Ciele: Analýza prenatálnych vzoriek za obdobie 2015–2020. Porovnanie miery detekcie klinicky relevantných variant cytogenetickou analýzou karyotypu a cytogenomickými metódami MLPA (Multiplex Ligation-Depent Probe Amplification) a mikročipmi (CMA – chromosomal microarray). Súbor a metodika: Analyzovaných bolo 1 029 prenatálnych vzoriek cytogenetickým hodnotením karyotypu (n = 1 029), cytogenomickými metódami MLPA (n = 144) a CMA (n = 111). Všetky nebalansované zmeny boli potvrdené metódou MLPA alebo CMA. Výsledky: Z analyzovaného súboru plodov, po odčítaní aneuploidií – 107 (10,40 %, n = 1 029), bolo analýzou karyotypu zachytených 22 štruktúrnych aberácií (2,39 %, n = 922) – deväť nebalansovaných zmien (0,98 %), 10 balansovaných zmien (1,08 %), jeden prípad nejasnej mozaiky (0,09 %), jeden prípad prítomnosti marker chromozómu (0,09 %) a jeden prípad diskordancie pohlavia (0,09 %). U 255 vzoriek s fyziologickým karyotypom indikovaných k cytogenomickému vyšetreniu bolo zachytených celkom osem (7,21 %, n = 111) patologických variant metódou CMA. Metódou MLPA bolo z týchto ôsmich patogénnych variant zachytených päť (3,47 %, n = 144). Celkový záchyt patogénnych variant metódami MLPA a CMA vrátane konfirmačných vyšetrení patologického karyotypu je 14 (5,14 %) a 17 (6,25 %) (n = 272). Záchyt patologických variant v skupine s izolovanými poruchami bol nižší než v skupine s mnohopočetnými poruchami (5,08 vs. 21,42 %). Záver: Potvrdila sa vyššia úspešnosť záchytu patologických variant so zmenou v počte kópií, metódou CMA než MLPA.
Objective: Analysis of prenatal samples from 2015 to 2020. Comparison detection rates of clinically relevant variants by cytogenetic karyotype analysis and cytogenomic MLPA (Multiplex Ligation-Depent Probe Amplification) and microarray methods (CMA – chromosomal microarray). Material and method: 1,029 prenatal samples were analyzed by cytogenetic karyotyping (N = 1,029), cytogenomic methods – MLPA (N = 144) and CMA (N = 111). All unbalanced changes were confirmed by MLPA or CMA. Results: From the analyzed set of fetuses, after subtraction of aneuploidies – 107 (10.40%, N = 1,029), 22 structural aberrations (2.39%, N = 922) – nine unbalanced changes (0.98%), 10 balanced changes (1.08%), one case of unclear mosaicism (0.09%), one case of presence of a marker chromosome (0.09%) and one case of sex discordance (0.09%) – were detected by karyotype analysis. A total of eight (7.21%, N = 111) pathological variants were detected by CMA in 255 samples with physiological karyotype indicated for cytogenomic examination. Five (3.47%, N = 144) of eight pathogenic variants were detected by MLPA method. The total capture of pathogenic variants by MLPA and CMA methods was 14 (5.14%) and 17 (6.25%) (N = 272), including confirmatory pathological karyotype testing. Detection of pathological variants in the isolated disorders group was lower than in the multiple disorders group (5.08 vs. 21.42%). Conclusion: A higher success rate for the detection of pathological copy number variation variants by the microarray method than by the MLPA method was confirmed.
- MeSH
- Clinical Studies as Topic MeSH
- Humans MeSH
- Microarray Analysis methods MeSH
- Mosaicism MeSH
- Multiplex Polymerase Chain Reaction methods MeSH
- Fetus MeSH
- Prenatal Diagnosis * MeSH
- Pregnancy MeSH
- DNA Copy Number Variations MeSH
- Congenital Abnormalities * diagnosis genetics MeSH
- Check Tag
- Humans MeSH
- Pregnancy MeSH
- Female MeSH
The development of clinically applicable portable sensors and multiplex protein biomarker assays is one of the most important goals of laboratory medicine today. Sensing strategies based on electrochemical devices are discussed in this overview, with special emphasis on detection principles derived from voltammetry, electrogenerated chemiluminescence, bipolar electrochemistry and impedance-based measurements. Up-to-date examples of electrochemical methods in biomedical research and development are highlighted here, including critical evaluation and future directions of the analysis, development and validation of new protein biomarkers.
