Biomolecular Detection and Quantification最新文献

{"title":"Guest editor's introduction for BDQ special issue: ‘Advanced Molecular Diagnostics for Biomarker Discovery’","authors":"Michael W. Pfaffl (Guest Editor)","doi":"10.1016/j.bdq.2015.09.003","DOIUrl":"10.1016/j.bdq.2015.09.003","url":null,"abstract":"","PeriodicalId":38073,"journal":{"name":"Biomolecular Detection and Quantification","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.bdq.2015.09.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34401262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Removal of between-run variation in a multi-plate qPCR experiment","authors":"Jan M. Ruijter ,&nbsp;Adrián Ruiz Villalba ,&nbsp;Jan Hellemans ,&nbsp;Andreas Untergasser ,&nbsp;Maurice J.B. van den Hoff","doi":"10.1016/j.bdq.2015.07.001","DOIUrl":"10.1016/j.bdq.2015.07.001","url":null,"abstract":"<div><p>Quantitative PCR (qPCR) is the method of choice in gene expression analysis. However, the number of groups or treatments, target genes and technical replicates quickly exceeds the capacity of a single run on a qPCR machine and the measurements have to be spread over more than 1 plate. Such multi-plate measurements often show similar proportional differences between experimental conditions, but different absolute values, even though the measurements were technically carried out with identical procedures. Removal of this between-plate variation will enhance the power of the statistical analysis on the resulting data. Inclusion and application of calibrator samples, with replicate measurements distributed over the plates, assumes a multiplicative difference between plates. However, random and technical errors in these calibrators will propagate to all samples on the plate. To avoid this effect, the systematic bias between plates can be removed with a correction factor based on all overlapping technical and biological replicates between plates. This approach removes the requirement for all calibrator samples to be measured successfully on every plate. This paper extends an already published factor correction method to the use in multi-plate qPCR experiments. The between-run correction factor is derived from the target quantities which are calculated from the quantification threshold, PCR efficiency and observed <em>C</em>_<em>q</em> value. To enable further statistical analysis in existing qPCR software packages, an efficiency-corrected <em>C</em>_<em>q</em> value is reported, based on the corrected target quantity and a PCR efficiency per target. The latter is calculated as the mean of the PCR efficiencies taking the number of reactions per amplicon per plate into account. Export to the RDML format completes an RDML-supported analysis pipeline of qPCR data ranging from raw fluorescence data, amplification curve analysis and application of reference genes to statistical analysis.</p></div>","PeriodicalId":38073,"journal":{"name":"Biomolecular Detection and Quantification","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.bdq.2015.07.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34401264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The potential of circulating extracellular small RNAs (smexRNA) in veterinary diagnostics—Identifying biomarker signatures by multivariate data analysis","authors":"Spornraft Melanie,&nbsp;Kirchner Benedikt,&nbsp;Michael W. Pfaffl,&nbsp;Riedmaier Irmgard","doi":"10.1016/j.bdq.2015.08.001","DOIUrl":"10.1016/j.bdq.2015.08.001","url":null,"abstract":"<div><p>Worldwide growth and performance-enhancing substances are used in cattle husbandry to increase productivity. In certain countries however e.g., in the EU, these practices are forbidden to prevent the consumers from potential health risks of substance residues in food. To maximize economic profit, ‘black sheep‘ among farmers might circumvent the detection methods used in routine controls, which highlights the need for an innovative and reliable detection method. Transcriptomics is a promising new approach in the discovery of veterinary medicine biomarkers and also a missing puzzle piece, as up to date, metabolomics and proteomics are paramount. Due to increased stability and easy sampling, circulating extracellular small RNAs (smexRNAs) in bovine plasma were small RNA-sequenced and their potential to serve as biomarker candidates was evaluated using multivariate data analysis tools.</p><p>After running the data evaluation pipeline, the proportion of miRNAs (microRNAs) and piRNAs (PIWI-interacting small non-coding RNAs) on the total sequenced reads was calculated. Additionally, top 10 signatures were compared which revealed that the readcount data sets were highly affected by the most abundant miRNA and piRNA profiles. To evaluate the discriminative power of multivariate data analyses to identify animals after veterinary drug application on the basis of smexRNAs, OPLS-DA was performed. In summary, the quality of miRNA models using all mapped reads for both treatment groups (animals treated with steroid hormones or the β-agonist clenbuterol) is predominant to those generated with combined data sets or piRNAs alone. Using multivariate projection methodologies like OPLS-DA have proven the best potential to generate discriminative miRNA models, supported by small RNA-Seq data. Based on the presented comparative OPLS-DA, miRNAs are the favorable smexRNA biomarker candidates in the research field of veterinary drug abuse.