4544060-15811500-303530-22733000 Faculty of Biotechnology Advanced Genetic Engineering and Gene Transfer BT308 Assignment 1 Microarray Dana Al Habbal161465 Submitted to

4544060-15811500-303530-22733000
Faculty of Biotechnology
Advanced Genetic Engineering and Gene Transfer
BT308
Assignment 1
Microarray
Dana Al Habbal161465
Submitted to: T.A Yara Ahmed
T.A Abdelrahman El-GammalMicroarray
Since the completion of the human genome project in 2001, many different technologies have evolved to better aid in the analysis of the sequenced genes. Among those is the microarray technology which enables researches to analyse the expression of many genes in a single reaction quickly and efficiently. Now the regions of DNA associated with the fundamentals of protein production and the causes of genetic anomalies can be studied ADDIN CSL_CITATION { “citationItems” : { “id” : “ITEM-1”, “itemData” : { “DOI” : “10.4103/0975-7406.100283”, “ISSN” : “0976-4879”, “abstract” : “Microarray is one of the most recent advances being used for cancer research; it provides assistance in pharmacological approach to treat various diseases including oral lesions. Microarray helps in analyzing large amount of samples which have either been recorded previously or new samples; it even helps to test the incidence of a particular marker in tumors. Till recently, microarray’s usage in dentistry has been very limited, but in future, as the technology becomes affordable, there may be increase in its usage. Here, we discuss the various techniques and applications of microarray or DNA chip. “, “author” : { “dropping-particle” : “”, “family” : “Govindarajan”, “given” : “Rajeshwar”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Duraiyan”, “given” : “Jeyapradha”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Kaliyappan”, “given” : “Karunakaran”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Palanisamy”, “given” : “Murugesan”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Journal of Pharmacy ; Bioallied Sciences”, “id” : “ITEM-1”, “issue” : “Suppl 2”, “issued” : { “date-parts” : “2012”, “8”, “1” }, “page” : “S310-S312”, “publisher” : “Medknow Publications ; Media Pvt Ltd”, “publisher-place” : “India”, “title” : “Microarray and its applications”, “type” : “article-journal”, “volume” : “4” }, “uris” : “http://www.mendeley.com/documents/?uuid=5dba7743-ee00-4082-9493-d89728664391” }, { “id” : “ITEM-2”, “itemData” : { “DOI” : “10.1186/1475-2859-6-4”, “ISSN” : “1475-2859”, “abstract” : “With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as: toxicology, evolutionary biology, drug development and production, disease characterization, diagnostics development, cellular physiology and stress responses, and forensics have benefiting from its use. However, for many researchers not familiar with microarrays, current articles and reviews often address neither the fundamental principles behind the technology nor the proper designing of experiments. Although, microarray technology is relatively simple, conceptually, its practice does require careful planning and detailed understanding of the limitations inherently present. Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Furthermore, this review is not meant to be comprehensive, but rather substantive; highlighting important concepts and detailing steps necessary to conduct and interpret microarray experiments. Collectively, the information included in this text will highlight the versatility of microarray technology and provide a glimpse of what the future may hold.”, “author” : { “dropping-particle” : “”, “family” : “Jaluria”, “given” : “Pratik”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Konstantopoulos”, “given” : “Konstantinos”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Betenbaugh”, “given” : “Michael”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Shiloach”, “given” : “Joseph”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Microbial Cell Factories”, “id” : “ITEM-2”, “issue” : “1”, “issued” : { “date-parts” : “2007” }, “page” : “4”, “title” : “A perspective on microarrays: current applications, pitfalls, and potential