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Journal of B.U.ON. : Official Journal... 2017Bioinformatics is one of the newest fields of biological research, and should be viewed broadly as the use of mathematical, statistical, and computational methods for... (Review)
Review
Bioinformatics is one of the newest fields of biological research, and should be viewed broadly as the use of mathematical, statistical, and computational methods for the processing and analysis of biological data. Over the last decade, the rapid growth of information and technology in both "genomics" and "omics" eras has been overwhelming for the laboratory scientists to process experimental results. Traditional gene-by-gene approaches in research are insufficient to meet the growth and demand of biological research in understanding the true biology. The massive amounts of data generated by new technologies as genomic sequencing and microarray chips make the management of data and the integration of multiple platforms of high importance; this is then followed by data analysis and interpretation to achieve biological understanding and therapeutic progress. Global views of analyzing the magnitude of information are necessary and traditional approaches to lab work have steadily been changing towards a bioinformatics era. Research is moving from being restricted to a laboratory environment to working with computers in a "virtual lab" environment. The present review article shall put light on this emerging field and its applicability towards cancer research.
Topics: Computational Biology; Humans; Microarray Analysis; Neoplasms; Proteomics
PubMed: 29155508
DOI: No ID Found -
Journal of Cellular and Molecular... Jan 2021To investigate the incidence and clinical significance of chromosomal mosaicism (CM) in prenatal diagnosis by G-banding karyotyping and chromosomal microarray analysis...
To investigate the incidence and clinical significance of chromosomal mosaicism (CM) in prenatal diagnosis by G-banding karyotyping and chromosomal microarray analysis (CMA). This is a single-centre retrospective study of invasive prenatal diagnosis for CM. From 5758 karyotyping results and 6066 CMA results, 104 foetal cases with CM were selected and analysed further. In total, 50% (52/104) of foetal cases with CM were affected by ultrasound-detectable phenotypes. Regardless of whether they were singleton or twin pregnancies, isolated structural defects in one system (51.35%, 19/37 in singletons; 86.67%, 13/15 in twins) and a single soft marker (18.92%, 7/37 in singletons; 13.33%, 2/15 in twins) were the most common ultrasound anomalies. Mosaic autosomal trisomy (19.23%, 20/104) was the most frequent type, and its rate was higher in phenotypic foetuses (28.85%, 15/52) than in non-phenotypic foetuses (9.62%, 5/52). There was no difference in mosaic fractions between phenotypic and non-phenotypic foetuses based on specimen sources or overall classification. Discordant mosaic results were observed in 16 cases (15.38%, 16/104) from different specimens or different testing methods. Genetic counselling and clinical management regarding CM in prenatal diagnosis remain challenging due to the variable phenotypes and unclear significance. Greater caution should be used in prenatal counselling, and more comprehensive assays involving serial ultrasound examinations, different specimens or testing methods verifications and follow-up should be applied.
Topics: Adult; Genetic Counseling; Humans; Karyotype; Karyotyping; Microarray Analysis; Mosaicism
PubMed: 33201576
DOI: 10.1111/jcmm.16080 -
ChemistryOpen Mar 2020Many proteins in living organisms are glycosylated. As their glycan patterns exhibit protein-, cell-, and tissue-specific heterogeneity, changes in the glycosylation... (Review)
Review
Many proteins in living organisms are glycosylated. As their glycan patterns exhibit protein-, cell-, and tissue-specific heterogeneity, changes in the glycosylation levels could serve as useful indicators of various pathological and physiological states. Thus, the identification of glycoprotein biomarkers from specific changes in the glycan profiles of glycoproteins is a trending field. Lectin microarrays provide a new glycan analysis platform, which enables rapid and sensitive analysis of complex glycans without requiring the release of glycans from the protein. Recent developments in lectin microarray technology enable high-throughput analysis of glycans in complex biological samples. In this review, we will discuss the basic concepts and recent progress in lectin microarray technology, the application of lectin microarrays in biomarker discovery, and the challenges and future development of this technology. Given the tremendous technical advancements that have been made, lectin microarrays will become an indispensable tool for the discovery of glycoprotein biomarkers.
Topics: Biomarkers; Glycoproteins; Glycosylation; Humans; Lectins; Microarray Analysis; Polysaccharides; Protein Array Analysis; Protein Conformation
PubMed: 32154049
DOI: 10.1002/open.201900326 -
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 -
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 -
Ultrasound in Obstetrics & Gynecology :... Mar 2021To evaluate the utility of expanded non-invasive prenatal screening (NIPS), compared with chromosomal microarray analysis (CMA), for the detection of chromosomal... (Comparative Study)
Comparative Study
OBJECTIVE
To evaluate the utility of expanded non-invasive prenatal screening (NIPS), compared with chromosomal microarray analysis (CMA), for the detection of chromosomal abnormalities in high-risk pregnancies.
METHODS
This was a multicenter retrospective study of singleton pregnancies at high risk for chromosomal abnormality. Patients who underwent expanded NIPS and CMA sequentially during pregnancy from 2015 to 2019 were included in the analysis. Pregnancies with a positive result for sex chromosome aneuploidy were excluded as the full details could not be retrieved. The utility of expanded NIPS and CMA for detection of chromosomal abnormalities in this cohort was compared by assessing the concordance between the results.
RESULTS
Of the 774 included high-risk pregnancies, 550 (71.1%) had a positive NIPS result, while a positive CMA result was detected in 308 (39.8%) cases. The rate of full or partial concordance between NIPS and CMA was 82.2%, 59.6% and 25.0% for trisomies 21, 18 and 13, respectively. For rare aneuploidies and segmental imbalances, NIPS and CMA results were fully or partially concordant in 7.5% and 33.3% of cases, respectively. Copy-number variants < 5 Mb were detected more often by CMA, with an incidence of 7.9% (61/774) compared with 3.1% (24/774) by NIPS. A genetic aberration was detected by CMA in 1 in 17 (5.8%) high-risk pregnancies that had a negative or non-reportable NIPS result.
