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Methods in Molecular Biology (Clifton,... 2016High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data...
High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data storage and computing power. Cloud computing offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and thus, it may represent the key technology for facing those issues. In fact, in the recent years it has been adopted for the deployment of different bioinformatics solutions and services both in academia and in the industry. Although this, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine. This chapter reviews main academic and industrial cloud-based bioinformatics solutions; with a special focus on microarray data analysis solutions and underlines main issues and problems related to the use of such platforms for the storage and analysis of patients data.
Topics: Cloud Computing; Computational Biology; Humans; Microarray Analysis
PubMed: 25863787
DOI: 10.1007/7651_2015_236 -
PeerJ 2023Invasive prenatal evaluation by chromosomal microarray analysis (CMA) and karyotyping might represent an important option in pregnant women, but limited reports have...
BACKGROUND
Invasive prenatal evaluation by chromosomal microarray analysis (CMA) and karyotyping might represent an important option in pregnant women, but limited reports have applied CMA and karyotyping of fetuses conceived by assisted reproductive technology (ART). This study aimed to examine the value of CMA and karyotyping in prenatal diagnosis after ART.
METHODS
This retrospective study included all singleton fetuses conceived by ART from January 2015 to December 2021. Anomalies prenatally diagnosed based on karyotyping and CMA were analyzed. Prevalence rates for various CMA and karyotyping results were stratified based on specific testing indications including isolated-and non-isolated ART groups. The rates of CMA findings with clinical significance (pathogenic/likely pathogenic) and karyotype anomalies were assessed and compared to those of local control individuals with naturally conceived pregnancies and without medical indications.
RESULTS
In total, 224 subjects were assessed by karyotyping and CMA. In the examined patients, chromosomal and karyotype abnormality rates were 3.57% (8/224) and 8.93% (20/224), respectively. This finding indicated a 5.35% (12/224)-incremental rate of abnormal CMA was obtained over karyotype analysis ( = 0.019). The risk of CMA with pathogenic findings for all pregnancies conceived by ART (5.80%, 13/224) was markedly elevated in comparison with the background value obtained in control individuals (1.47%, 9/612; = 0.001). In addition, risk of CMA with clinically pathogenic results in isolated ART groups was significant higher compared to the background risk reported in the control cohort ( = 0.037).
CONCLUSIONS
Prenatal diagnosis including karyotyping and CMA is recommended for fetuses conceived by ART, with or without ultrasound findings.
Topics: Pregnancy; Female; Humans; Retrospective Studies; Prenatal Diagnosis; Karyotyping; Microarray Analysis; Fetus; Karyotype
PubMed: 36684682
DOI: 10.7717/peerj.14678 -
Nature Reviews. Molecular Cell Biology Dec 2015Lipids tailor membrane identities and function as molecular hubs in all cellular processes. However, the ways in which lipids modulate protein function and structure are... (Review)
Review
Lipids tailor membrane identities and function as molecular hubs in all cellular processes. However, the ways in which lipids modulate protein function and structure are poorly understood and still require systematic investigation. In this Innovation article, we summarize pioneering technologies, including lipid-overlay assays, lipid pull-down assays, affinity-purification lipidomics and the liposome microarray-based assay (LiMA), that will enable protein-lipid interactions to be deciphered on a systems level. We discuss how these technologies can be applied to the charting of system-wide networks and to the development of new pharmaceutical strategies.
Topics: Animals; Cell Membrane; Humans; Lipid Metabolism; Lipids; Lipoproteins; Liposomes; Microarray Analysis; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins
PubMed: 26507169
DOI: 10.1038/nrm4080 -
BMC Pregnancy and Childbirth Nov 2020To explore the application value of chromosomal microarray analysis (CMA) in prenatal diagnosis. (Comparative Study)
Comparative Study
BACKGROUND
To explore the application value of chromosomal microarray analysis (CMA) in prenatal diagnosis.
METHODS
The results of chromosome karyotype analysis and CMA of 477 cases undergoing amniocentesis were analyzed. The results of the no ultrasound abnormality group and the ultrasound abnormality group were compared separately. Within the ultrasound abnormality group, the results of the ultrasound structural malformation group, the ultrasound soft index abnormality group, and other ultrasound abnormality (including abnormal amniotic fluid volume and fetal growth restriction) groups were compared.
