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The Journal of Molecular Diagnostics :... Sep 2019An enduring goal of personalized medicine in cancer is the ability to identify patients who are likely to respond to specific therapies. Our growing understanding of the... (Review)
Review
An enduring goal of personalized medicine in cancer is the ability to identify patients who are likely to respond to specific therapies. Our growing understanding of the biology and molecular signatures of individual tumor types has facilitated the identification of predictive biomarkers and has led to an increasing number of diagnostic tests to be performed, often as serial and distinct assays on limited tumor specimens. The biomarker diagnostics field has been revolutionized by next-generation sequencing (NGS), which provides a comprehensive overview of the genomic profile of a tumor. Many preanalytic variables can influence the accuracy and reliability of NGS results. Standardization of preanalytic variables is, however, complicated by the plethora of specimen acquisition and processing methods. Variables across the tissue journey, including specimen acquisition, specimen fixation, and sectioning, as well as postfixation processing, such as nucleic acid extraction, library preparation, and choice of sequencing methods, are critical for the reliability of NGS analysis; thus, standardization would be beneficial. In this article, each step in the tissue journey is outlined, with specific focus on preanalytic variables that can influence NGS results. Practical considerations for standardization of these variables are provided to facilitate accurate, reliable, and reproducible NGS-based molecular characterization of tumors, ultimately informing diagnosis and guiding treatment.
Topics: Gene Library; High-Throughput Nucleotide Sequencing; Humans; Neoplasms; Precision Medicine; Sequence Analysis, DNA; Specimen Handling
PubMed: 31251989
DOI: 10.1016/j.jmoldx.2019.05.004 -
Microbiology Spectrum Jan 2019In the decade and a half since the introduction of next-generation sequencing (NGS), the technical feasibility, cost, and overall utility of sequencing have changed... (Review)
Review
In the decade and a half since the introduction of next-generation sequencing (NGS), the technical feasibility, cost, and overall utility of sequencing have changed dramatically, including applications for infectious disease epidemiology. Massively parallel sequencing technologies have decreased the cost of sequencing by more than 6 orders or magnitude over this time, with a corresponding increase in data generation and complexity. This review provides an overview of the basic principles, chemistry, and operational mechanics of current sequencing technologies, including both conventional Sanger and NGS approaches. As the generation of large amounts of sequence data becomes increasingly routine, the role of bioinformatics in data analysis and reporting becomes all the more critical, and the successful deployment of NGS in public health settings requires careful consideration of changing information technology, bioinformatics, workforce, and regulatory requirements. While there remain important challenges to the sustainable implementation of NGS in public health, in terms of both laboratory and bioinformatics capacity, the impact of these technologies on infectious disease surveillance and outbreak investigations has been nothing short of revolutionary. Understanding the important role that NGS plays in modern public health laboratory practice is critical, as is the need to ensure appropriate workforce, infrastructure, facilities, and funding consideration for routine NGS applications, future innovation, and rapidly scaling NGS-based infectious disease surveillance and outbreak response activities. *This article is part of a curated collection.
Topics: Computational Biology; DNA; Data Analysis; Gene Library; High-Throughput Nucleotide Sequencing; Humans; Sequence Analysis, DNA
PubMed: 30737915
DOI: 10.1128/microbiolspec.AME-0005-2018 -
Protein & Cell Jun 2010As one of the key technologies in biomedical research, DNA sequencing has not only improved its productivity with an exponential growth rate but also been applied to new... (Review)
Review
As one of the key technologies in biomedical research, DNA sequencing has not only improved its productivity with an exponential growth rate but also been applied to new areas of application over the past few years. This is largely due to the advent of newer generations of sequencing platforms, offering ever-faster and cheaper ways to analyze sequences. In our previous review, we looked into technical characteristics of the next-generation sequencers and provided prospective insights into their future development. In this article, we present a brief overview of the advantages and shortcomings of key commercially available platforms with a focus on their suitability for a broad range of applications.
Topics: Animals; DNA-Binding Proteins; Epigenomics; Gene Expression Profiling; Genomics; High-Throughput Nucleotide Sequencing; Humans; Nanostructures; RNA, Small Untranslated
PubMed: 21204006
DOI: 10.1007/s13238-010-0065-3 -
Value in Health : the Journal of the... Sep 2018Next-generation sequencing (NGS) technologies have seen variable adoption in the clinic. This is partly due to a lack of clinical and economic studies, with the latter... (Review)
Review
BACKGROUND
Next-generation sequencing (NGS) technologies have seen variable adoption in the clinic. This is partly due to a lack of clinical and economic studies, with the latter increasingly challenged to examine patient preferences for health and nonhealth outcomes (e.g., false-positive rate).
