Question

are studied) Compare and contrast DNA microarrays (DNA chips) to RNA sequencing (RNA-Seq). .

Answer 1

DNA chips is also known as DNA microarray analysis. In this technique microscopic DNA spots are attached to a solid surface and their collection together is called as DNA microarray analysis.

Aim: It is used to study mutations in a gene. It can be used in clinical diagnosis of a disease.

Method: At first the DNA sample containing the gene of interest is collected along with a control DNA sample without the gene of interest. The double stranded DNA sample is first separated to convert it into a single stranded DNA. Now this single stranded DNA is reduced in length and a fluorescent dye is added to this fragment. Usually a green dye is used for the DNA sample to be tested. Whereas, the controlled DNA sample is labelled with a red colour dye. The microarray chip contains synthetic DNA sequences and now these labelled DNA are inserted into the DNA chip and allowed to hybridise.

interpretation: The identification of the gene mutation is done as follows, if there is mutation of the gene of interest then sample DNA will bind to the sequences of mutated gene of interest on the microarray chip. And if there is no mutation of gene of interest then the the DNA sample will bind to the sequences of normal gene, that is the gene without mutation.

RNA sequencing is a method used to study the sequences of RNA present in a sample and also quantify the RNA present in the sample.It basically studies the transcriptome in gene expression.

Aim: to identify gene expression as well as gene fusion etc

Method: At first the RNA is converted into cDNA fragments. They are sequenced using adaptors of NGS workflow. This is followed by amplification of fragments. As a result of this, short sequences reads are produced.

Interpretation: These reads produced are aligned against the genome sequence of interest and computational technology is used for the same. The expression level of the transcripts are analysed using statistical tools

Contrast:

DNA hybridisation method requires specific probe whereas RNA sequencing depends on the detection of transcripts and does not require specific probe or genome for analysis. There is an issue of cross hybridisation in DNA microarray analysis but there is no such issue incase of RNA sequencing. DNA microarray analysis can be used to study only mutation in a gene and it is not a quantitative method.RNA sequencing on the other hand is a quantitative method and can determine the quantity of RNA present in the sample. The RNA sequencing method is more sensitive and accurate as compared to DNA microarray analysis. Cost of RNA sequencing is much cheaper and it has very low background noise.