developing cancer (10-15 years) with one of the highest frequencies in the world's population. Many countries have implemented various CRC screening programs, but have not achieved the desired compliance. Colonoscopy - considered the gold standard for CRC screening - has its limitations as well as the other techniques used, such as irrigoscopy, sigmoidoscopy, fecal blood and hemoglobin tests. The biomarker septin 9 has been found to be hypermethylated in nearly 100% of tissue neoplasia specimens and detected in circulating DNA fractions of CRC patients. A commercially available assay for septin 9 has been developed with moderate sensitivity (∼70%) and specificity (∼90%) and a second generation assay, Epi proColon 2.0 (Epigenomics AG), shows increased sensitivity (∼92%). The performance of the assay proved to be independent of tumor site and reaches a high sensitivity of 77%, even in early cancer stages (I and II). Furthermore, septin 9 was recently used in follow-up studies for detection of early recurrence of CRC. This article evaluates the opportunities, known limitations and future perspectives of the recently introduced Epi proColon(®) 2.0 test, which is based on the detection of aberrantly methylated DNA of the v2 region of the septin 9 gene in plasma.
TL;DR: Molecular analysis of circulating cell-free DNA offers a novel, minimally invasive method that can be performed at multiple time-points and plausibly better represents the prevailing molecular profile of the cancer.
Abstract: The optimal choice of cancer therapy depends upon analysis of the tumor genome for druggable molecular alterations. The spatial and temporal intratumor heterogeneity of cancers creates substantial challenges, as molecular profile depends on time and site of tumor tissue collection. To capture the entire molecular profile, multiple biopsies from primary and metastatic sites at different time points would be required, which is not feasible for ethical or economic reasons. Molecular analysis of circulating cell-free DNA offers a novel, minimally invasive method that can be performed at multiple time-points and plausibly better represents the prevailing molecular profile of the cancer. Molecular analysis of this cell-free DNA offers multiple clinically useful applications, such as identification of molecular targets for cancer therapy, monitoring of tumor molecular profile in real time, detection of emerging molecular aberrations associated with resistance to particular therapy, determination of cancer prognosis and diagnosis of cancer recurrence or progression.
TL;DR: The role of KRAS mutation testing is poised to expand, likely in a setting of combinatorial therapeutic strategy and requiring additional mutation testing of its upstream and/or downstream effectors.
Abstract: Activating mutation of KRAS plays a significant role in the pathogenesis of common human malignancies and molecular testing of KRAS mutation has emerged as an essential biomarker in the current practice of clinical oncology. The presence of KRAS mutation is generally associated with clinical aggressiveness of the cancer and reduced survival of the patient. Therapeutically, KRAS mutation testing has maximum utility in stratifying metastatic colorectal carcinoma and lung cancer patients for treatment with targeted therapy. Diagnostically, KRAS mutation testing is useful in the workup of pancreaticobiliary and thyroid cancers, particularly using cytological specimens. In the era of precision medicine, the role of KRAS mutation testing is poised to expand, likely in a setting of combinatorial therapeutic strategy and requiring additional mutation testing of its upstream and/or downstream effectors.
TL;DR: The information obtained from the characterization of this body fluid compartment in human samples is discussed in the context of its usefulness as diagnostic resource for several pathologies, including cancer, inflammatory, vascular and metabolic diseases.
Abstract: Biomarkers are of great importance for prediction, diagnosis and monitoring the progression and therapeutic success of a disease. Whole body fluids, such as blood or urine, constitute the main desired biological source to identify these markers, mostly due to the minimally invasive procedures used to collect them. An additional benefit of studying these biological fluids that has been demonstrated by many different groups is that they contain cell-released extracellular vesicles, carrying a cargo of lipids, proteins and nucleic acids that reflects cell/tissue origin and, remarkably, cellular status. In this review, the information obtained from the characterization of this body fluid compartment in human samples is discussed in the context of its usefulness as diagnostic resource for several pathologies, including cancer, inflammatory, vascular and metabolic diseases. The review shows the great variety of methods used for this purpose as well as the different types of molecules that could serve as specific or common disease markers.
TL;DR: An overview of the current use of EVs in CVD and a discussion of the need for robust and easy isolation technologies for plasma EV subsets are presented to bring this promising field towards clinical application in the patient are presented.
Abstract: Cardiovascular disease (CVD) is the leading cause of death worldwide and its prevalence is expected to rise rapidly worldwide in the coming decades. Atherosclerosis, the syndrome underlying CVD, is a chronic progressive disease of the arteries already present at a young age. Strokes, heart attacks and heart failure are acute CVD events that occur after decades, however, and require timely diagnosis and treatment. Plasma extracellular vesicles (EVs) are microstructures with a lipid bilayer membrane involved in hemostasis, inflammation and injury. Both EV-counts and EV-content are associated with CVD and the identification of plasma EVs is a novel source of blood-based biomarkers with the potential to improve diagnosis and prognosis of CVD. Presented in this review is an overview of the current use of EVs in CVD and a discussion of the need for robust and easy isolation technologies for plasma EV subsets. This is needed to bring this promising field towards clinical application in the patient.
TL;DR: A review of the currently available literature with more speculative arguments about the potential interpretation and application of VOC analysis is provided in this paper, which provides an overview of the main relevant aspects of this promising field of research.
