Posted: September 20th, 2022

Chromosomal microarray

Computer Sciences and Information Technology
Topic:
Chromosomal microarray
Read the attached paper and answer the 3 questions

1. What is AOH? How can it be detected with CMA, and what does the presence of AOH indicate (what is the potential clinical significance of AOH)?

2. In Figure 5, why were more AOH’s detected using affymetrix platform than other platforms? Does the variation in the number of AOH detected by the different platforms affect the main conclusion of this paper? Why or why not?

3. What are the different parameters the authors used to determine the quality of DNA isolated from blood vs saliva? What do these parameters indicate?
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Chromosomal Microarray
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1. What is AOH? How can it be detected with CMA, and what does the presence of AOH indicate (what is the potential clinical significance of AOH)?
Absence of heterozygosity (AOH) is indicative of uniparental disomy or identity by descent, which can be detected through Chromosomal Microarray (CMA) platforms using SNP genotyping.in the research experiment, Agilent CMA testing would be done as per manufacturer’s instructions, and the images would be extracted through the Feature Extraction Software and the Agilent Genomic Workbench software version 7.0 for analyzing data. AOH would be detected through defined by a minimum of 10 probes and >2 Mb.in the blood and saliva samples. The research indicated that the detection of AOH in saliva DNA is still warranted, especially in the clinically significant AOH cases. The presence of AOH is of potential clinical significance because it shows the loss of a parent’s contribution to the cell, which could have arisen from deletion, gene conversion, loss of chromosome, or mitotic recombination.
2. In Figure 5, why were more AOH’s detected using the Affymetrix platform than other platforms? Does the variation in the number of AOH detected by the different platforms affect this paper’s main conclusion? Why or why not?
More AOH’s were detected in the Affymetrix platform because the platform has been based on SNP genotyping and higher resolution, thus demonstrating more consistency in the paired specimens of blood and saliva. The research indicated that the detection of AOH was limited due to a limited number of AOH variations in the specimens. The research indicated that they could not accurately assess the direct concordance between the paired DNA and saliva DNA. The paper’s main conclusion was strong support towards using saliva DNA as a reliable alternative for detecting clinical copy number aberrations; hence, it has also been informed by the variation of detecting AOH in different platforms. Notably, the research points out that it is essential to use additional samples that have clinically significant copy-neutral AOH is required for adequate detection of AOH.
3. What are the different parameters the authors used to determine the quality of DNA isolated from blood vs. saliva? What do these parameters indicate?
● The UV spectrophotometry absorbance was used to analyze the quality of the twenty samples of saliva and blood, each of which had its bacterial content. There were no significant differences in the blood and saliva samples as they demonstrated A260/280 and A260/230 ratios. This demonstrated that the saliva DNA was comparable to blood DNA.
● The quantity of Microbial DNA in which the median percentage of bacterial DNA in human saliva collected was approximately 12%. Through the CMA platforms experiments, the research would find that DNA collected high bacterial content in saliva would produce quality CMA metrics comparable to blood DNA.

References
Reiner, J., Karger, L., Cohen, N., Mehta, L., Edelmann, L., & Scott, S. A. (2017). Chromosomal microarray detection of constitutional copy number variation using saliva DNA. The Journal of Molecular Diagnostics, 19(3), 397-403.

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