RESULTS
Abnormal chromosome and CMA results were found in a total of 71 cases (15.88%, 71/447), which can be broken down into a total of 23 karyotype abnormalities (5.15%, 23/447), consisting of 18 cases of aneuploidy (4.03%, 18/447), 2 cases of unbalanced chromosome rearrangements (0.44%, 2/447), and 3 cases of chimerism (0.67%, 3/447); 17 cases with detection of pathogenic copy number variations (pCNVs) (3.80%, 17/447); and 31 cases of detection of clinical variants of unknown significance (VOUS) (6.93%, 31/447). CMA detected 3.8% more genetic abnormalities than karyotype analysis (in addition to the abnormalities detected simultaneously by karyotype analysis). Between the no ultrasound abnormality group and the ultrasound abnormality group, there was an extremely significant difference in the detection rate of an abnormal chromosomal karyotype (P < 0.01) and of VOUS (P < 0.01), but there was no significant difference in the detection rate of pCNV (P > 0.05). Comparing the ultrasound structural malformation group, the ultrasound soft index abnormality group, and the other ultrasound abnormality group, there were no significant differences in the detection rate of abnormal chromosomal karyotypes (P > 0.05), pCNV (P > 0.05) or VOUS (P > 0.05).
CONCLUSIONS
The detection rate of chromosomal karyotype abnormalities in prenatal diagnosis in cases with no ultrasound abnormalities was higher. For cases with fetal ultrasound structural abnormalities, when compared with traditional karyotype analysis, CMA can improve the detection rate of fetal genetic abnormalities. However, the no ultrasound abnormality group also had a high VOUS abnormality detection rate, so it is necessary to strictly define the CMA indications.
Topics: Adult; Amniocentesis; Chromosome Disorders; DNA Copy Number Variations; Female; Fetus; Genetic Testing; Humans; Karyotyping; Microarray Analysis; Pregnancy; Prenatal Diagnosis; Ultrasonography, Prenatal; Young Adult
PubMed: 33198662
DOI: 10.1186/s12884-020-03368-y -
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 -
Briefings in Bioinformatics Jul 2016Predictive, preventive, personalized and participatory (P4) medicine is an emerging medical model that is based on the customization of all medical aspects (i.e.... (Review)
Review
Predictive, preventive, personalized and participatory (P4) medicine is an emerging medical model that is based on the customization of all medical aspects (i.e. practices, drugs, decisions) of the individual patient. P4 medicine presupposes the elucidation of the so-called omic world, under the assumption that this knowledge may explain differences of patients with respect to disease prevention, diagnosis and therapies. Here, we elucidate the role of some selected omics sciences for different aspects of disease management, such as early diagnosis of diseases, prevention of diseases, selection of personalized appropriate and optimal therapies based on molecular profiling of patients. After introducing basic concepts of P4 medicine and omics sciences, we review some computational tools and approaches for analysing selected omics data, with a special focus on microarray and mass spectrometry data, which may be used to support P4 medicine. Some applications of biomarker discovery and pharmacogenomics and some experiences on the study of drug reactions are also described.
Topics: Humans; Mass Spectrometry; Microarray Analysis; Precision Medicine
PubMed: 26351205
DOI: 10.1093/bib/bbv076 -
Methods in Molecular Biology (Clifton,... 2023The diversity of the antigen-specific humoral immune response reflects the interaction of the immune system with pathogens and autoantigens. Peptide microarray analysis... (Review)
Review
The diversity of the antigen-specific humoral immune response reflects the interaction of the immune system with pathogens and autoantigens. Peptide microarray analysis opens up new perspectives for the use of antibodies as diagnostic biomarkers and provides unique access to a more differentiated view on humoral responses to disease. This review focuses on the latest applications of peptide microarrays for the serologic medical diagnosis of autoimmunity, infectious diseases (including COVID-19), and cancer.
Topics: Autoantibodies; Autoantigens; Biomarkers; COVID-19; Humans; Microarray Analysis; Neoplasms; Peptides; Protein Array Analysis
PubMed: 36152276
DOI: 10.1007/978-1-0716-2732-7_1 -
Analytical Chemistry Jun 2023Microarrays have been widely used for multiplexed bioassays. Fabrication of a conventional microarray typically requires a complex microarray spotter, using which...
