Advanced microtechnologies for detection of chromosome abnormalities by fluorescent in situ hybridization

Kwasny, Dorota; Vedarethinam, Indumathi; Shah, Pranjul Jaykumar; Silahtaroglu, Asli; Tümer, Zeynep; Svendsen, Winnie Edith

doi:10.1007/s10544-011-9622-7

Cited by 13 publications

(10 citation statements)

References 16 publications

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“…Even with the introduction of genomic technologies like microarray analysis and exome sequencing, FISH analysis will still be an integral part of genetic diagnosis (Parisi et al, 2012; Wei et al, 2013; Martin and Warburton, 2015). Microfluidic devices for miniaturized and automatic FISH applications are currently under development (Vedarethinam et al, 2010; Kwasny et al, 2012; Kao et al, 2015). The validation of these devices in the near future and the available of more disease-specific probes will further enhance and expand the diagnostic FISH application.…”

Section: Discussionmentioning

confidence: 99%

Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

Cui

Shu

2016

Front. Cell Dev. Biol.

175

125

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Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH techniques have visualized intra-nuclear genomic structure and sub-cellular transcriptional dynamics of many genes and revealed their functions in various biological processes.

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Section: Discussionmentioning

confidence: 99%

Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

Cui

Shu

2016

Front. Cell Dev. Biol.

175

125

View full text Add to dashboard Cite

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“…In the following, we review the different microfluidic platforms and approaches for carrying out FISH assays on-chip. We significantly extend on earlier reviews by Kwasny et al on microfluidic FISH for chromosome abnormalities [33], by Sato on microfluidic FISH for analysis of circulating tumor cells [34] and a historic FISH review with microfluidic FISH outlook by Huber et al [35]. Here, we include microfluidic platforms across the full range of samples, from cells to tissue, from mammalian to microbial samples.…”

Section: Introductionmentioning

confidence: 93%

FISH and chips: a review of microfluidic platforms for FISH analysis

Rodriguez-Mateos

Azevedo

Almeida

et al. 2020

Med Microbiol Immunol

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Fluorescence in situ hybridization (FISH) allows visualization of specific nucleic acid sequences within an intact cell or a tissue section. It is based on molecular recognition between a fluorescently labeled probe that penetrates the cell membrane of a fixed but intact sample and hybridizes to a nucleic acid sequence of interest within the cell, rendering a measurable signal. FISH has been applied to, for example, gene mapping, diagnosis of chromosomal aberrations and identification of pathogens in complex samples as well as detailed studies of cellular structure and function. However, FISH protocols are complex, they comprise of many fixation, incubation and washing steps involving a range of solvents and temperatures and are, thus, generally time consuming and labor intensive. The complexity of the process, the relatively high-priced fluorescent probes and the fairly high-end microscopy needed for readout render the whole process costly and have limited wider uptake of this powerful technique. In recent years, there have been attempts to transfer FISH assay protocols onto microfluidic lab-on-a-chip platforms, which reduces the required amount of sample and reagents, shortens incubation times and, thus, time to complete the protocol, and finally has the potential for automating the process. Here, we review the wide variety of approaches for lab-on-chip-based FISH that have been demonstrated at proof-of-concept stage, ranging from FISH analysis of immobilized cell layers, and cells trapped in arrays, to FISH on tissue slices. Some researchers have aimed to develop simple devices that interface with existing equipment and workflows, whilst others have aimed to integrate the entire FISH protocol into a fully autonomous FISH on-chip system. Whilst the technical possibilities for FISH on-chip are clearly demonstrated, only a small number of approaches have so far been converted into off-the-shelf products for wider use beyond the research laboratory. Keywords Microfluidics-assisted FISH • µFISH • Microfluidics • Lab-on-a-Chip (LOC) • Fluorescence in situ hybridization (FISH) Edited by Volkhard A. J. Kempf.

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“…Even with the introduction of genomic technologies, such as microarray analysis and exome sequencing, the FISH analysis still cannot be substituted in the field of genetic diagnosis [38][39][40]. Micro-fluidic devices for miniaturized and automatic FISH applications are currently under development [41][42][43]. Further research on the identification of more diseases specific probes and labeling methods will give strength to validate these platforms in diagnostics FISH POC settings.…”

Section: Referencesmentioning

confidence: 99%

MicroRNA amplification and detection technologies: opportunities and challenges for point of care diagnostics

Dave

Ngo

Pernestig

et al. 2019

Laboratory Investigation

172

128

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The volume of point of care (POC) testing continues to grow steadily due to the increased availability of easy-to-use devices, thus making it possible to deliver less costly care closer to the patient site in a shorter time relative to the central laboratory services. A novel class of molecules called microRNAs have recently gained attention in healthcare management for their potential as biomarkers for human diseases. The increasing interest of miRNAs in clinical practice has led to an unmet need for assays that can rapidly and accurately measure miRNAs at the POC. However, the most widely used methods for analyzing miRNAs, including Northern blot-based platforms, in situ hybridization, reverse transcription qPCR, microarray, and next-generation sequencing, are still far from being used as ideal POC diagnostic tools, due to considerable time, expertize required for sample preparation, and in terms of miniaturizations making them suitable platforms for centralized labs. In this review, we highlight various existing and upcoming technologies for miRNA amplification and detection with a particular emphasis on the POC testing industries. The review summarizes different miRNA targets and signals amplification-based assays, from conventional methods to alternative technologies, such as isothermal amplification, paper-based, oligonucleotide-templated reaction, nanobead-based, electrochemical signalingbased, and microfluidic chip-based strategies. Based on critical analysis of these technologies, the possibilities and feasibilities for further development of POC testing for miRNA diagnostics are addressed and discussed.

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Advanced microtechnologies for detection of chromosome abnormalities by fluorescent in situ hybridization

Cited by 13 publications

References 16 publications

Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

FISH and chips: a review of microfluidic platforms for FISH analysis

MicroRNA amplification and detection technologies: opportunities and challenges for point of care diagnostics

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