What are gene chips-Microarray

 Let us talk about microarrary: Basic principle for clinicians: A microarray is a laboratory tool used to detect the expression of thousands of genes at the same time. The DNA molecules attached to each slide act as probes to detect gene expression, which is also known as the transcriptome or the set of messenger RNA (mRNA) transcripts expressed by a group of genes. How to carry out such complicated “difficult –to –understand” tests?? - To perform a microarray analysis, mRNA molecules are typically collected from both an experimental sample and a reference sample. For example, the reference sample could be collected from a healthy individual, and the experimental sample could be collected from an individual with a disease like cancer. The two mRNA samples are then converted into complementary DNA (cDNA), and each sample is labeled with a fluorescent probe of a different color. For instance, the experimental cDNA sample may be labeled with a red fluorescent dye, whereas the reference cDNA may be labeled with a green fluorescent dye.

What are gene  chips???   DNA microarrays are microscope slides that are printed with thousands of tiny spots in defined positions, with each spot containing a known DNA sequence or gene. Often, these slides are referred to as gene chips or DNA chips. The DNA molecules attached to each slide act as probes to detect gene expression, which is also known as the transcriptome or the set of messenger RNA (mRNA) transcripts expressed by a group of genes.

What is DNA Microarray?? Ans:-DNA Microarray is a kind of “Molecular Biology research”. Microarray is   one such technology which enables the researchers to investigate and address issues which were once thought to be non traceable. One can analyze the expression of many genes in a single reaction quickly and in an efficient manner

What do we mean by  DNA  probes?? Ans:- Thousands of spotted samples known as probes (with known identity) are immobilized on a solid support (a microscope glass slides or silicon chips or nylon membrane). The spots can be DNA, cDNA, or oligonucleotides. These are used to determine complementary binding of the unknown sequences thus allowing parallel analysis for gene expression and gene discovery. An experiment with a single DNA chip can provide information on thousands of genes simultaneously. An orderly arrangement of the probes on the support is important as the location of each spot on the array is used for the identification of a gene

The principle of microarray?? Ans; A typical microarray experiment involves the hybridization of an mRNA molecule to the DNA template from which it is originated. Many DNA samples are used to construct an array. The amount of mRNA bound to each site on the array indicates the expression level of the various genes. This number may run in thousands. All the data is collected and a profile is generated for gene expression in the cell.

What is hybridization??? Ans:-The two samples are then mixed together and allowed to bind to the microarray slide. The process in which the cDNA molecules bind to the DNA probes on the slide is called hybridization. Following hybridization, the microarray is scanned to measure the expression of each gene printed on the slide. If the expression of a particular gene is higher in the experimental sample than in the reference sample, then the corresponding spot on the microarray appears red. But if the, if the expression in the experimental sample  is lower than in the reference sample, then the spot appears green. Finally, if there is equal expression in the two samples, then the spot appears yellow. The data gathered through microarrays can be used to create gene expression profiles, which show simultaneous changes in the expression of many genes in response to a particular condition or treatment.

ABC of Microarray technology & We the clinicians!!!  :- It essentially compare the differences if any, between   RNA prepared from suspected  diseased cells and RNA prepared from normal cells . I hope this will suffice. If one is thirsty to know details, well I am afraid she/ he will forget details of microarray technology   even I describe some basic aspects of microarray.

       Microarray technology is a powerful technique used to compare differences in gene expression between two mRNA samples. Comparing RNA prepared from diseased cells and RNA prepared from normal cells one will be able to  identify a   set of genes that play key roles in some diseases.

 Kinds of microarray testing –simplifying for the clinicians:-Microarray experiments can for the clinicians can  be categorized in three ways:A) Microarray Expression Analysis B) Microarray for Mutation Analysis C) Comparative Genomic Hybridization. Let us view all such procedures.

1. Microarray Expression Analysis: In this experimental setup, the cDNA derived from the mRNA of known genes is immobilized. The sample has genes from both the normal as well as the diseased tissues. Spots with more intensity are obtained for diseased tissue gene if the gene is over expressed in the diseased condition. This expression pattern is then compared to the expression pattern of a gene responsible for a disease.

2. Microarray for Mutation Analysis: For this analysis, the researchers use gDNA. The genes might differ from each other by as less as a single nucleotide base.

A single base difference between two sequences is known as Single Nucleotide Polymorphism (SNP) and detecting them is known as SNP detection.

3. Comparative Genomic Hybridization: It is used for the identification in the increase or decrease of the important chromosomal fragments harboring genes involved in a disease.

Applications of Microarrays

Gene Discovery: DNA Microarray technology helps in the identification of new genes, know about their functioning and expression levels under different conditions.

Disease Diagnosis: DNA Microarray technology helps researchers learn more about different diseases such as heart diseases, mental illness, infectious disease and especially the study of cancer. Until recently, different types of cancer have been classified on the basis of the organs in which the tumors develop. Now, with the evolution of microarray technology, it will be possible for the researchers to further classify the types of cancer on the basis of the patterns of gene activity in the tumor cells. This will tremendously help the pharmaceutical community to develop more effective drugs as the treatment strategies will be targeted directly to the specific type of cancer.

Drug Discovery: Microarray technology has extensive application in Pharmacogenomics. Pharmacogenomics is the study of correlations between therapeutic responses to drugs and the genetic profiles of the patients. Comparative analysis of the genes from a diseased and a normal cell will help the identification of the biochemical constitution of the proteins synthesized by the diseased genes. The researchers can use this information to synthesize drugs which combat with these proteins and reduce their effect.