uses”, “type” : “article-journal”, “volume” : “6” }, “uris” : “http://www.mendeley.com/documents/?uuid=80298669-07f4-4c0a-9053-3dbb45dc8b2f” }, { “id” : “ITEM-3”, “itemData” : { “DOI” : “10.1128/CMR.00019-09”, “ISSN” : “0893-8512”, “abstract” : “Summary: The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform’s advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles. “, “author” : { “dropping-particle” : “”, “family” : “Miller”, “given” : “Melissa B”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Tang”, “given” : “Yi-Wei”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Clinical Microbiology Reviews”, “id” : “ITEM-3”, “issue” : “4”, “issued” : { “date-parts” : “2009”, “10” }, “page” : “611-633”, “publisher” : “American Society for Microbiology (ASM)”, “title” : “Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology”, “type” : “article-journal”, “volume” : “22” }, “uris” : “http://www.mendeley.com/documents/?uuid=f9595aaf-29d4-449d-b778-94512c8eea26” }, { “id” : “ITEM-4”, “itemData” : { “DOI” : “10.1038/sj.onc.1206865”, “ISSN” : “0950-9232 (Print)”, “PMID” : “14528274”, “abstract” : “Cancer is a highly variable disease with multiple heterogeneous genetic and epigenetic changes. Functional studies are essential to understanding the complexity and polymorphisms of cancer. The final deciphering of the complete human genome, together with the improvement of high throughput technologies, is causing a fundamental transformation in cancer research. Microarray is a new powerful tool for studying the molecular basis of interactions on a scale that is impossible using conventional analysis. This technique makes it possible to examine the expression of thousands of genes simultaneously. This technology promises to lead to improvements in developing rational approaches to therapy as well as to improvements in cancer diagnosis and prognosis, assuring its entry into clinical practice in specialist centers and hospitals within the next few years. Predicting who will develop cancer and how this disease will behave and respond to therapy after diagnosis will be one of the potential benefits of this technology within the next decade. In this review, we highlight some of the recent developments and results in microarray technology in cancer research, discuss potentially problematic areas associated with it, describe the eventual use of microarray technology for clinical applications and comment on future trends and issues.”, “author” : { “dropping-particle” : “”, “family” : “Russo”, “given” : “Giuseppe”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Zegar”, “given” : “Charles”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Giordano”, “given” : “Antonio”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Oncogene”, “id” : “ITEM-4”, “issue” : “42”, “issued” : { “date-parts” : “2003”, “9” }, “language” : “eng”, “page” : “6497-6507”, “publisher-place” : “England”, “title” : “Advantages and limitations of microarray technology in human cancer.”, “type” : “article-journal”, “volume” : “22” }, “uris” : “http://www.mendeley.com/documents/?uuid=e42cd131-ea6c-48fe-91d3-7f5e51164265” } , “mendeley” : { “formattedCitation” : “(Govindarajan, Duraiyan, Kaliyappan, & Palanisamy, 2012; Jaluria, Konstantopoulos, Betenbaugh, & Shiloach, 2007; Miller & Tang, 2009; Russo, Zegar, & Giordano, 2003)”, “plainTextFormattedCitation” : “(Govindarajan, Duraiyan, Kaliyappan, & Palanisamy, 2012; Jaluria, Konstantopoulos, Betenbaugh, & Shiloach, 2007; Miller & Tang, 2009; Russo, Zegar, & Giordano, 2003)”, “previouslyFormattedCitation” : “(Govindarajan, Duraiyan, Kaliyappan, & Palanisamy, 2012; Jaluria, Konstantopoulos, Betenbaugh, & Shiloach, 2007; Miller & Tang, 2009; Russo, Zegar, & Giordano, 2003)” }, “properties” : { }, “schema” : “https://github.com/citation-style-language/schema/raw/master/csl-citation.json” }(Govindarajan, Duraiyan, Kaliyappan, & Palanisamy, 2012; Jaluria, Konstantopoulos, Betenbaugh, & Shiloach, 2007; Miller & Tang, 2009; Russo, Zegar, & Giordano, 2003).
Principle and Mechanism
The concept of the microarray was derived from Southern blotting and is based on conducting parallel expression of multiple genes in one reaction. A basic microarray experiment is composed of a chip/microscope glass/nylon membrane containing many wells with different DNA sequences hybridized on it.
