-
Methods in Molecular Biology (Clifton,... 2022Microarrays are broadly used in the omic investigation and have several areas of applications in biology and medicine, providing a significant amount of data for a...
Microarrays are broadly used in the omic investigation and have several areas of applications in biology and medicine, providing a significant amount of data for a single experiment. Different kinds of microarrays are available, identifiable by characteristics such as the type of probes, the surface used as support, and the method used for the target detection. To better deal with microarray datasets, the development of microarray data analysis protocols simple to use as well as able to produce accurate reports, and comprehensible results arise. The object of this paper is to provide a general protocol showing how to choose the best software tool to analyze microarray data, allowing to efficiently figure out genomic/pharmacogenomic biomarkers.
Topics: Data Analysis; Gene Expression Profiling; Genomics; Microarray Analysis; Oligonucleotide Array Sequence Analysis; Software
PubMed: 34902134
DOI: 10.1007/978-1-0716-1839-4_17 -
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 -
American Journal of Human Genetics Aug 2021Chromosomal aberrations including structural variations (SVs) are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard...
Chromosomal aberrations including structural variations (SVs) are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard cytogenetics. Drawbacks of these tests are a very low resolution (karyotyping) and the inability to detect balanced SVs or indicate the genomic localization and orientation of duplicated segments or insertions (copy number variant [CNV] microarrays). Here, we investigated the ability of optical genome mapping (OGM) to detect known constitutional chromosomal aberrations. Ultra-high-molecular-weight DNA was isolated from 85 blood or cultured cells and processed via OGM. A de novo genome assembly was performed followed by structural variant and CNV calling and annotation, and results were compared to known aberrations from standard-of-care tests (karyotype, FISH, and/or CNV microarray). In total, we analyzed 99 chromosomal aberrations, including seven aneuploidies, 19 deletions, 20 duplications, 34 translocations, six inversions, two insertions, six isochromosomes, one ring chromosome, and four complex rearrangements. Several of these variants encompass complex regions of the human genome involved in repeat-mediated microdeletion/microduplication syndromes. High-resolution OGM reached 100% concordance compared to standard assays for all aberrations with non-centromeric breakpoints. This proof-of-principle study demonstrates the ability of OGM to detect nearly all types of chromosomal aberrations. We also suggest suited filtering strategies to prioritize clinically relevant aberrations and discuss future improvements. These results highlight the potential for OGM to provide a cost-effective and easy-to-use alternative that would allow comprehensive detection of chromosomal aberrations and structural variants, which could give rise to an era of "next-generation cytogenetics."
Topics: Chromosome Aberrations; Chromosome Disorders; Chromosome Mapping; Cytogenetic Analysis; DNA Copy Number Variations; Genome, Human; Humans; Karyotyping; Microarray Analysis
PubMed: 34237280
DOI: 10.1016/j.ajhg.2021.05.012 -
Genes Mar 2021In 1959, 63 years after the death of John Langdon Down, Jérôme Lejeune discovered trisomy 21 as the genetic reason for Down syndrome. Screening for Down syndrome has... (Review)
Review
In 1959, 63 years after the death of John Langdon Down, Jérôme Lejeune discovered trisomy 21 as the genetic reason for Down syndrome. Screening for Down syndrome has been applied since the 1960s by using maternal age as the risk parameter. Since then, several advances have been made. First trimester screening, combining maternal age, maternal serum parameters and ultrasound findings, emerged in the 1990s with a detection rate (DR) of around 90-95% and a false positive rate (FPR) of around 5%, also looking for trisomy 13 and 18. With the development of high-resolution ultrasound, around 50% of fetal anomalies are now detected in the first trimester. Non-invasive prenatal testing (NIPT) for trisomy 21, 13 and 18 is a highly efficient screening method and has been applied as a first-line or a contingent screening approach all over the world since 2012, in some countries without a systematic screening program. Concomitant with the rise in technology, the possibility of screening for other genetic conditions by analysis of cfDNA, such as sex chromosome anomalies (SCAs), rare autosomal anomalies (RATs) and microdeletions and duplications, is offered by different providers to an often not preselected population of pregnant women. Most of the research in the field is done by commercial providers, and some of the tests are on the market without validated data on test performance. This raises difficulties in the counseling process and makes it nearly impossible to obtain informed consent. In parallel with the advent of new screening technologies, an expansion of diagnostic methods has begun to be applied after invasive procedures. The karyotype has been the gold standard for decades. Chromosomal microarrays (CMAs) able to detect deletions and duplications on a submicroscopic level have replaced the conventional karyotyping in many countries. Sequencing methods such as whole exome sequencing (WES) and whole genome sequencing (WGS) tremendously amplify the diagnostic yield in fetuses with ultrasound anomalies.
Topics: Chromosome Disorders; Female; Genetic Testing; Humans; Microarray Analysis; Pregnancy; Prenatal Diagnosis
PubMed: 33805390
DOI: 10.3390/genes12040501 -
Advances in Biochemical... 2024Microarrays are widely utilized in bioanalysis. Electrochemical biosensing techniques are often applied in microarray-based assays because of their simplicity, low cost,... (Review)
Review
Microarrays are widely utilized in bioanalysis. Electrochemical biosensing techniques are often applied in microarray-based assays because of their simplicity, low cost, and high sensitivity. In such systems, the electrodes and sensing elements are arranged in arrays, and the target analytes are detected electrochemically. These sensors can be utilized for high-throughput bioanalysis and the electrochemical imaging of biosamples, including proteins, oligonucleotides, and cells. In this chapter, we summarize recent progress on these topics. We categorize electrochemical biosensing techniques for array detection into four groups: scanning electrochemical microscopy, electrode arrays, electrochemiluminescence, and bipolar electrodes. For each technique, we summarize the key principles and discuss the advantages, disadvantages, and bioanalysis applications. Finally, we present conclusions and perspectives about future directions in this field.
Topics: Biosensing Techniques; Electrochemical Techniques; Microarray Analysis; Electrodes; Humans
PubMed: 37306698
DOI: 10.1007/10_2023_229 -
Obstetrics and Gynecology Apr 2019
Topics: Chromosome Aberrations; Congenital Abnormalities; Female; Humans; Microarray Analysis; Oligonucleotide Array Sequence Analysis; Pregnancy; Ultrasonography, Prenatal
PubMed: 30913183
DOI: 10.1097/AOG.0000000000003208 -
Faraday Discussions Oct 2019Glycan microarrays have become a powerful technology to study biological processes, such as cell-cell interaction, inflammation, and infections. Yet, several challenges,... (Review)
Review
Glycan microarrays have become a powerful technology to study biological processes, such as cell-cell interaction, inflammation, and infections. Yet, several challenges, especially in multivalent display, remain. In this introductory lecture we discuss the state-of-the-art glycan microarray technology, with emphasis on novel approaches to access collections of pure glycans and their immobilization on surfaces. Future directions to mimic the natural glycan presentation on an array format, as well as in situ generation of combinatorial glycan collections, are discussed.
Topics: Animals; Bioprinting; Click Chemistry; Equipment Design; Glycomics; Humans; Microarray Analysis; Polysaccharides
PubMed: 31298252
DOI: 10.1039/c9fd00080a -
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 -
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 -
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