</p></div>","PeriodicalId":38073,"journal":{"name":"Biomolecular Detection and Quantification","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.bdq.2015.08.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34401265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microfluidic droplet-based PCR instrumentation for high-throughput gene expression profiling and biomarker discovery","authors":"Christopher J. Hayes ,&nbsp;Tara M. Dalton","doi":"10.1016/j.bdq.2015.04.003","DOIUrl":"10.1016/j.bdq.2015.04.003","url":null,"abstract":"<div><p>PCR is a common and often indispensable technique used in medical and biological research labs for a variety of applications. Real-time quantitative PCR (RT-qPCR) has become a definitive technique for quantitating differences in gene expression levels between samples. Yet, in spite of this importance, reliable methods to quantitate nucleic acid amounts in a higher throughput remain elusive. In the following paper, a unique design to quantify gene expression levels at the nanoscale in a continuous flow system is presented. Fully automated, high-throughput, low volume amplification of deoxynucleotides (DNA) in a droplet based microfluidic system is described. Unlike some conventional qPCR instrumentation that use integrated fluidic circuits or plate arrays, the instrument performs qPCR in a continuous, micro-droplet flowing process with droplet generation, distinctive reagent mixing, thermal cycling and optical detection platforms all combined on one complete instrument. Detailed experimental profiling of reactions of less than 300<!--> <!-->nl total volume is achieved using the platform demonstrating the dynamic range to be 4 order logs and consistent instrument sensitivity. Furthermore, reduced pipetting steps by as much as 90% and a unique degree of hands-free automation makes the analytical possibilities for this instrumentation far reaching. In conclusion, a discussion of the first demonstrations of this approach to perform novel, continuous high-throughput biological screens is presented. The results generated from the instrument, when compared with commercial instrumentation, demonstrate the instrument reliability and robustness to carry out further studies of clinical significance with added throughput and economic benefits.</p></div>","PeriodicalId":38073,"journal":{"name":"Biomolecular Detection and Quantification","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.bdq.2015.04.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34401261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A glance at the applications of Singular Spectrum Analysis in gene expression data","authors":"Hossein Hassani ,&nbsp;Zara Ghodsi","doi":"10.1016/j.bdq.2015.04.001","DOIUrl":"10.1016/j.bdq.2015.04.001","url":null,"abstract":"<div><p>In recent years Singular Spectrum Analysis (SSA) has been used to solve many biomedical issues and is currently accepted as a potential technique in quantitative genetics studies. Presented in this article is a review of recent published genetics studies which have taken advantage of SSA. Since Singular Value Decomposition (SVD) is an important stage of this technique which can also be used as an independent analytical method in gene expression data, we also briefly touch upon some areas of the application of SVD. The review finds that at present, the most prominent area of applying SSA in genetics is filtering and signal extraction, which proves that SSA can be considered as a valuable aid and promising method for genetics analysis.</p></div>","PeriodicalId":38073,"journal":{"name":"Biomolecular Detection and Quantification","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.bdq.2015.04.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34400272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development, validation and quantitative assessment of an enzymatic assay suitable for small molecule screening and profiling: A case-study","authors":"Vicente Sancenon,&nbsp;Wei Hau Goh,&nbsp;Aishwarya Sundaram,&nbsp;Kai Shih Er,&nbsp;Nidhi Johal,&nbsp;Svetlana Mukhina,&nbsp;Grant Carr,&nbsp;Saravanakumar Dhakshinamoorthy","doi":"10.1016/j.bdq.2015.03.001","DOIUrl":"10.1016/j.bdq.2015.03.001","url":null,"abstract":"<div><p>The successful discovery and subsequent development of small molecule inhibitors of drug targets relies on the establishment of robust, cost-effective, quantitative, and physiologically relevant <em>in vitro</em> assays that can support prolonged screening and optimization campaigns. The current study illustrates the process of developing and validating an enzymatic