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Methods in Molecular Biology (Clifton,... 2022Microarrays are experimental methods that can provide information about gene expression and SNP data that hold great potential for new understanding, driving advances in...
Microarrays are experimental methods that can provide information about gene expression and SNP data that hold great potential for new understanding, driving advances in functional genomics and clinical and molecular biology. Cluster analysis is used to analyze data that are not a priori to contain any specific subgroup. The goal is to use the data itself to recognize meaningful and informative subgroups. Also, cluster analysis helps data reduction purposes, exposes hidden patterns, and generates hypotheses regarding the relationship between genes and phenotypes. This chapter outlines a collection of cluster methods suitable for the analysis of microarray data sets.
Topics: Algorithms; Cluster Analysis; Gene Expression; Gene Expression Profiling; Genomics; Microarray Analysis; Oligonucleotide Array Sequence Analysis
PubMed: 34902133
DOI: 10.1007/978-1-0716-1839-4_16 -
Chemical Society Reviews Oct 2022Through their specific interactions with proteins, cellular glycans play key roles in a wide range of physiological and pathological processes. One of the main goals of... (Review)
Review
Through their specific interactions with proteins, cellular glycans play key roles in a wide range of physiological and pathological processes. One of the main goals of research in the areas of glycobiology and glycomedicine is to understand glycan-protein interactions at the molecular level. Over the past two decades, glycan microarrays have become powerful tools for the rapid evaluation of interactions between glycans and proteins. In this review, we briefly describe methods used for the preparation of glycan probes and the construction of glycan microarrays. Next, we highlight applications of glycan microarrays to rapid profiling of glycan-binding patterns of plant, animal and pathogenic lectins, as well as other proteins. Finally, we discuss other important uses of glycan microarrays, including the rapid analysis of substrate specificities of carbohydrate-active enzymes, the quantitative determination of glycan-protein interactions, discovering high-affinity or selective ligands for lectins, and identifying functional glycans within cells. We anticipate that this review will encourage researchers to employ glycan microarrays in diverse glycan-related studies.
Topics: Animals; Carbohydrates; Lectins; Ligands; Microarray Analysis; Polysaccharides
PubMed: 36111958
DOI: 10.1039/d2cs00452f -
Analytical Biochemistry Dec 2023Microarrays are powerful tools for high-throughput bioassays that can extract information from tens of thousands of micro-spots consisting of biomolecules. This... (Review)
Review
Microarrays are powerful tools for high-throughput bioassays that can extract information from tens of thousands of micro-spots consisting of biomolecules. This information is invaluable to many applications, such as drug discovery and disease diagnostics. Different applications of these microarrays need spots of different shapes, sizes, and chemistries to achieve their goals. Micro/nano-fabrication techniques are used to make microarrays with different feature structures and array densities for required assay procedures. Understanding these fabrication methods is essential to creating an effective microarray. The purpose of this article is to critically review fabrication methods used in recent microarray-based bioassay studies. We summarized commonly used microarray fabrication techniques and filled the gap in recent literature on relevant topics. We discussed recent examples of how microarrays were fabricated and used in a variety of bioassays. Specifically, we examined microarray printing, various microlithography techniques, and microfluidics-based microarray fabrication. We evaluated how their application shaped the fabrication methods and compared their performance based on different applications. In the end, we discussed current challenges and outlined potential future directions. This review addressed the gap in literature and provided important insights for choosing appropriate fabrication techniques towards different applications.
Topics: Microarray Analysis; Microfluidics; Biological Assay
PubMed: 37914004
DOI: 10.1016/j.ab.2023.115369 -
Clinical and Experimental Obstetrics &... 2017Genome copy number variation (CNV) is an important cause of genetic and developmental disorders. In recent years, chromosomal microarray analysis (CMA) technology to... (Review)
Review
Genome copy number variation (CNV) is an important cause of genetic and developmental disorders. In recent years, chromosomal microarray analysis (CMA) technology to test for genomic copy number variation has been developed and gradually applied in prenatal diagnostics, offering high diagnostic ability. Here, the authors summarise the CMA established in clinical settings, as well as the significance and clinical application of the standard analyses. They also emphatically discuss the key problems in the establishment process of the platform in prenatal diagnostics in the clinic.