OBJECTIVES
To conduct a structured review of studies valuing patients' preference-based utility for NGS outcomes, to highlight identified methodological challenges, and to consider how studies addressed identified challenges.
METHODS
We searched MEDLINE (PubMed), Embase (Ovid), and Web of Science for published studies examining outcomes from health care decisions informed by NGS. We focused our search on direct elicitations of preference-based utility. We reviewed included studies and qualitatively grouped and summarized stated challenges and solutions by theme.
RESULTS
Eleven studies were included. Most of them (n = 6) used discrete choice experiments to value utility. We categorized challenges into four themes: 1) valuing the full range of NGS outcomes, 2) accounting for accuracy and uncertainty surrounding effectiveness, 3) allowing for simultaneous multiple and cascading risks, and 4) incorporating downstream consequences. Studies found strong evidence of utility for NGS information, regardless of health improvement. Investigators addressed challenges by simplifying complex choices, by including health outcomes alongside nonhealth outcomes, and by using multiple elicitation techniques.
CONCLUSIONS
The breadth and complexity of NGS-derived information makes the technology a unique and challenging application for utility valuation. Failing to account for the utility or disutility of NGS-related nonhealth outcomes may lead to overinvestment or underinvestment in NGS, and so there is a need for research addressing unresolved challenges.
Topics: Cost-Benefit Analysis; Decision Making; High-Throughput Nucleotide Sequencing; Humans; Outcome Assessment, Health Care; Technology Assessment, Biomedical
PubMed: 30224107
DOI: 10.1016/j.jval.2018.06.010 -
Briefings in Bioinformatics Nov 2014Advances in next-generation sequencing (NGS) technologies have greatly improved our ability to detect genomic variants for biomedical research. In particular, NGS... (Review)
Review
Advances in next-generation sequencing (NGS) technologies have greatly improved our ability to detect genomic variants for biomedical research. In particular, NGS technologies have been recently applied with great success to the discovery of mutations associated with the growth of various tumours and in rare Mendelian diseases. The advance in NGS technologies has also created significant challenges in bioinformatics. One of the major challenges is quality control of the sequencing data. In this review, we discuss the proper quality control procedures and parameters for Illumina technology-based human DNA re-sequencing at three different stages of sequencing: raw data, alignment and variant calling. Monitoring quality control metrics at each of the three stages of NGS data provides unique and independent evaluations of data quality from differing perspectives. Properly conducting quality control protocols at all three stages and correctly interpreting the quality control results are crucial to ensure a successful and meaningful study.
Topics: Computational Biology; DNA; Gene Library; High-Throughput Nucleotide Sequencing; Humans; Neoplasms; Polymorphism, Single Nucleotide; Quality Control; Sequence Alignment; Sequence Analysis, DNA
PubMed: 24067931
DOI: 10.1093/bib/bbt069 -
Mutagenesis Sep 2014Demand for new technologies that deliver fast, inexpensive and accurate genome information has never been greater. This challenge has catalysed the rapid development of... (Review)
Review
Demand for new technologies that deliver fast, inexpensive and accurate genome information has never been greater. This challenge has catalysed the rapid development of advances in next-generation sequencing (NGS). The generation of large volumes of sequence data and the speed of data acquisition are the primary advantages over previous, more standard methods. In 2013, the Food and Drug Administration granted marketing authorisation for the first high-throughput NG sequencer, Illumina's MiSeqDx, which allowed the development and use of a large number of new genome-based tests. Here, we present a review of template preparation, nucleic acid sequencing and imaging, genome assembly and alignment approaches as well as recent advances in current and near-term commercially available NGS instruments. We also outline the broad range of applications for NGS technologies and provide guidelines for platform selection to best address biological questions of interest. DNA sequencing has revolutionised biological and medical research, and is poised to have a similar impact on the practice of medicine. This tool is but one of an increasing arsenal of developing tools that enhance our capabilities to identify, quantify and functionally characterise the components of biological networks that keep us healthy or make us sick. Despite advances in other 'omic' technologies, DNA sequencing and analysis, in many respects, have played the leading role to date. The new technologies provide a bridge between genotype and phenotype, both in man and model organisms, and have revolutionised how risk of developing a complex human disease may be assessed. The generation of large DNA sequence data sets is producing a wealth of medically relevant information on a large number of individuals and populations that will potentially form the basis of truly individualised medical care in the future.