- MeSH
- Biomarkers analysis MeSH
- Biosensing Techniques methods MeSH
- Electrochemical Techniques methods MeSH
- Humans MeSH
- Microarray Analysis methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
miRNA profile of luminal breast cancer subtyptes in Slovak womenCieľ štúdie: Aberantná expresia krátkych, nekódujúcich molekúl RNA (miRNA) sa podieľa na vzniku, progresii a metastázovaní karcinómu prsníka. Úroveň expresie vybraných miRNA je úzko spojená nielen s imunohistochemickým profilom a histopatologickými parametrami, ale aj s klinickými výsledkami, prognózou a terapeutickou odpoveďou. Cieľom tohto výskumu bola analýza celého spektra miRNA metódou microarray a zadefinovanie panelu relevantných miRNA objasňujúcich biologickú charakteristiku luminálnych podtypov karcinómu prsníka. Typ štúdie: Prierezová, základný výskum. Názov a sídlo pracoviska: Martinské centrum pre biomedicínu, Jesseniova lekárska fakulta v Martine, Univerzita Komenského v Bratislave, Martin, Slovenská republika. Metodika: Sledovaný súbor pozostával zo 16 tkanív Luminal A/Luminal B karcinómu prsníka a 16 tkanív prsného tkaniva bez patologického nálezu. miRNA profil sa analyzoval microarray technológiou na sklíčku SurePrint G3 Human miRNA kit v.21, ktoré obsahuje 2549 miRNA. Výsledky sa hodnotili knižnicou AgiMicroRNA Bioconductor library v rámci balíka Limma. Výsledky: Analýza najnižšej hodnoty FDR p-value a najvyššej hodnoty logFC označila za najdôležitejšiu onkogénnu miRNA s vyššou expresiou v súbore nádorových tkanív v porovnaní s normálnymi tkanivami miR-182, nasledovala miR-21, miR-342-3p a miR-342-5p a miR6826. Medzi miRNA s nižšou expresiou dominovala miR-4324 a kluster miR-99a/let7c/miR-125b. Záver: Získané výsledky prispievajú k biologickej charakterizácií skupiny luminálnych typov karcinómu prsníka, ponúkajú východisko pre nadväzujúce projekty v kontexte objasnenia príslušných signálnych dráh mechanizmov karcinogenézy a sľubujú nové a inovatívne možnosti cielenej terapie zameranej na špecifické miRNA zapojené v dôležitých mechanizmoch karcinogenézy.
Objective: Aberrant expression of short, non-coding RNA molecules (miRNA) leads to breast cancer initiation, progression and metastasing. The miRNA expression level associates with imunohistochemical profile, histopathological parameters, clinical outcomes, prognoses and therapeutical response. The aim of this study was to analyse the whole spectrum of miRNA by microarray method and to define relevant miRNAs describing biological characteristics of luminal breast cancer subtypes. Design: Cross-sectional study, basic research. Setting: Biomedical center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia. Methods: We analysed 16 tissue samples of Luminal A/B breast cancer types and 16 breast tissue samples without pathological findings. The microarray technology by Agilent was used to analyse 2549 miRNAs by SurePrint G3 Human miRNA kit v.21. The results were assessed by AgiMicroRNA Bioconductor library within Limma pack. Results: The analyses of the lowest FDR p-value and the highest logFC value selected the oncomiR miR-182 as the most dominant with higher expression in cancer tissues than in normal tissues, followed by miR-21, miR342-3p/5p and miR-6826. The miR-4324 and cluster of miR-99a/let7c/miR-125b dominated in the group of miRNAs with lower expression in cancer tissues compared to normal tissues. Conclusion: The first results of this study complement biological characteristics of luminal breast cancer subptypes, represent basis for follow-up projects focused on the clarification of relevant signaling pathways and promise new and innovative breast cancer treatment based on the precise, tailored therapy by targeting specific miRNAs involved in the most important carcinogenesis mechanisms.