The mechanism involves the hybridization of an mRNA molecule to its complementary source DNA. Many DNA samples are used to construct an array called probes that are immobilized onto the plate containing either 34 or 96 wells; each well has a size of less than 200 microns. These probes are known DNA sequences. The probes may also be cDNA or oligonucleotides depending on the unknown samples. Quantification of the mRNA strands bound to their complementary DNA or cDNA probes indicates the expression level of that mRNA. The data can then be assimilated for the function of the mRNA based on it hybridizing with the DNA probe as well as which tissue expresses high levels of this particular mRNA to deduce its function within the tissue. Generally, the sample mRNA or sequence to be tested is labelled with a probe. The exact steps can be summarized as first extracting mRNA, then conducting a reverse-transcription PCR to cDNA, labelling the cDNA, hybridizing the cDNA to the probes on the plate, and scanning the plates to determine and quantify the fluorescence emission. Most common labelling of cDNA is using fluorochrome dyes Cy3 (green) and Cy5 (red). An integral step within the process is normalization of the intensity of the fluorescence after obtaining the results ADDIN CSL_CITATION { “citationItems” : { “id” : “ITEM-1”, “itemData” : { “DOI” : “10.4103/0975-7406.100283”, “ISSN” : “0976-4879”, “abstract” : “Microarray is one of the most recent advances being used for cancer research; it provides assistance in pharmacological approach to treat various diseases including oral lesions. Microarray helps in analyzing large amount of samples which have either been recorded previously or new samples; it even helps to test the incidence of a particular marker in tumors. Till recently, microarray’s usage in dentistry has been very limited, but in future, as the technology becomes affordable, there may be increase in its usage. Here, we discuss the various techniques and applications of microarray or DNA chip. “, “author” : { “dropping-particle” : “”, “family” : “Govindarajan”, “given” : “Rajeshwar”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Duraiyan”, “given” : “Jeyapradha”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Kaliyappan”, “given” : “Karunakaran”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Palanisamy”, “given” : “Murugesan”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Journal of Pharmacy ; Bioallied Sciences”, “id” : “ITEM-1”, “issue” : “Suppl 2”, “issued” : { “date-parts” : “2012”, “8”, “1” }, “page” : “S310-S312”, “publisher” : “Medknow Publications ; Media Pvt Ltd”, “publisher-place” : “India”, “title” : “Microarray and its applications”, “type” : “article-journal”, “volume” : “4” }, “uris” : “http://www.mendeley.com/documents/?uuid=5dba7743-ee00-4082-9493-d89728664391” }, { “id” : “ITEM-2”, “itemData” : { “DOI” : “10.1186/1475-2859-6-4”, “ISSN” : “1475-2859”, “abstract” : “With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as: toxicology, evolutionary biology, drug development and production, disease characterization, diagnostics development, cellular physiology and stress responses, and forensics have benefiting from its use. However, for many researchers not familiar with microarrays, current articles and reviews often address neither the fundamental principles behind the technology nor the proper designing of experiments. Although, microarray technology is relatively simple, conceptually, its practice does require careful planning and detailed understanding of the limitations inherently present. Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Furthermore, this review is not meant to be comprehensive, but rather substantive; highlighting important concepts and detailing steps necessary to conduct and interpret microarray experiments. Collectively, the information included in this text will highlight the versatility of microarray technology and provide a glimpse of what the future may hold.”, “author” : { “dropping-particle” : “”, “family” : “Jaluria”, “given” : “Pratik”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Konstantopoulos”, “given” : “Konstantinos”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Betenbaugh”, “given” : “Michael”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Shiloach”, “given” : “Joseph”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Microbial Cell Factories”, “id” : “ITEM-2”, “issue” : “1”, “issued” : { “date-parts” : “2007” }, “page” : “4”, “title” : “A perspective on microarrays: current applications, pitfalls, and potential uses”, “type” : “article-journal”, “volume” : “6” }, “uris” : “http://www.mendeley.com/documents/?uuid=80298669-07f4-4c0a-9053-3dbb45dc8b2f” }, { “id” : “ITEM-3”, “itemData” : { “DOI” : “10.1128/CMR.00019-09”, “ISSN” : “0893-8512”, “abstract” : “Summary: The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform’s advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles. “, “author” : { “dropping-particle” : “”, “family” : “Miller”, “given” : “Melissa B”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Tang”, “given” : “Yi-Wei”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Clinical Microbiology Reviews”, “id” : “ITEM-3”, “issue” : “4”, “issued” : { “date-parts” : “2009”, “10” }, “page” : “611-633”, “publisher” : “American Society for Microbiology (ASM)”, “title” : “Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology”, “type” : “article-journal”, “volume” : “22” }, “uris” : “http://www.mendeley.com/documents/?uuid=f9595aaf-29d4-449d-b778-94512c8eea26” }, { “id” : “ITEM-4”, “itemData” : { “DOI” : “10.1038/sj.onc.1206865”, “ISSN” : “0950-9232 (Print)”, “PMID” : “14528274”, “abstract” : “Cancer is a highly variable disease with multiple heterogeneous genetic and epigenetic changes. Functional studies are essential to understanding the complexity and polymorphisms of cancer. The final deciphering of the complete human genome, together with the improvement of high throughput technologies, is causing a fundamental transformation in cancer research. Microarray is a new powerful tool for studying the molecular basis of interactions on a scale that is impossible using conventional analysis. This technique makes it possible to examine the expression of thousands of genes simultaneously. This technology promises to lead to improvements in developing rational approaches to therapy as well as to improvements in cancer diagnosis and prognosis, assuring its entry into clinical practice in specialist centers and hospitals within the next few years. Predicting who will develop cancer and how this disease will behave and respond to therapy after diagnosis will be one of the potential benefits of this technology within the next decade. In this review, we highlight some of the recent developments and results in microarray technology in cancer research, discuss potentially problematic areas associated with it, describe the eventual use of microarray technology for clinical applications and comment on future trends and issues.”, “author” : { “dropping-particle” : “”, “family” : “Russo”, “given” : “Giuseppe”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Zegar”, “given” : “Charles”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Giordano”, “given” : “Antonio”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Oncogene”, “id” : “ITEM-4”, “issue” : “42”, “issued” : { “date-parts” : “2003”, “9” }, “language” : “eng”, “page” : “6497-6507”, “publisher-place” : “England”, “title” : “Advantages and limitations of microarray technology in human cancer.”, “type” : “article-journal”, “volume” : “22” }, “uris” : “http://www.mendeley.com/documents/?uuid=e42cd131-ea6c-48fe-91d3-7f5e51164265” } , “mendeley” : { “formattedCitation” : “(Govindarajan et al., 2012; Jaluria et al., 2007; Miller & Tang, 2009; Russo et al., 2003)”, “plainTextFormattedCitation” : “(Govindarajan et al., 2012; Jaluria et al., 2007; Miller & Tang, 2009; Russo et al., 2003)”, “previouslyFormattedCitation” : “(Govindarajan et al., 2012; Jaluria et al., 2007; Miller & Tang, 2009; Russo et al., 2003)” }, “properties” : { }, “schema” : “https://github.com/citation-style-language/schema/raw/master/csl-citation.json” }(Govindarajan et al., 2012; Jaluria et al., 2007; Miller & Tang, 2009; Russo et al., 2003).

Figure SEQ Figure * ARABIC 1. This figure shows the expected results after conducting the microarray experiment. Notice the different colours which represent the reference and test samples hybridizing to their complementary strands and the intensity of the colours representing the expression levels ADDIN CSL_CITATION { “citationItems” : { “id” : “ITEM-1”, “itemData” : { “DOI” : “10.1128/CMR.00019-09”, “ISSN” : “0893-8512”, “abstract” : “Summary: The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform’s advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles. “, “author” : { “dropping-particle” : “”, “family” : “Miller”, “given” : “Melissa B”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Tang”, “given” : “Yi-Wei”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Clinical Microbiology Reviews”, “id” : “ITEM-1”, “issue” : “4”, “issued” : { “date-parts” : “2009”, “10” }, “page” : “611-633”, “publisher” : “American Society for Microbiology (ASM)”, “title” : “Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology”, “type” : “article-journal”, “volume” : “22” }, “uris” : “http://www.mendeley.com/documents/?uuid=f9595aaf-29d4-449d-b778-94512c8eea26” } , “mendeley” : { “formattedCitation” : “(Miller ; Tang, 2009)”, “plainTextFormattedCitation” : “(Miller ; Tang, 2009)”, “previouslyFormattedCitation” : “(Miller ; Tang, 2009)” }, “properties” : { }, “schema” : “https://github.com/citation-style-language/schema/raw/master/csl-citation.json” }(Miller & Tang, 2009).