CONCLUSION
CMA allows for comprehensive detection of genome-wide chromosomal abnormalities in high-risk pregnancies. CMA should be offered instead of expanded NIPS for high-risk pregnancies. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.
Topics: Adult; Chromosome Aberrations; Chromosome Disorders; Female; Humans; Microarray Analysis; Noninvasive Prenatal Testing; Pregnancy; Pregnancy, High-Risk; Reproducibility of Results; Retrospective Studies; Young Adult
PubMed: 32198896
DOI: 10.1002/uog.22021 -
Bioinformatics (Oxford, England) Feb 2013Microarrays are commonly used to detect changes in gene expression between different biological samples. For this purpose, many analysis tools have been developed that...
SUMMARY
Microarrays are commonly used to detect changes in gene expression between different biological samples. For this purpose, many analysis tools have been developed that offer visualization, statistical analysis and more sophisticated analysis methods. Most of these tools are designed specifically for messenger RNA microarrays. However, today, more and more different microarray platforms are available. Changes in DNA methylation, microRNA expression or even protein phosphorylation states can be detected with specialized arrays. For these microarray technologies, the number of available tools is small compared with mRNA analysis tools. Especially, a joint analysis of different microarray platforms that have been used on the same set of biological samples is hardly supported by most microarray analysis tools. Here, we present InCroMAP, a tool for the analysis and visualization of high-level microarray data from individual or multiple different platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation and protein modification datasets. Several methods are offered that allow for an integrated analysis of data from those platforms. The available features of InCroMAP range from visualization of DNA methylation data over annotation of microRNA targets and integrated gene set enrichment analysis to a joint visualization of data from all platforms in the context of metabolic or signalling pathways.
AVAILABILITY
InCroMAP is freely available as Java™ application at www.cogsys.cs.uni-tuebingen.de/software/InCroMAP, including a comprehensive user's guide and example files.
Topics: DNA Methylation; Gene Expression; Gene Expression Profiling; MicroRNAs; Oligonucleotide Array Sequence Analysis; Protein Array Analysis; Proteins; RNA, Messenger; Software
PubMed: 23257199
DOI: 10.1093/bioinformatics/bts709 -
Acta Biochimica Et Biophysica Sinica Mar 2011Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as... (Review)
Review
Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer, diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics, proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as high-throughput, miniaturized, and capable of parallel analysis, protein microarrays have already become an important technology platform for systems biology. In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays, and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.
Topics: Antibodies; Humans; Immobilized Proteins; Membrane Proteins; Microarray Analysis; Microdissection; Molecular Probes; Protein Array Analysis; Proteome; Systems Biology
PubMed: 21257623
DOI: 10.1093/abbs/gmq127 -
Prenatal Diagnosis May 2023The aim of this study was to determine the diagnostic yield of exome sequencing (ES) above that of chromosomal microarray analysis (CMA) or karyotyping in fetuses with... (Meta-Analysis)
Meta-Analysis Review
The aim of this study was to determine the diagnostic yield of exome sequencing (ES) above that of chromosomal microarray analysis (CMA) or karyotyping in fetuses with isolated fetal growth restriction (FGR). This was a systematic review conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Selected studies included those with (a) only fetuses with FGR in the absence of fetal structural anomalies and (b) negative CMA or karyotyping results. Only positive variants classified as likely pathogenic or pathogenic determined as causative of the fetal phenotype were considered. A negative CMA or karyotype result was treated as the reference standard. Eight studies with data on ES diagnostic yield, including 146 fetuses with isolated FGR, were identified. Overall, a pathogenic variant determined as potentially causative of the fetal phenotype was found in 17 cases, resulting in a 12% (95% CI: 7%-18%) incremental performance pool of ES. The vast majority were studied before 32 weeks'gestation. In conclusion, a monogenic disorder was prenatally found in association with apparently isolated FGR in 12% of these fetuses.
Topics: Pregnancy; Humans; Female; Fetal Growth Retardation; Exome Sequencing; Ultrasonography, Prenatal; Karyotyping; Microarray Analysis
PubMed: 36869857
DOI: 10.1002/pd.6339 -
Briefings in Functional Genomics &... Dec 2007Microarray based transcription profiling is now a consolidated methodology and has widespread use in areas such as pharmacogenomics, diagnostics and drug target... (Review)
Review
Microarray based transcription profiling is now a consolidated methodology and has widespread use in areas such as pharmacogenomics, diagnostics and drug target identification. Large-scale microarray studies are also becoming crucial to a new way of conceiving experimental biology. A main issue in microarray transcription profiling is data analysis and mining. When microarrays became a methodology of general use, considerable effort was made to produce algorithms and methods for the identification of differentially expressed genes. More recently, the focus has switched to algorithms and database development for microarray data mining. Furthermore, the evolution of microarray technology is allowing researchers to grasp the regulative nature of transcription, integrating basic expression analysis with mRNA characteristics, i.e. exon-based arrays, and with DNA characteristics, i.e. comparative genomic hybridization, single nucleotide polymorphism, tiling and promoter structure. In this article, we will review approaches used to detect differentially expressed genes and to link differential expression to specific biological functions.
Topics: Animals; Gene Expression Profiling; Microarray Analysis; Quality Control; Statistics as Topic
PubMed: 18216026
DOI: 10.1093/bfgp/elm034