A precise understanding of the gene expression profiles of individual tumors is

Question

A precise understanding of the gene expression profiles of individual tumors is critical to understanding cancer treatment and prognosis. In LGS we discussed several techniques that can be used in the clinic to compare various aspects of the control of gene expression between normal cells/tissue and tumor cells/tissue. Technologies used in clinical oncology that we did not discuss in LGS include microarray analysis and next generation sequencing.

Microarray analysis is a method that allows researchers to examine the expression level of a very large number of genes at one time, and can be used to compare the expression levels of nearly every gene in the human genome between tumor tissue and normal tissue in a single experiment. Microarray analysis costs ~$1,000 per sample, and results in a knowledge of all of the genes whose expression has changed in a particular patient’s tumor.

Next generation sequencing (NGS) technology allows the sequence of the entire human genome from one cell culture or tissue to be determined in roughly one day. NGS costs ~$10,000 per sample, and it results in a knowledge of every mutation that is present in a particular patient’s tumor.

Though we did not discuss microarray analysis or NGS, the descriptions above give you all the information you need in order to compare and contrast the clinical utility of various gene expression profiling technologies. In your answer, include the following: (A) Compare and contrast the information that can be generated by Bisulfite Sequencing, Chromatin IP (ChIP), microarray analysis, and NGS; (B) describe the strengths and limitations of microarray analysis relative to NGS, and those of NGS relative to microarray analysis; (C) state whether you would expect microarray analysis or NGS to be more powerful for understanding gene expression profiles, and why you came to this conclusion.

Explanation / Answer

A) Comparison and contrast on information generated by Bisulphite sequencing, ChiP, Microarray analysis and NGS.

Bisulphite sequencing uses bisulphite to treat strands of DNA, specifically methylated cytosine residues. The methylated cytosine will induce single nucleotide polymorphisms but the un-methylated cytosines get converted to uracil. In case of tumor studies, hyper or hypomethylation may bring about decreased stability of gene or also may result in loss of function. ChiP is mainly used to understand the interaction of protien and DNA.It helps to identify areas in the genome where histone binding occurs, thereby understanding if any modifications in binding has occured. Microarray and NGS methods are high content sequencing methods that allows screening of many gene segments in a short time. It also gives a method to profile different gene expression pattern and screen may drugs and biologics that can inhibit the expression.

B)   Strengths and limitations of microarray analysis Vs NGS

Strengths:

Limitation:

C) Microarray analysis is more powerful as it helps to understand gene expression profiles of the entire genome. This is because this technique deciphers the expression levels of each of the genes. It is also powerful technique as it helps to screen any drugs that can inhibit the expression of the gene.

Related Questions

Navigate

• Browse (All)
• Browse A
• Subjects

Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.