Types
The types of microarrays can be categorized based on the type of immobilized probe into:
DNA microarray
Protein microarray
Peptide microarray
Cellular microarray
Tissue microarray
Phenotype microarray
Antibody microarray
Reverse phase protein microarray
The types may also be classified according to the objective of the experiment into:
Expression analysis: usually used to compare expression of diseased vs. normal genes.

Mutation analysis: usually used to identify point mutations or SNPs.

Comparative genomic analysis: usually used to measure the expression level is segments of chromosomes related to diseases.
Finally, the categorization may also be based on the chip/channel itself and the experimental design into:
Single channel approach
Multiple channel approach
Speciality approaches such as using beads ADDIN CSL_CITATION { “citationItems” : { “id” : “ITEM-1”, “itemData” : { “DOI” : “10.4103/0975-7406.100283”, “ISSN” : “0976-4879”, “abstract” : “Microarray is one of the most recent advances being used for cancer research; it provides assistance in pharmacological approach to treat various diseases including oral lesions. Microarray helps in analyzing large amount of samples which have either been recorded previously or new samples; it even helps to test the incidence of a particular marker in tumors. Till recently, microarray’s usage in dentistry has been very limited, but in future, as the technology becomes affordable, there may be increase in its usage. Here, we discuss the various techniques and applications of microarray or DNA chip. “, “author” : { “dropping-particle” : “”, “family” : “Govindarajan”, “given” : “Rajeshwar”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Duraiyan”, “given” : “Jeyapradha”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Kaliyappan”, “given” : “Karunakaran”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Palanisamy”, “given” : “Murugesan”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Journal of Pharmacy & Bioallied Sciences”, “id” : “ITEM-1”, “issue” : “Suppl 2”, “issued” : { “date-parts” : “2012”, “8”, “1” }, “page” : “S310-S312”, “publisher” : “Medknow Publications & Media Pvt Ltd”, “publisher-place” : “India”, “title” : “Microarray and its applications”, “type” : “article-journal”, “volume” : “4” }, “uris” : “http://www.mendeley.com/documents/?uuid=5dba7743-ee00-4082-9493-d89728664391” }, { “id” : “ITEM-2”, “itemData” : { “DOI” : “10.1186/1475-2859-6-4”, “ISSN” : “1475-2859”, “abstract” : “With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as: toxicology, evolutionary biology, drug development and production, disease characterization, diagnostics development, cellular physiology and stress responses, and forensics have benefiting from its use. However, for many researchers not familiar with microarrays, current articles and reviews often address neither the fundamental principles behind the technology nor the proper designing of experiments. Although, microarray technology is relatively simple, conceptually, its practice does require careful planning and detailed understanding of the limitations inherently present. Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Furthermore, this review is not meant to be comprehensive, but rather substantive; highlighting important concepts and detailing steps necessary to conduct and interpret microarray experiments. Collectively, the information included in this text will highlight the versatility of microarray technology and provide a glimpse of what the future may hold.”, “author” : { “dropping-particle” : “”, “family” : “Jaluria”, “given” : “Pratik”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Konstantopoulos”, “given” : “Konstantinos”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Betenbaugh”, “given” : “Michael”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Shiloach”, “given” : “Joseph”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Microbial Cell Factories”, “id” : “ITEM-2”, “issue” : “1”, “issued” : { “date-parts” : “2007” }, “page” : “4”, “title” : “A perspective on microarrays: current applications, pitfalls, and potential uses”, “type” : “article-journal”, “volume” : “6” }, “uris” : “http://www.mendeley.com/documents/?uuid=80298669-07f4-4c0a-9053-3dbb45dc8b2f” }, { “id” : “ITEM-3”, “itemData” : { “DOI” : “10.1128/CMR.00019-09”, “ISSN” : “0893-8512”, “abstract” : “Summary: The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. 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Figure SEQ Figure * ARABIC 2. Representation of single channel (one colour) microarray vs. multiple channels (two colours) microarray emphasizing that the overall steps are the same; however, there are differences in the method of detection whether it is labelling the reference and test samples differently (multiple channels) or applying the same label (single channel) ADDIN CSL_CITATION { “citationItems” : { “id” : “ITEM-1”, “itemData” : { “DOI” : “10.1128/CMR.00019-09”, “ISSN” : “0893-8512”, “abstract” : “Summary: The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform’s advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles. “, “author” : { “dropping-particle” : “”, “family” : “Miller”, “given” : “Melissa B”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Tang”, “given” : “Yi-Wei”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Clinical Microbiology Reviews”, “id” : “ITEM-1”, “issue” : “4”, “issued” : { “date-parts” : “2009”, “10” }, “page” : “611-633”, “publisher” : “American Society for Microbiology (ASM)”, “title” : “Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology”, “type” : “article-journal”, “volume” : “22” }, “uris” : “http://www.mendeley.com/documents/?uuid=f9595aaf-29d4-449d-b778-94512c8eea26” } , “mendeley” : { “formattedCitation” : “(Miller & Tang, 2009)”, “plainTextFormattedCitation” : “(Miller & Tang, 2009)”, “previouslyFormattedCitation” : “(Miller & Tang, 2009)” }, “properties” : { }, “schema” : “https://github.com/citation-style-language/schema/raw/master/csl-citation.json” }(Miller & Tang, 2009).

Advantages
Provides data for large numbers of genes
Can be conducted in one reaction instead of multiple reactions
Results obtained are fast and reaction is relatively easy
Can easily provide links between disease progression and associated genes and their expression levels
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Disadvantages
Chips/plates are expensive to produce
The plates have a short shelf life
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Applications
Microarray technology has a wide range of applications within every industry, but the most promising applications are:
Gene discovery: through microarrays, gene function and expression levels may be determined according to the variable cellular conditions.

Drug discovery: microarrays are extensively used in the field of pharmacogenomics which is the study of individualized therapy based on treatments dependant on the genetic profile of an individual. Through identification of diseased genes, the proteins synthesized by them can be isolated and targeted by drugs.

Disease diagnosis: genes associated with the progression of diseases may be assessed for in one reaction to determine which are pivotal. For example, cancer has been classified based on its genetic pattern instead of just based on the tumor growth.