Abstract: Breath analysis via electronic nose is a technique oriented around volatile organic compound (VOC) profiling in exhaled breath for diagnostic and prognostic purposes. This approach, when supported by methodologies for VOC identification, has been often referred to as metabolomics or breathomics. Although breath analysis may have a substantial impact on clinical practice, as it may allow early diagnosis and large-scale screening strategies while being noninvasive and inexpensive, some technical and methodological limitations must be solved, together with crucial interpretative issues. By integrating a review of the currently available literature with more speculative arguments about the potential interpretation and application of VOC analysis, the authors aim to provide an overview of the main relevant aspects of this promising field of research.
TL;DR: The current state of the art, benefits and challenges of metabolomics are outlined to create an understanding of metabolites studies from the experimental design to data analysis.
Abstract: Small molecules within biological systems provide powerful insights into the biological roles, processes and states of organisms. Metabolomics is the study of the concentrations, structures and interactions of these thousands of small molecules, collectively known as the metabolome. Metabolomics is at the interface between chemistry, biology, statistics and computer science, requiring multidisciplinary skillsets. This presents unique challenges for researchers to fully utilize the information produced and to capture its potential diagnostic power. A good understanding of study design, sample preparation, analysis methods and data analysis is essential to get the right answers for the right questions. We outline the current state of the art, benefits and challenges of metabolomics to create an understanding of metabolomics studies from the experimental design to data analysis.
TL;DR: The challenges and opportunities of using targeted resequencing (TRS) panels for diagnosing monogenetic disorders and working with TRS panels also poses new challenges in variant interpretation, data handling and bioinformatic analyses.
Abstract: Next-generation sequencing (NGS) will soon be used for clinically heterogeneous, inherited disorders and the increasing number of disease-causing genes reported. Diagnostic laboratories therefore need to decide which NGS methods they are going to invest in and how to implement them. We discuss here the challenges and opportunities of using targeted resequencing (TRS) panels for diagnosing monogenetic disorders. Of the different NGS approaches available, TRS panels offer the opportunity to sequence and analyze a limited set of predetermined target genes. At present, TRS panels offer better base-pair coverage, running times, costs and dataset handling than other NGS applications such as whole genome sequencing and whole exome sequencing. However, working with TRS panels also poses new challenges in variant interpretation, data handling and bioinformatic analyses. To optimize the analyses, TRS panel testing should be performed by bioinformaticians, clinicians and laboratory staff in close collaboration.
TL;DR: New technologies that allow rapid isolation of biomarkers directly from blood will permit seamless sample-to-answer solutions that enable next-generation point-of-care molecular diagnostics.
Abstract: As we move into the era of individualized cancer treatment, the need for more sophisticated cancer diagnostics has emerged. Cell-free (cf) nucleic acids (cf-DNA, cf-RNA) and other cellular nanoparticulates are now considered important and selective biomarkers. There is great hope that blood-borne cf-nucleic acids can be used for ‘liquid biopsies’, replacing more invasive tissue biopsies to analyze cancer mutations and monitor therapy. Conventional techniques for cf-nucleic acid biomarker isolation from blood are generally time-consuming, complicated and expensive. They require relatively large blood samples, which must be processed to serum or plasma before isolation of biomarkers can proceed. Such cumbersome sample preparation also limits the widespread use of powerful, downstream genomic analyses, including PCR and DNA sequencing. These limitations also preclude rapid, point-of-care diagnostic applications. Thus, new technologies that allow rapid isolation of biomarkers directly from blood will permit s...
TL;DR: Recommendations how to perform robust and highly accurate targeted preamplification in combination with qPCR or next-generation sequencing are provided.
Abstract: Objective: Quantification of small molecule numbers often requires preamplification to generate enough copies for accurate downstream enumerations. Here, we studied experimental parameters in targeted preamplification and their effects on downstream quantitative real-time PCR (qPCR). Methods: To evaluate different strategies, we monitored the preamplification reaction in real-time using SYBR Green detection chemistry followed by melting curve analysis. Furthermore, individual targets were evaluated by qPCR. Result: The preamplification reaction performed best when a large number of primer pairs was included in the primer pool. In addition, preamplification efficiency, reproducibility and specificity were found to depend on the number of template molecules present, primer concentration, annealing time and annealing temperature. The amount of nonspecific PCR products could also be reduced about 1000-fold using bovine serum albumin, glycerol and formamide in the preamplification. Conclusion: On the basis of ...
TL;DR: Whole-genome-NGS techniques that allow deep sequencing of nucleic acids, data mining and sorting out of sequences of pathogens without any a priori hypothesis will likely soon become a standard procedure in microbiological diagnosis.
Abstract: Non-targeted identification of microbes is now possible directly in biological samples, based on whole-genome-NGS (WG-NGS) techniques that allow deep sequencing of nucleic acids, data mining and sorting out of sequences of pathogens without any a priori hypothesis. WG-NGS was first only used as a research tool due to its cost, complexity and lack of standardization. Recent improvements in sample preparation and bioinformatics pipelines and decrease in cost now allow actionable diagnostics in patients. The potency and limits of WG-NGS and possible future indications are discussed here. WG-NGS will likely soon become a standard procedure in microbiological diagnosis.