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Progress in Neuro-psychopharmacology &... Jan 2016Major depressive disorder (MDD) is a serious health concern worldwide. Currently there are no predictive tests for the effectiveness of any particular antidepressant in... (Review)
Review
Major depressive disorder (MDD) is a serious health concern worldwide. Currently there are no predictive tests for the effectiveness of any particular antidepressant in an individual patient. Thus, doctors must prescribe antidepressants based on educated guesses. With the recent advent of scientific research, genome-wide gene expression microarray studies are widely utilized to analyze hundreds of thousands of biomarkers by high-throughput technologies. In addition to the candidate-gene approach, the genome-wide approach has recently been employed to investigate the determinants of MDD as well as antidepressant response to therapy. In this review, we mainly focused on gene expression studies with genome-wide approaches using RNA derived from peripheral blood cells. Furthermore, we reviewed their limitations and future directions with respect to the genome-wide gene expression profiling in MDD pathogenesis as well as in antidepressant therapy.
Topics: Animals; Antidepressive Agents; Biomarkers; Depressive Disorder, Major; Gene Expression; Gene Expression Profiling; Humans; Microarray Analysis; Treatment Outcome
PubMed: 25708651
DOI: 10.1016/j.pnpbp.2015.02.008 -
Cold Spring Harbor Protocols Jul 2019Gene expression profiling typically requires microgram quantities of mRNA, which can be difficult to obtain. In such cases, RNA must be amplified to have enough material...
Gene expression profiling typically requires microgram quantities of mRNA, which can be difficult to obtain. In such cases, RNA must be amplified to have enough material for microarray labeling and hybridization. This protocol generates amplified antisense RNA (aRNA) from limited quantities of total RNA. It is designed around maximizing yield and product length while minimizing template-independent side reactions. Template-independent reactions compete with the desired template-dependent reaction, an undesirable situation that becomes more severe as less RNA template is used. Amplification products dominated by template-independent product result in greatly reduced sensitivity and compression of differences in microarray hybridization experiments. Most notably, the oligo(dT) primer used in reverse transcription (RT) yields a high-molecular-weight product in the in vitro transcription (IVT) reaction independent of any cDNA template. This protocol therefore limits the amount of primer used by using small cDNA synthesis volumes. In addition, high-molecular-weight, template-independent product is generated in the presence of biotinylated NTPs and the absence of any polymer when excessive amounts of T7 RNA polymerase activity are used. Template-dependent product of questionable molecular weight and limited functionality in downstream reactions can also be produced with excessive T7 RNA polymerase activity. Essentially, more yield is not always better. Here, a single round of amplification typically results in a fivefold to 20-fold mass conversion of starting material. If the first-round aRNA is used as a template for a second round of amplification, 200- to 400-fold amplification is typical.
Topics: Gene Expression Profiling; Microarray Analysis; Nucleic Acid Amplification Techniques; RNA; RNA, Antisense
PubMed: 31262957
DOI: 10.1101/pdb.prot096420 -
Methods in Molecular Biology (Clifton,... 2017Structurally diverse glycans are expressed by all animate beings and exert diverse biological functions through specific interactions with glycan binding proteins...
Structurally diverse glycans are expressed by all animate beings and exert diverse biological functions through specific interactions with glycan binding proteins (GBPs). In humans, glycan-GBP interactions are implicated in many disease-relevant processes in development, infection and immune response to bacterial and viral pathogens. Recent progress in chemical synthesis, including automated glycan assembly, has facilitated access to complex glycans that cannot be isolated from biological material. Glycan immobilization on microarrays allows rapid, multiplexed glycan-GBP interaction studies to reveal biological functions. Synthetic glycan microarrays have enabled, for instance, the identification of glycan ligands for lectins, the definition of vaccine antigens, revealed viral glycan receptors and can serve as diagnostic tools for human disease. Here, we describe the methods to fabricate custom glycan microarrays that are used to examine glycan-GBP binding specificities. Conjugation-ready synthetic glycans are covalently attached to microarray surfaces through nucleophilic linker moieties. Microarrays are incubated with GBPs, and binding events are quantitatively detected by fluorescent signals. These methods are readily adaptable to a multitude of purposes from basic research to biomedical applications.
Topics: Amines; Carrier Proteins; Microarray Analysis; Polysaccharides; Protein Binding; Sulfhydryl Compounds
PubMed: 27873210
DOI: 10.1007/978-1-4939-6584-7_15 -
Methods in Molecular Biology (Clifton,... 2022Glycan binding proteins (GBPs) possess the unique ability to regulate a wide variety of biological processes through interactions with highly modifiable cell surface...
Glycan binding proteins (GBPs) possess the unique ability to regulate a wide variety of biological processes through interactions with highly modifiable cell surface glycans. While many studies demonstrate the impact of glycan modification on GBP recognition and activity, the relative contribution of subtle changes in glycan structure on GBP binding can be difficult to define. To overcome limitations in the analysis of GBP-glycan interactions, recent studies utilized glycan microarray platforms containing hundreds of structurally defined glycans. These studies not only provided important information regarding GBP-glycan interactions in general but have also resulted in significant insight into binding specificity and biological activity of the galectin family. We will describe the methods used when employing glycan microarray platforms to examine galectin-glycan binding specificity and function.