- MeSH
- Clinical Studies as Topic MeSH
- Humans MeSH
- MicroRNAs analysis MeSH
- Microarray Analysis methods MeSH
- Breast Neoplasms * genetics MeSH
- Check Tag
- Humans MeSH
- Female MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
Interactions between glycans and glycan binding proteins are essential for numerous processes in all kingdoms of life. Glycan microarrays are an excellent tool to examine protein-glycan interactions. Here, we present a microbe-focused glycan microarray platform based on oligosaccharides obtained by chemical synthesis. Glycans were generated by combining different carbohydrate synthesis approaches including automated glycan assembly, solution-phase synthesis, and chemoenzymatic methods. The current library of more than 300 glycans is as diverse as the mammalian glycan array from the Consortium for Functional Glycomics and, due to its microbial focus, highly complementary. This glycan platform is essential for the characterization of various classes of glycan binding proteins. Applications of this glycan array platform are highlighted by the characterization of innate immune receptors and bacterial virulence factors as well as the analysis of human humoral immunity to pathogenic glycans.
- MeSH
- Antigens, Bacterial chemistry immunology MeSH
- CHO Cells MeSH
- Cricetulus MeSH
- Species Specificity MeSH
- Glycomics MeSH
- Immune System MeSH
- Lectins MeSH
- Humans MeSH
- Microarray Analysis methods MeSH
- Oligosaccharides MeSH
- Polysaccharides chemistry classification immunology MeSH
- Recombinant Proteins MeSH
- Carrier Proteins chemistry MeSH
- Protein Binding MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The review brings a comprehensive overview of recent developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) to analysis, microscale isolation, purification, and physicochemical and biochemical characterization of peptides in the years 2015, 2016, and ca. up to the middle of 2017. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis (sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, and detection) are described. New developments in particular CE and CEC methods are presented and several types of their applications to peptide analysis are reported: qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC methods to provide important physicochemical characteristics of peptides are demonstrated.
- MeSH
- Amino Acids chemistry MeSH
- Chemical Fractionation MeSH
- Electrophoresis, Capillary methods MeSH
- Humans MeSH
- Microarray Analysis methods MeSH
- Peptide Mapping MeSH
- Peptides analysis isolation & purification MeSH
- Stereoisomerism MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
The scope of the study was to apply Phenotype Biolog MicroArray (PM) technology to test the antibiotic sensitivity of the bacterial strains isolated from on-site wastewater treatment facilities. In the first step of the study, the percentage values of resistant bacteria from total heterotrophic bacteria growing on solid media supplemented with various antibiotics were determined. In the untreated wastewater, the average shares of kanamycin-, streptomycin-, and tetracycline-resistant bacteria were 53, 56, and 42%, respectively. Meanwhile, the shares of kanamycin-, streptomycin-, and tetracycline-resistant bacteria in the treated wastewater were 39, 33, and 29%, respectively. To evaluate the antibiotic susceptibility of the bacteria present in the wastewater, using the phenotype microarrays (PMs), the most common isolates from the treated wastewater were chosen: Serratia marcescens ss marcescens, Pseudomonas fluorescens, Stenotrophomonas maltophilia, Stenotrophomonas rhizophila, Microbacterium flavescens, Alcaligenes faecalis ss faecalis, Flavobacterium hydatis, Variovorax paradoxus, Acinetobacter johnsonii, and Aeromonas bestiarum. The strains were classified as multi-antibiotic-resistant bacteria. Most of them were resistant to more than 30 antibiotics from various chemical classes. Phenotype microarrays could be successfully used as an additional tool for evaluation of the multi-antibiotic resistance of environmental bacteria and in preliminary determination of the range of inhibition concentration.