Topics: DNA Copy Number Variations; Female; Genetic Diseases, Inborn; Humans; Microarray Analysis; Pregnancy; Prenatal Diagnosis
PubMed: 29746015
DOI: No ID Found -
Acta Microbiologica Et Immunologica... Mar 2019The pan-genomic microarray technique is used for environmental and/or clinical studies. Although microarray is an accurate and sharp diagnostic tool, the expertized... (Review)
Review
The pan-genomic microarray technique is used for environmental and/or clinical studies. Although microarray is an accurate and sharp diagnostic tool, the expertized bioinformaticians were able to minimize the outcome biases and maximize the flexibility and accuracy of the technique. The knowledge of bioinformatics plays a key role in association with probe designing and the utilization of correct probe sets and platforms. This technique is divided into two parts as dry lab (in silico studies) and wet lab (in vitro studies). Each part covers the other and are known as complementary divisions. In the case of microarray probe designing, a wide range of software, tools, and databases are necessary. Obviously, the application of right databases, software, and tools decreases the probable biases in the outcomes. Due to the importance of suitable probe designing, this article has focused its look onto a variety of online/offline databases, software, and tools.
Topics: Computational Biology; Internet; Microarray Analysis; Oligonucleotide Array Sequence Analysis; Oligonucleotide Probes
PubMed: 30010394
DOI: 10.1556/030.65.2018.028 -
Methods in Molecular Biology (Clifton,... 2017Speed and throughput are vital ingredients for discovery driven, "-omics" research. The small molecule microarray (SMM) succeeds at delivering phenomenal screening... (Review)
Review
Speed and throughput are vital ingredients for discovery driven, "-omics" research. The small molecule microarray (SMM) succeeds at delivering phenomenal screening throughput and versatility. The concept at the heart of the technology is elegant, yet simple: by presenting large collections of molecules in high density on a flat surface, one is able to interrogate all possible interactions with desired targets, in just a single step. SMMs have become established as the choice platform for screening, lead discovery, and molecular characterization. This introduction describes the principles governing microarray construction and use, focusing on practical challenges faced when conducting SMM experiments. It will explain the key design considerations and lay the foundation for the chapters that follow. (An earlier version of this chapter appeared in Small Molecule Microarrays: Methods and Protocols, published in 2010.).
Topics: Microarray Analysis; Small Molecule Libraries
PubMed: 27873196
DOI: 10.1007/978-1-4939-6584-7_1 -
Annals of Allergy, Asthma & Immunology... Jul 2021To give an overview and describe the strengths and weaknesses of immunoglobulin E (IgE) microarray and other multiplex assays that have been developed and are being used... (Review)
Review
OBJECTIVE
To give an overview and describe the strengths and weaknesses of immunoglobulin E (IgE) microarray and other multiplex assays that have been developed and are being used for allergy diagnostics.
DATA SOURCES
Queries for IgE microarray and multiplex assays were conducted with PubMed and Google Scholar, searching for primary articles and review papers.
STUDY SELECTIONS
We focused on articles written in English on commercially available IgE multiplex assays that were reported in the allergy and immunology literature.
RESULTS
Several commercial IgE assays that use microarray or other multiplex technology have been developed, and some have been implemented into clinical practice in Europe and Asia, with the Immuno Solid-Phase Allergen Chip being the most widely studied. Results of these assays generally correlate with results using "singleplex" IgE assays (eg, ImmunoCAP), though there can be variability among products and among allergens. A strength of the microarray technology is that IgE to a large number of allergens can be detected simultaneously in a single test, and only a small amount of patient serum is required. Cost, inadequate sensitivity under some scenarios, and difficulties with data interpretation, in some cases of 100 or more allergens, can be limitations.
CONCLUSION
IgE microarray assays are already a valuable tool in research applications. These assays, and also other forms of IgE multiplex assays, are likely to play an important role in the clinical practice of allergy in the future. Additional studies focused on clinical outcomes, and the development of more targeted allergen panels could facilitate increased clinical use.
Topics: Allergens; Humans; Hypersensitivity; Immunoglobulin E; Immunologic Tests; Microarray Analysis; Technology Assessment, Biomedical
PubMed: 33450398
DOI: 10.1016/j.anai.2021.01.003 -
Methods in Molecular Biology (Clifton,... 2022Gene expression microarrays are one of the most widely used high-throughput technologies in molecular biology, with applications such as identification of disease...