Topics: Carrier Proteins; Galectins; Microarray Analysis; Polysaccharides; Protein Binding
PubMed: 35320525
DOI: 10.1007/978-1-0716-2055-7_9 -
Current Opinion in Pediatrics Dec 2014Prenatal diagnostic and screening tests are routinely offered to all women in pregnancy. Advances in technology have led to an expansion in available testing. As... (Review)
Review
PURPOSE OF REVIEW
Prenatal diagnostic and screening tests are routinely offered to all women in pregnancy. Advances in technology have led to an expansion in available testing. As technology improves, women are facing increasingly complex decisions regarding the quantity and quality of information they wish to have regarding their fetus.
RECENT FINDINGS
Professional guidelines support the use of chromosomal microarray analysis as a first-tier test in place of standard karyotype for the evaluation of fetal chromosomes when one or more anomaly is detected by ultrasound. These same guidelines indicate that either chromosomal microarray analysis or standard karyotype can be offered for prenatal diagnosis with a phenotypically normal fetus. Additionally, recent work continues to validate the use of noninvasive prenatal testing for the detection of aneuploidy in the high-risk population. This testing utilizes cell-free DNA in the maternal circulation to predict fetal karyotype with greater sensitivity and specificity than maternal serum screening or first trimester screening. Data continue to accumulate supporting noninvasive prenatal testing use in an all-risk or low-risk population. Additionally, noninvasive prenatal testing is clinically available to screen for a select number of microdeletion syndromes, broadening the scope of population-based screening to include conditions not previously evaluated, although there are limited data available regarding this application.
SUMMARY
As prenatal diagnosis becomes increasingly complex, there is a need for the education of both patients and providers regarding the benefits and limitations of the testing strategies available to them.
Topics: Aneuploidy; Female; Humans; Mass Screening; Microarray Analysis; Pregnancy; Prenatal Diagnosis
PubMed: 25211161
DOI: 10.1097/MOP.0000000000000145 -
Pediatric Endocrinology Reviews : PER Sep 2015Chromosomal microarray analysis (CMA) is a technology used for the detection of clinically-significant microdeietions or duplications, with a high sensitivity for... (Review)
Review
Chromosomal microarray analysis (CMA) is a technology used for the detection of clinically-significant microdeietions or duplications, with a high sensitivity for submicroscopic aberrations. It is able to detect changes as small as 5-10Kb in size - a resolution up to 1000 times higher than that of conventional karyotyping. CMA is used for uncovering copy number variants (CNVs) thought to play an important role in the pathogenesis of a variety of disorders, primarily neurodevelopmental disorders and congenital anomalies. CMA may be applied in the prenatal or postnatal setting, with unique benefits and limitations in each setting. The growing use of CMA makes it essential for practicing physicians to understand the principles of this technology and be aware of its powers and limitations.
Topics: Adult; Chromosomes; Female; Genetic Testing; Humans; Infant, Newborn; Karyotyping; Microarray Analysis; Pregnancy; Prenatal Diagnosis
PubMed: 26540760
DOI: No ID Found -
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 (Pā<ā0.01) and of VOUS (Pā<ā0.01), 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 -
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 -
BMC Pregnancy and Childbirth Jul 2023The aim of this study was to investigate the incidence of chromosome anomalies in different types of congenital gastrointestinal obstruction and assess pregnancy...
OBJECTIVE
The aim of this study was to investigate the incidence of chromosome anomalies in different types of congenital gastrointestinal obstruction and assess pregnancy outcomes of fetuses with congenital gastrointestinal obstruction.
METHODS
A total of 64 cases with gastrointestinal obstruction between January 2014 and December 2020 were enrolled in this study. They were divided into three groups according to sonographic images. Group A: isolated upper gastrointestinal obstruction; Group B: isolated lower gastrointestinal obstruction; Group C: non-isolated gastrointestinal obstruction. The rate of chromosome anomalies in different groups was calculated. Pregnant women with amniocentesis were followed up by medical records and telephone. The follow-up included pregnancy outcomes and development of the live born infants.
RESULT
From January 2014 to December 2020, there were 64 fetus with congenital gastrointestinal obstruction underwent chromosome microarray analysis(CMA), the overall detection rate of CMA testing was 14.1%(9/64). The detection rate of Group A, B and C were 16.2%, 0 and 25.0% respectively. 9 fetuses with abnormal CMA results were all terminated. Among 55 fetuses with normal chromosomes, 10(18.2%) fetuses were not found to have any gastrointestinal obstruction after birth. 17(30.9%) fetuses were diagnosed with gastrointestinal obstruction and underwent surgical treatment after birth, one of which had lower gastrointestinal obstruction combined with biliary obstruction and died due to liver cirrhosis. 11(20.0%) pregnancy were terminated due to multiple abnormalities. 5(9.1%) fetuses were intrauterine death. 3(5.5%) fetuses were neonatal deaths. 9(16.4%) fetuses were lost to follow-up.
CONCLUSION
It is crucial to understand whether the gastrointestinal tract abnormality is isolated or associated to other findings. The risk of chromosomal abnormalities in fetuses with isolated lower gastrointestinal obstruction is lower than upper gastrointestinal obstruction. While genetic abnormalities excluded, a promising prognosis is expected for fetuses with congenital gastrointestinal obstruction.
Topics: Infant, Newborn; Pregnancy; Female; Humans; Pregnancy Outcome; Ultrasonography, Prenatal; Prenatal Diagnosis; Chromosome Aberrations; Fetus; Chromosomes; Microarray Analysis; Intestinal Obstruction
PubMed: 37422671
DOI: 10.1186/s12884-023-05828-7