assay for the discovery of small molecule inhibitors using alkaline phosphatase from bovine intestine as model target. The assay development workflow includes an initial phase of optimization of assay materials, reagents, and conditions, continues with a process of miniaturization and automation, and concludes with validation by quantitative measurement of assay performance and signal variability. The assay is further evaluated for dose–response and mechanism-of-action studies required to support structure–activity-relationship studies. Emphasis is placed on the most critical aspects of assay optimization and other relevant considerations, including the technology, assay materials, buffer constituents, reaction conditions, liquid handling equipment, analytical instrumentation, and quantitative assessments. Examples of bottlenecks encountered during assay development and strategies to address them are provided.</p></div>","PeriodicalId":38073,"journal":{"name":"Biomolecular Detection and Quantification","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.bdq.2015.03.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34400270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proximity assays for sensitive quantification of proteins","authors":"Christina Greenwood ,&nbsp;David Ruff ,&nbsp;Sara Kirvell ,&nbsp;Gemma Johnson ,&nbsp;Harvinder S. Dhillon ,&nbsp;Stephen A. Bustin","doi":"10.1016/j.bdq.2015.04.002","DOIUrl":"10.1016/j.bdq.2015.04.002","url":null,"abstract":"<div><p>Proximity assays are immunohistochemical tools that utilise two or more DNA-tagged aptamers or antibodies binding in close proximity to the same protein or protein complex. Amplification by PCR or isothermal methods and hybridisation of a labelled probe to its DNA target generates a signal that enables sensitive and robust detection of proteins, protein modifications or protein–protein interactions. Assays can be carried out in homogeneous or solid phase formats and <em>in situ</em> assays can visualise single protein molecules or complexes with high spatial accuracy. These properties highlight the potential of proximity assays in research, diagnostic, pharmacological and many other applications that require sensitive, specific and accurate assessments of protein expression.</p></div>","PeriodicalId":38073,"journal":{"name":"Biomolecular Detection and Quantification","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.bdq.2015.04.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34400271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aims & Scope","authors":"","doi":"10.1016/S2214-7535(15)00029-7","DOIUrl":"https://doi.org/10.1016/S2214-7535(15)00029-7","url":null,"abstract":"","PeriodicalId":38073,"journal":{"name":"Biomolecular Detection and Quantification","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S2214-7535(15)00029-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"137429033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons","authors":"Nathan D. Olson ,&nbsp;Steven P. Lund ,&nbsp;Justin M. Zook ,&nbsp;Fabiola Rojas-Cornejo ,&nbsp;Brian Beck ,&nbsp;Carole Foy ,&nbsp;Jim Huggett ,&nbsp;Alexandra S. Whale ,&nbsp;Zhiwei Sui ,&nbsp;Anna Baoutina ,&nbsp;Michael Dobeson ,&nbsp;Lina Partis ,&nbsp;Jayne B. Morrow","doi":"10.1016/j.bdq.2015.01.004","DOIUrl":"10.1016/j.bdq.2015.01.004","url":null,"abstract":"<div><p>This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from <em>Escherichia coli</em> O157:H7 strain EDL933 and <em>Listeria monocytogenes</em> serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing^®, or Ion Torrent PGM^®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.</p></div>","PeriodicalId":38073,"journal":{"name":"Biomolecular Detection and Quantification","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.bdq.2015.01.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34400268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the performance of the Oxford Nanopore Technologies MinION","authors":"T. Laver ,&nbsp;J. Harrison ,&nbsp;P.A. O’Neill ,&nbsp;K. Moore ,&nbsp;A. Farbos ,&nbsp;K. Paszkiewicz ,&nbsp;D.J. Studholme","doi":"10.1016/j.bdq.2015.02.001","DOIUrl":"10.1016/j.bdq.2015.02.001","url":null,"abstract":"<div><p>The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G<!--> <!-->+<!--> <!-->C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2<!--> <!-->kb and 1<!--> <!-->kb respectively, while the longest single read was 98<!--> <!-->kb. The whole length of a 5<!--> <!-->kb rRNA operon was covered by a single read. As the first nanopore-based single molecule sequencer available to researchers, the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhance contiguity of de novo assembly when used in conjunction with Illumina MiSeq data.</p></div>","PeriodicalId":38073,"journal":{"name":"Biomolecular Detection and Quantification","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.bdq.2015.02.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54134026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}