Gene expression microarrays are one of the most widely used high-throughput technologies in molecular biology, with applications such as identification of disease mechanisms and development of diagnostic and prognostic gene signatures. However, the success of these tasks is often limited because microarray analysis does not account for the complex relationships among genes, their products, and overall signaling and regulatory cascades. Incorporating protein-protein interaction data into microarray analysis can help address these challenges. This chapter reviews how protein-protein interactions can help with microarray analysis, leading to benefits such as better explanations of disease mechanisms, more complete gene annotations, improved prioritization of genes for future experiments, and gene signatures that generalize better to new data.
Topics: Biological Phenomena; Computational Biology; Gene Expression Profiling; Microarray Analysis; Molecular Sequence Annotation
PubMed: 34902122
DOI: 10.1007/978-1-0716-1839-4_5 -
Zhonghua Fu Chan Ke Za Zhi Mar 2023To explore the diagnostic value of chromosome karyotype analysis, chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in microcephaly. A total of 9...
To explore the diagnostic value of chromosome karyotype analysis, chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in microcephaly. A total of 9 cases of microcephaly fetuses diagnosed by prenatal ultrasound or children with microcephaly diagnosed after birth were selected from the Sixth Affiliated Hospital of Guangzhou Medical University from January 2014 to August 2022.Karyotype analysis and/or CMA were used to detect. The cases with negative karyotype analysis and CMA results were further sequenced by trio-based WES (Trio-WES). Then the coding genes contained in the pathogenic copy number variation (CNV) fragments were analyzed by gene ontology (GO) enrichment. The genes related to the development of the central nervous system contained in the pathogenic CNV and the pathogenic genes found by Trio-WES were combined for gene interaction network analysis. In this study, 9 cases of microcephaly were recruited, with the time of diagnosis ranged from 23 weeks of gestation to 7 years after birth, and the head circumference of fetus or children ranged from 18.3 to 42.5 cm (-7SD to -2SD). Karyotype analysis was detected in all 9 cases and no abnormality result was found. Eight cases were detected by CMA, and one abnormal was found. Five cases were detected by Trio-WES, and two cases were detected with likely pathogenic genes. The GO enrichment analysis of the coding gene in the 4p16.3 microdeletion (pathogenic CNV) region showed that: in biological process, it was mainly concentrated in phototransduction, visible light; in terms of molecular function, it was mainly concentrated in fibroblast growth factor binding; in terms of cell components, it was mainly concentrated in rough endoplasmic reticulum. Gene interaction network analysis suggested that CDC42 gene could interact with CTBP1, HTT and ASPM gene. CMA could be used as a first-line detection technique for microcephaly. When the results of chromosome karyotype analysis and/or CMA are negative, Trio-WES could improve the detection rate of pathogenicity of microcephaly.
Topics: Female; Humans; Pregnancy; DNA Copy Number Variations; Fetus; Karyotype; Karyotyping; Microarray Analysis; Microcephaly; Prenatal Diagnosis; Infant, Newborn
PubMed: 36935194
DOI: 10.3760/cma.j.cn112141-20221102-00675 -
Annual Review of Analytical Chemistry... Jun 2017Advances in scientific instrumentation have allowed experimentalists to evaluate well-known systems in new ways and to gain insight into previously unexplored or poorly... (Review)
Review
Advances in scientific instrumentation have allowed experimentalists to evaluate well-known systems in new ways and to gain insight into previously unexplored or poorly understood phenomena. Within the growing field of multianalyte physiometry (MAP), microphysiometers are being developed that are capable of electrochemically measuring changes in the concentration of various metabolites in real time. By simultaneously quantifying multiple analytes, these devices have begun to unravel the complex pathways that govern biological responses to ischemia and oxidative stress while contributing to basic scientific discoveries in bioenergetics and neurology. Patients and clinicians have also benefited from the highly translational nature of MAP, and the continued expansion of the repertoire of analytes that can be measured with multianalyte microphysiometers will undoubtedly play a role in the automation and personalization of medicine. This is perhaps most evident with the recent advent of fully integrated noninvasive sensor arrays that can continuously monitor changes in analytes linked to specific disease states and deliver a therapeutic agent as required without the need for patient action.
Topics: Biomarkers; Biosensing Techniques; Electrochemical Techniques; Electrophoresis; Humans; Microarray Analysis; Pharmaceutical Preparations; Point-of-Care Systems
PubMed: 28605606
DOI: 10.1146/annurev-anchem-061516-045334