Microarrays have been widely used for multiplexed bioassays. Fabrication of a conventional microarray typically requires a complex microarray spotter, using which nanoliter bioreagent (e.g., antibody and cells) droplets are delivered onto a glass slide. However, arraying a delicate bioreagent in nanoliter volumes could cause the loss of bioactivity and needs a complex microarray spotter. Further, mixing of different bioreagents in a multiplexed assay leads to cross-reactions, producing false positive signals that impair assay reproducibility and scalability. In this work, we propose a new microarray format, named "compartmentalized linker array (CLA)", that consists of pre-prepared storable microarrays of chemical linkers in microliter compartments. CLA can be used for binding and patterning bioreagents into microarrays by simply pipetting and incubating bioreagent solutions in compartments. Using commonly used aminosilane linker-based antibody microarray, we developed CLA and demonstrated its application for a multiplexed sandwich immunoassay measuring three cancer-related proteins. A "two-phase" blocking system was established for de-activating background regions on glass where no linker molecules are present. Storage conditions of the CLA chip were explored and demonstrated for long-term storage. In a multiplexed immunoassay, low pg/mL sensitivity was achieved for all the three proteins, comparable to those of conventional assays. Moreover, CLA can be potentially used for other applications beyond protein assays, making microarray technology transferrable and widely available for the biological and biomedical research community.
Topics: Protein Array Analysis; Reproducibility of Results; Microarray Analysis; Proteins; Immunoassay; Antibodies
PubMed: 37267452
DOI: 10.1021/acs.analchem.3c01442 -
Clinical and Experimental Allergy :... Aug 2016During the last decades component-resolved diagnostics either as singleplex or multiplex measurements has been introduced into the field of clinical allergology,... (Review)
Review
During the last decades component-resolved diagnostics either as singleplex or multiplex measurements has been introduced into the field of clinical allergology, providing important information that cannot be obtained from extract-based tests. Here we review recent studies that demonstrate clinical applications of the multiplex microarray technique in the diagnosis and risk assessment of allergic patients, and its usefulness in studies of allergic diseases. The usefulness of ImmunoCAP ISAC has been validated in a wide spectrum of allergic diseases like asthma, allergic rhinoconjunctivitis, atopic dermatitis, eosinophilic esophagitis, food allergy and anaphylaxis. ISAC provides a broad picture of a patient's sensitization profile from a single test, and provides information on specific and cross-reactive sensitizations that facilitate diagnosis, risk assessment, and disease management. Furthermore, it can reveal unexpected sensitizations which may explain anaphylaxis previously categorized as idiopathic and also display for the moment clinically non-relevant sensitizations. ISAC can facilitate a better selection of relevant allergens for immunotherapy compared with extract testing. Microarray technique can visualize the allergic march and molecular spreading in the preclinical stages of allergic diseases, and may indicate that the likelihood of developing symptomatic allergy is associated with specific profiles of sensitization to allergen components. ISAC is shown to be a useful tool in routine allergy diagnostics due to its ability to improve risk assessment, to better select relevant allergens for immunotherapy as well as detecting unknown sensitization. Multiplex component testing is especially suitable for patients with complex symptomatology.
Topics: Allergens; Cross Reactions; Humans; Hypersensitivity; Immunotherapy; Microarray Analysis; Phenotype; Risk Assessment
PubMed: 27196983
DOI: 10.1111/cea.12761 -
Methods in Molecular Biology (Clifton,... 2022Microarray technology is fully established among the research fields in genetic domain. Academia and industrial researchers investigate and analyze genes' expression to...
Microarray technology is fully established among the research fields in genetic domain. Academia and industrial researchers investigate and analyze genes' expression to obtain more and more useful information about given organisms, with the aim to perform better disease diagnosis and prediction, accurate medical data analysis, etc. Analyzing gene expression data, often available in raw form, implies a huge amount of analytical and computational complexities and therefore, innovative and intelligent mechanisms have to be designed to obtain useful information from this precious data. This chapter proposes a multiagent algorithm for building a distributed algorithm for DNA Microarray management. A collection of agents, in which each one representing a Microarray (or chip), execute in parallel a sequence of simple operations exploiting local information, and an organized virtual structure is built at global level. A word embeddings approach, able to capture the semantic context and represent Microarrays with vectors, is employed to map the chips, so allowing advanced agents' operations. A similarity-based overlay network of agents is brought out and an efficient management system of DNA Microarray is enabled. The generated virtual structure allows executing of informed operations, such as range queries, in a large dataset containing unstructured data. Preliminary results were confirm the validity of the algorithm proposed.
Topics: Algorithms; Oligonucleotide Array Sequence Analysis; Semantics
PubMed: 34902121
DOI: 10.1007/978-1-0716-1839-4_4