User:Friedchickenprincess/Methylation specific oligonucleotide microarray

Summary: For this article, I aim to expand the scope of sources in which the article is based in. I want to improve and add to the information about how it works, as well as fine-tuning details: explaining what amplicons are, why and how the oligonucleotide probes bind to unmethylated and methylated CpG sites, and so on. Additionally, I want to expand on its impact in cancer research. I will find more medical references to show its use (or possible use) in the cancer research field. Furthermore, I want to extend this into how it could benefit epigenetic research as a whole.

'''This is not a bad idea. Please starting getting used to linking to things to make them easier to find. See how I have altered your "For this article" so that it is hotlinked to the article. Just use the link tool on the control bar at the top to create such things.'''

'''This is definately a viable idea. Above you say that you will find more references. But you are supposed to provide at least one such review reference here. So please find a recent review and add it. Also don't settle for one source. Hunt for more in Pubmed. Also, for this one you should read company website that sell such kits. Medical science always involves expensive/lucrative kits for doing the science. Companies will explain stuff to you on their web sites. You can't let the article become an ad but you can learn for company sites as well. -- Dr. Atkinson'''

Summary 2 (after comment above):

Firstly, I want to clarify and specify steps in the methylation specific oligonucleotide (MSO) microarray. Below I list the specific edits I intend to put in:

- after first paragraph, add that it can analyze methylation patterns of many CpG sites along many genes concurrently - in some MSO microarrays, it can take 12 samples at a time; "with 27,578 DNA methylation measurements per sample, there are 330,936 possible measurements per experiment"

--> this shows how it is a very effective way of examining CpG islands across the genome and many genes - clarify that the presence of bisulfite deaminates unmethylated cytosines into uracil

- after "converted to thymine," add: "This transformation allows for discrimination of the daughter strands in the process of annealing and hybridization"

- the probes are used as a "solid support" for oligonucleotides "- the 3' terminus of a oligonucleotide probe is cut right before the CpG sites, and then 'arrayed on glass slides by attaching to the surface via their 5' ends'"Furthermore, I would like to add the reasons in which MSO microarray is useful in epigenetic research compared to other methods:

- Other methods restrict research to "sequences whose motifs are restricted;" however, in MSO microarray, its employment of bisulfite can analyze more CpG sites

- It can get a lot of measurements from small samples

Upon researching for this technique, I came across the website of Illumina Inc, which produces many genome-analyzing programs and products. They created the Infinium HumanMethylation27 BeadChip, which utilizes MSO microarray as well, but instead of probes used beads. I learned the following, which I believe would be useful in understanding this technique:

- Oligonucleotide probes use allele-specific primer annealing to hybridize to specific CpG loci: either the methylated (C) or unmethylated (T)

This answers my question of why and how the oligonucleotide probes bind to CpG sites.

Additionally, I found extensive information about MSO microarray's implications for cancer research.

- A CpG dinucleotide that has an abnormally methylated cytosine is common in cancer