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Annals of Medicine Dec 2023To evaluate the clinical utility of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in foetuses with oligohydramnios.
OBJECTIVES
To evaluate the clinical utility of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in foetuses with oligohydramnios.
METHODS
In this retrospective study, 126 fetuses with oligohydramnios at our centre from 2018 to 2021 were reviewed. The results of CMA and WES were analysed.
RESULTS
One hundred and twenty-four cases underwent CMA and 32 cases underwent WES. The detection rate of pathogenic/likely pathogenic (P/LP) copy number variant (CNV) by CMA was 1.6% (2/124). WES revealed P/LP variants in 21.8% (7/32) of the foetuses. Six (85.7%, 6/7) foetuses showed an autosomal recessive inheritance pattern. Three (42.9%, 3/7) variants were involved in the renin-angiotensin-aldosterone system (RAAS), which are the known genetic causes of autosomal recessive renal tubular dysgenesis (ARRTD).
CONCLUSION
CMA has low diagnostic utility for oligohydramnios, while WES offers obvious advantages in improving the detection rate. WES should be recommended for fetuses with oligohydramnios.
Topics: Pregnancy; Female; Humans; Retrospective Studies; Exome Sequencing; Oligohydramnios; Microarray Analysis; Fetus; Prenatal Diagnosis
PubMed: 37243546
DOI: 10.1080/07853890.2023.2215539 -
Biotechnology Journal Feb 2021High-throughput systems allow screening and analysis of large number of samples simultaneously under same conditions. Over recent years, high-throughput systems have... (Review)
Review
High-throughput systems allow screening and analysis of large number of samples simultaneously under same conditions. Over recent years, high-throughput systems have found applications in fields other than drug discovery like bioprocess industries, pollutant detection, material microarrays, etc. With the introduction of materials in such HT platforms, the screening system has been enabled for solid phases apart from conventional solution phase. The use of biomaterials has further facilitated cell-based assays in such platforms. Here, the authors have focused on the recent developments in biomaterial-based platforms including the fabricationusing contact and non-contact methods and utilization of such platforms for discovery of novel biomaterials exploiting interaction of biological entities with surface and bulk properties. Finally, the authors have elaborated on the application of the biomaterial-based high-throughput platforms in tissue engineering and regenerative medicine, cancer and stem cell studies. The studies show encouraging applications of biomaterial microarrays. However, success in clinical applicability still seems to be a far off task majorly due to absence of robust characterization and analysis techniques. Extensive focus is required for developing personalized medicine, analytical tools and storage/shelf-life of cell laden microarrays.
Topics: Biocompatible Materials; Drug Discovery; High-Throughput Screening Assays; Microarray Analysis; Regenerative Medicine; Tissue Engineering
PubMed: 32914497
DOI: 10.1002/biot.202000288 -
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 -
Prenatal Diagnosis Aug 2023This study aimed to assess the diagnostic yield of prenatal genetic testing using trio whole exome sequencing (WES) and trio whole genome sequencing (WGS) in pregnancies...
OBJECTIVE
This study aimed to assess the diagnostic yield of prenatal genetic testing using trio whole exome sequencing (WES) and trio whole genome sequencing (WGS) in pregnancies with fetal anomalies by comparing the results with conventional chromosomal microarray (CMA) analysis.
METHODS
A total of 40 pregnancies with fetal anomalies or increased nuchal translucency (NT ≥ 5 mm) were included between the 12th and 21st week of gestation. Trio WES/WGS and CMA were performed in all cases.
RESULTS
The trio WES/WGS analysis increased the diagnostic yield by 25% in cases with negative CMA results. Furthermore, all six chromosomal aberrations identified by CMA were independently detected by WES/WGS analysis. In total, 16 out of 40 cases obtained a genetic sequence variant, copy number variant, or aneuploidy explaining the phenotype, resulting in an overall WES/WGS diagnostic yield of 40%. WES analysis provided a more reliable identification of mosaic sequence variants than WGS because of its higher sequencing depth.
CONCLUSIONS
Prenatal WES/WGS proved to be powerful diagnostic tools for fetal anomalies, surpassing the diagnostic yield of CMA. They have the potential to serve as standalone methods for prenatal diagnosis. The study highlighted the limitations of WGS in accurately detecting mosaic variants, which is particularly relevant when analyzing chorionic villus samples.
Topics: Female; Humans; Pregnancy; Prenatal Diagnosis; Whole Genome Sequencing; Exome Sequencing; Microarray Analysis; Congenital Abnormalities; Genetic Variation
PubMed: 37355983
DOI: 10.1002/pd.6402 -
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,... 2022Microarray analyses usually result in a list of differential genes that need to be annotated to link them the phenotype being studied, help planning validation...
Microarray analyses usually result in a list of differential genes that need to be annotated to link them the phenotype being studied, help planning validation experiments and interpretation of the results. Pathway enrichment analyses are frequently used for such purpose, where pathways are human created models of molecular activities and processes. While different types of pathway enrichment are available, we focus this protocol on the most frequent type-overrepresentation analysis. Many databases collect different sets of pathways and curate different sets of genes for the same pathways, so it is important to carefully choose the most suitable pathway source to perform enrichment analysis. To provide a comprehensive pathway analysis, in this protocol we will use pathDIP, which supports comprehensive enrichment analysis by integrating 22 main pathway databases. We will also describe the steps needed to visualize the enriched pathways using GSOAP.
Topics: Computational Biology; Databases, Factual; Gene Expression Profiling; Humans; Microarray Analysis
PubMed: 34902127
DOI: 10.1007/978-1-0716-1839-4_10 -
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 -
Cold Spring Harbor Protocols Sep 2019Competitive hybridization of labeled nucleic acids to a microarray is conceptually similar to other hybridization methods, such as Southern blotting. For massively...
Competitive hybridization of labeled nucleic acids to a microarray is conceptually similar to other hybridization methods, such as Southern blotting. For massively multiplexed microarrays, the adoption of two-color hybridization schemes has been a significant advance. The use of two colors-typically Cy3- and Cy5-labeled nucleic acids-makes it possible to control for factors that affect hybridization intensity, including the number of labeled nucleotides and the of each oligonucleotide. Thus, the difference in intensity among spots on a microarray can be quantified and analyzed to assess biological phenomena, like changes in gene expression or details of transcript structure. This protocol for hybridization is conceptually straightforward-"cold" (nonfluorescent) blocking nucleotide is added to the mixed nucleic acid material, Hybridization buffer is added, and the mixture is applied to the microarray surface. Hybridization occurs overnight, after which the microarray is washed and scanned.
Topics: Nucleic Acid Hybridization; Nucleic Acids; Oligonucleotide Array Sequence Analysis; Solutions
PubMed: 31481490
DOI: 10.1101/pdb.prot096487 -
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