Toxicological research: the changes in the genetic profiles of an individual based on exposure to toxins can be reported through the study of toxicogenomics which is dependent on microarray technology ADDIN CSL_CITATION { “citationItems” : { “id” : “ITEM-1”, “itemData” : { “DOI” : “10.4103/0975-7406.100283”, “ISSN” : “0976-4879”, “abstract” : “Microarray is one of the most recent advances being used for cancer research; it provides assistance in pharmacological approach to treat various diseases including oral lesions. Microarray helps in analyzing large amount of samples which have either been recorded previously or new samples; it even helps to test the incidence of a particular marker in tumors. Till recently, microarray’s usage in dentistry has been very limited, but in future, as the technology becomes affordable, there may be increase in its usage. Here, we discuss the various techniques and applications of microarray or DNA chip. “, “author” : { “dropping-particle” : “”, “family” : “Govindarajan”, “given” : “Rajeshwar”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Duraiyan”, “given” : “Jeyapradha”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Kaliyappan”, “given” : “Karunakaran”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Palanisamy”, “given” : “Murugesan”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Journal of Pharmacy ; Bioallied Sciences”, “id” : “ITEM-1”, “issue” : “Suppl 2”, “issued” : { “date-parts” : “2012”, “8”, “1” }, “page” : “S310-S312”, “publisher” : “Medknow Publications ; Media Pvt Ltd”, “publisher-place” : “India”, “title” : “Microarray and its applications”, “type” : “article-journal”, “volume” : “4” }, “uris” : “http://www.mendeley.com/documents/?uuid=5dba7743-ee00-4082-9493-d89728664391” }, { “id” : “ITEM-2”, “itemData” : { “DOI” : “10.1186/1475-2859-6-4”, “ISSN” : “1475-2859”, “abstract” : “With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as: toxicology, evolutionary biology, drug development and production, disease characterization, diagnostics development, cellular physiology and stress responses, and forensics have benefiting from its use. However, for many researchers not familiar with microarrays, current articles and reviews often address neither the fundamental principles behind the technology nor the proper designing of experiments. Although, microarray technology is relatively simple, conceptually, its practice does require careful planning and detailed understanding of the limitations inherently present. Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Furthermore, this review is not meant to be comprehensive, but rather substantive; highlighting important concepts and detailing steps necessary to conduct and interpret microarray experiments. 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However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform’s advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles. “, “author” : { “dropping-particle” : “”, “family” : “Miller”, “given” : “Melissa B”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” }, { “dropping-particle” : “”, “family” : “Tang”, “given” : “Yi-Wei”, “non-dropping-particle” : “”, “parse-names” : false, “suffix” : “” } , “container-title” : “Clinical Microbiology Reviews”, “id” : “ITEM-3”, “issue” : “4”, “issued” : { “date-parts” : “2009”, “10” }, “page” : “611-633”, “publisher” : “American Society for Microbiology (ASM)”, “title” : “Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology”, “type” : “article-journal”, “volume” : “22” }, “uris” : “http://www.mendeley.com/documents/?uuid=f9595aaf-29d4-449d-b778-94512c8eea26” }, { “id” : “ITEM-4”, “itemData” : { “DOI” : “10.1038/sj.onc.1206865”, “ISSN” : “0950-9232 (Print)”, “PMID” : “14528274”, “abstract” : “Cancer is a highly variable disease with multiple heterogeneous genetic and epigenetic changes. Functional studies are essential to understanding the complexity and polymorphisms of cancer. The final deciphering of the complete human genome, together with the improvement of high throughput technologies, is causing a fundamental transformation in cancer research. Microarray is a new powerful tool for studying the molecular basis of interactions on a scale that is impossible using conventional analysis. This technique makes it possible to examine the expression of thousands of genes simultaneously. This technology promises to lead to improvements in developing rational approaches to therapy as well as to improvements in cancer diagnosis and prognosis, assuring its entry into clinical practice in specialist centers and hospitals within the next few years. Predicting who will develop cancer and how this disease will behave and respond to therapy after diagnosis will be one of the potential benefits of this technology within the next decade. 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References
ADDIN Mendeley Bibliography CSL_BIBLIOGRAPHY Govindarajan, R., Duraiyan, J., Kaliyappan, K., & Palanisamy, M. (2012). Microarray and its applications. Journal of Pharmacy & Bioallied Sciences, 4(Suppl 2), S310–S312. https://doi.org/10.4103/0975-7406.100283
Jaluria, P., Konstantopoulos, K., Betenbaugh, M., & Shiloach, J. (2007). A perspective on microarrays: current applications, pitfalls, and potential uses. Microbial Cell Factories, 6(1), 4. https://doi.org/10.1186/1475-2859-6-4
Miller, M. B., & Tang, Y.-W. (2009). Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology. Clinical Microbiology Reviews, 22(4), 611–633. https://doi.org/10.1128/CMR.00019-09
Russo, G., Zegar, C., & Giordano, A. (2003). Advantages and limitations of microarray technology in human cancer. Oncogene, 22(42), 6497–6507. https://doi.org/10.1038/sj.onc.1206865