You are studying a type of lung cancer. You obtain normal and tumor tissue from
ID: 180774 • Letter: Y
Question
You are studying a type of lung cancer. You obtain normal and tumor tissue from a patient. You perform a comparative genome hybridization (CGH) array analysis. DNA derived from normal tissue is labeled with a red fluorescent tag. DNA derived from tumor tissue is labeled with green fluorescent tag. Results from a small section of the microarray grid are shown. Y = yellow spot, G = green spot, R = red spot You wish to identify potential oncogenes. Which of these spots would you choose to study further for oncogenic properties? Explain your answer. Apart from the CGH array you also perform microarray expression analysis. You label the samples similar to the CGH array analysis. (cDNA derived from normal tissue - red fluorescent tag, cDNA derived from tumor tissue - green fluorescent tag). What color would you expect in the expression array for spots containing sequences for genes in your potential list of oncogenes based on the CGH array, if your prediction was correct? Explain your answer.Explanation / Answer
Comparative Genome Hybridization (CGH) is a technique used to perform genome-wide screening of chromosomal abnormalities like copy number variation. This is basically to detect any chromosomal gain or loss.
To detect such abnormalities in cancerous tissue, a normal and tumour tissue is labelled differently. In this case, normal tissue is labelled with red fluorescent tag and tumour tissue with green fluorescent tag. These samples are then mixed (1:1) and hybridized to microarray chip. After scanning microarray chip if we obtain equal intensity of red and green signal i.e. yellow there is no change in that chromosomal region. If we obtain red and green signal there is potential loss and gain of chromosomal segment respectively. If there is loss of DNA in tumour tissue more amount of normal sample binds to nucleotide strands on microarray giving red signal. If there is gain of DNA in tumour tissue more amount of this binds to array giving green signal.
Answer to question 1: We would choose red and green spots to study further for oncogenic properties.
If we do expression analysis of these potential oncogenes we would obtain following results.
For microarray expression analysis RNA is extracted from both normal and tumour tissue. This RNA is converted into cDNA. cDNA from normal tissue is labelled with red fluorescent tag and that from tumour tissue is labelled with green fluorescent tag. When this samples are hybridized onto chip and scanned following results would be obtained.
In CGH array, chromosomal regions which gave red signal and possibly had loss of DNA in tumour tissue would give red signal in expression analysis because genes will not be expressed in the regions which had DNA loss in tumour tissue. Hence we would get red signal mostly from the cDNA of normal tissue.
In CGH array, chromosomal regions which gave green signal and possibly had gain in DNA in tumour tissue would give green signal in expression analysis because of DNA gain and more copies of genes in tumour tissue. Hence we would get green signal mostly from the cDNA of tumour tissue.
Answer for question 2: Signals colours will remain same and will be interpreted as explained above.
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