- MeSH
- Anti-Bacterial Agents pharmacology MeSH
- Bacteria classification drug effects genetics isolation & purification MeSH
- Drug Resistance, Bacterial MeSH
- Water Purification instrumentation MeSH
- Microarray Analysis methods MeSH
- Wastewater chemistry microbiology MeSH
- Publication type
- Journal Article MeSH
- Evaluation Study MeSH
Metallothioneins (MTs), low molecular mass cysteine-rich proteins, which are able to bind up to 20 monovalent and up to 7 divalent heavy metal ions are widely studied due to their functions in detoxification of metals, scavenging free radicals and cells protection against the oxidative stress. It was found that the loss of the protective effects of MT leads to an escalation of pathogenic processes and carcinogenesis. The most extensive area is MTs expression for oncological applications, where the information about gene patterns is helpful for the identification biological function, resistance to drugs and creating the correct chemotherapy. In other medical applications the effect of oxidative stress to cell lines exposed to heavy metals and hydrogen peroxide is studied as well as influence of drugs and cytokines on MTs expression and MTs expression in the adipose tissue. The precise detection of low metallothionein concentrations and its isoforms is necessary to understand the connection between quantity and isoforms of MTs to size, localization and type of cancer. This information is necessary for well-timed therapy and increase the chance to survival. Microarray chips appear as good possibility for finding all information about expression of MTs genes and isoforms not only in cancer, but also in other diseases, especially diabetes, obesity, cardiovascular diseases, ageing, osteoporosis, psychiatric disorders and as the effects of toxic drugs and pollutants, which is discussed in this review.
- MeSH
- Humans MeSH
- Metallothionein analysis genetics metabolism MeSH
- Microarray Analysis methods MeSH
- Neoplasms diagnosis genetics metabolism MeSH
- Oxidative Stress physiology MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
BACKGROUND: Activation of the immune system plays a pathogenic role in the process of myocardial remodeling in patients with supraventricular arrhythmias. The intensity of this process is associated with the effectiveness of electrical cardioversion and radiofrequency catheter ablation (RFA). The aim of this study was to test the ability of the biochip microarray to detect immune parameters in patients with supraventricular arrhythmias undergoing RFA treatment. METHODS: We used a biochip-based microarray system to determine multiple immune parameters in a group of 35 patients who had undergone RFA for atrioventricular nodal reentry tachycardia (AVNRT), atrial flutter (AFL) and atrial fibrillation (AF). RESULTS: Before the procedure, serum IL-6 and VEGF levels were significantly increased in patients with atrial fibrillation compared to patients with AVNRT (IL-6: 6.4±6.3 ng/L vs. 1.5±0.7 ng/L, P < 0.01; VEGF: 132.4±74 ng/L vs. 88.5±56.4 ng/L, P < 0.01). After the procedure, serum IL-6, VEGF, IFN-γ and MCP-1 levels significantly increased compared to baseline (IL-6: 5.2±4.8 ng/L vs. 2.9±2.1 ng/L, P < 0.01; VEGF: 195.8±160 ng/L vs. 119.8± 110 ng/L, P < 0.05; IFN-γ: 3.1±1.2 ng/L vs. 2.3±0.6 ng/L, P < 0.05; MCP-1: 104.1±84.5 ng/L vs. 54.5±50 ng/L, P < 0.05). Serum IL-6 and IFN-γ were associated with the number of RFA applications (IL-6: r = 0.56, n 33; IFN-γ: r = 0.47, n 33). CONCLUSIONS: This study showed that biochip-based microarray can be useful in the detection of immune activation in patients with arrhythmias and can detect myocardial injury after RF procedures.