Topics: Computational Biology; Genetics, Medical; Genome, Human; Genotype; High-Throughput Nucleotide Sequencing; Humans; Phenotype; Sequence Analysis, DNA
PubMed: 25150023
DOI: 10.1093/mutage/geu031 -
Human Genomics Jun 2016In order to optimally integrate the use of high-throughput sequencing (HTS) as a tool in clinical diagnostics of likely monogenic disorders, we have created a... (Review)
Review
BACKGROUND
In order to optimally integrate the use of high-throughput sequencing (HTS) as a tool in clinical diagnostics of likely monogenic disorders, we have created a multidisciplinary "Genome Clinic Task Force" at the University Hospitals of Geneva, which is composed of clinical and molecular geneticists, bioinformaticians, technicians, bioethicists, and a coordinator.
METHODS AND RESULTS
We have implemented whole exome sequencing (WES) with subsequent targeted bioinformatics analysis of gene lists for specific disorders. Clinical cases of heterogeneous Mendelian disorders that could potentially benefit from HTS are presented and discussed during the sessions of the task force. Debate concerning the interpretation of identified variants and the content of the final report constitutes a major part of the task force's work. Furthermore, issues related to bioethics, genetic counseling, quality control, and reimbursement are also addressed.
CONCLUSIONS
This multidisciplinary task force has enabled us to create a platform for regular exchanges between all involved experts in order to deal with the multiple complex issues related to HTS in clinical practice and to continuously improve the diagnostic use of HTS. In addition, this task force was instrumental to formally approve the reimbursement of HTS for molecular diagnosis of Mendelian disorders in Switzerland.
Topics: Exome; Genetic Diseases, Inborn; High-Throughput Nucleotide Sequencing; Humans; Molecular Diagnostic Techniques; Public Health Administration; Reimbursement Mechanisms; Sequence Analysis, DNA; Switzerland
PubMed: 27353043
DOI: 10.1186/s40246-016-0080-4 -
TheScientificWorldJournal 2014The world has now entered into a new era of genomics because of the continued advancements in the next generation high throughput sequencing technologies, which includes... (Review)
Review
The world has now entered into a new era of genomics because of the continued advancements in the next generation high throughput sequencing technologies, which includes sequencing by synthesis-fluorescent in situ sequencing (FISSEQ), pyrosequencing, sequencing by ligation using polony amplification, supported oligonucleotide detection (SOLiD), sequencing by hybridization along with sequencing by ligation, and nanopore technology. Great impacts of these methods can be seen for solving the genome related problems of plant and animal kingdom that will open the door of a new era of genomics. This may ultimately overcome the Sanger sequencing that ruled for 30 years. NGS is expected to advance and make the drug discovery process more rapid.
Topics: Drug Discovery; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA
PubMed: 24688432
DOI: 10.1155/2014/802437 -
Molecular Ecology Resources Sep 2016Evolutionary biologists from Darwin forward have dreamed of having data that would elucidate our understanding of evolutionary history and the diversity of life....
Evolutionary biologists from Darwin forward have dreamed of having data that would elucidate our understanding of evolutionary history and the diversity of life. Sequence capture is a relatively old DNA technology, but its use is growing rapidly due to advances in (i) massively parallel DNA sequencing approaches and instruments, (ii) massively parallel bait construction, (iii) methods to identify target regions and (iv) sample preparation. We give a little historical context to these developments, summarize some of the important advances reported in this special issue and point to further advances that can be made to help fulfill Darwin's dream.
Topics: Biological Evolution; Biology; DNA; Genetic Variation; Genotyping Techniques; High-Throughput Nucleotide Sequencing; History, 20th Century; History, 21st Century; Nucleic Acid Hybridization; Specimen Handling
PubMed: 27454358
DOI: 10.1111/1755-0998.12574 -
International Journal of Molecular... Nov 2020Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different... (Review)
Review
Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.
Topics: Aptamers, Nucleotide; Base Sequence; Benchmarking; Gene Library; High-Throughput Nucleotide Sequencing; Humans; Ligands; Nucleic Acid Conformation; Nucleic Acids; Precision Medicine; SELEX Aptamer Technique
PubMed: 33233573
DOI: 10.3390/ijms21228774