- MeSH
- Tachycardia, Atrioventricular Nodal Reentry blood immunology surgery MeSH
- Biomarkers metabolism MeSH
- Adult MeSH
- Epidermal Growth Factor metabolism MeSH
- Interferon-gamma metabolism MeSH
- Interleukin-6 metabolism MeSH
- Catheter Ablation methods MeSH
- Middle Aged MeSH
- Humans MeSH
- Microarray Analysis methods MeSH
- Young Adult MeSH
- Case-Control Studies MeSH
- Vascular Endothelial Growth Factor A metabolism MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Young Adult MeSH
- Male MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Evaluation Study MeSH
- Research Support, Non-U.S. Gov't MeSH
S nástupem NGS a zvláště sekvenování transkriptomu došlo k nové specializaci microarray technologie a jejímu rozvoji k novým prakticky nenahraditelným nástrojům diagnostiky. Jakkoliv se objevují názory, že NGS zcela nahradí microarrays, trendy vyplývající z odborných článků, výzkumné a klinické praxe hovoří o výrazně rozdílném vývoji. NGS zejména v oblasti měření DNA exprese a transkriptomu skutečně přináší potenciál získání relativně kvalitativně bohatší informace, která se využívá zejména při hledání neznámých sekvencí, nicméně u analýz aplikovaných a známých sekvencí si microarrays naopak udržují dominantní postavení. Zcela unikátní platformou jsou tzv. VIPTM čipy, které přinesly možnost provádět populační studie s DNA až 10 tisíc jedinců v 10lokusech. Zároveň je opomíjen fakt, že současné sekvenační technologie mohou přinést informace pouze o DNA, na rozdíl od široké škály biomarkerových sond, které lze kotvit a tudíž analyzovat na substrátu microarrays, včetně proteinových biočipů, které zaznamenali velký boom především v poslední dekádě a těší se praktickému a klinickému využití.
With the advent of NGS and especially the transcriptome sequencing, a novel specialization of microarray technology has taken place and its development towards new practically indispensable diagnostic tools. Although it has been argued that NGS will eventually replace microarrays, the trends inferred from scientific articles, the research and clinical practice as well as the actual principal difference between these technologies, corroborate a significantly different development. In particular, in the measurement of DNA expression, NGS has brought the potential of obtaining a relatively richer qualitative information, which is used mainly for finding unknown sequences, however, microarrays conversely maintain dominance in the case of applied analyses and of known sequences. Furthermore, in the last decade, an entirely unique platform, called VIPTM microarrays, has been developed, which enabled to carry out cost -effectively population -based studies of DNA of up to 10,000 individuals in 10 loci. Moreover, another fact has been condoned, i.e. the current sequencing technologies can address only information related to DNA. Microarrays, to the contrary, permit immobilizing a wide spectrum of biomarker probes on the substrate and thus analyze a variety starting from DNA through proteins, small molecules, cells, tissues and others. As a consequence, the two technologies seem to be rather in a convenient complementarity than in any real competition.
Edukační publikace se zabývá v první části využitím čipů v imunochemii pro mikroanalýzu. Je uveden přehled podkladových materiálů a značek, jakož i senzitivita jednotlivých technologií. Vysvětluje se možnost imobilizace a detekce proteinů pomocí planárního vlnovodu. Ukazuje se používání čipů při paralelní kompetitivní imunoanalýze, sendvičové imunoanalýze a fluorescenční imunoanalýze na mikrokuličkách. Druhá část je věnována kapilární elektroforéze a jejímu využití k separaci po kompetitivní a nekompetitivní homogenní imunoanalýze, a heterogenní imunoanalýze. Diskutují se možnosti detekce analytu jako laserem indukovaná fluorescence, enzymové značky, chemiluminiscence, ampérometrie, UV/VIS absorbance, hmotnostní spektrometrie a povrchová plazmonová rezonance.
The first part of the educational article covers chip application for microarray in immunochemistry. An outline of surface chemistries and labelings is presented, as well as the sensitivity of various technologies. Protein immobilization and detection using planar waveguide technology is clarified. Chip applications are shown in parallel competitive immunoassay, sandwich immunoassay and fluorescent microsphere immunoassay. The second part covers capillary electrophoresis and its use for separation after competitive and non-competitive homogeneous immunoassay or heterogeneous immunoassay. The following possibilities of analyte detection are discussed: laser-induced fluorescence, enzyme labels, chemiluminiscence, amperometry, UV/VIS absorbance, mass spectrometry and surface plasmon resonance.
