User talk:AMF2718/sandbox

--- In the introductory paragraph, although the section is easily accessible for non-experts, the section is also extremely vague and does not do a very good job of grasping the key points of the page in a concise manner. For example, it could briefly mention different types of digital PCR or introduce the possible applications of this novel technique and then go into detail in the respective sections.

The PCR basics section can be renamed to the limitations of PCR and this section can be used to connect the limitations of traditional PCR to the advantages of digital PCR.

In the next section, more types of digital PCR can be mentioned along with double droplet PCR. In the section about double droplet PCR, the editors do an excellent job of summarizing the technique, but poorly elaborate on the advantages and disadvantages of this technique. The editors briefly add in the advantages, but they could also contrast it with the limitations of ddPCR as well as compare it to the advantages and disadvantages of the traditional PCR method.

In the following section about the dPCR working principle, it talks about a key advantage of digital PCR over traditional PCR, but this advantage should be highlighted and explicitly mentioned in order to emphasize the ingenuity of the dPCR technique.

The next section that talks about the technique's applications is not very detailed or developed at all. The editors briefly mention that this technique can be used to detect genetic-based disease, but gives no method or explanation of how this technique can be applied. The section then jumps to vaguely mention its connection to genetic prenatal diagnostics, but gives no examples on how. Lastly, the section highlights the technique's sensitivity and precision, but does not give an application of how these key advantages can be applied.

The development section of this page appears to be somewhat incoherent. For example, instead of mentioning every stepping stone to the technique it is known as today, a possible option to make this section more coherent would be to elucidate on the major key developments and take out the developments that do not hold much importance in the development of the technique it is known as today.

The last section titled "Comparison to Traditional PCR" seems to be redundant of other sections and can be eliminated entirely. This section primarily compares different types of PCR to ddPCR and thus, can be easily incorporated into the previous sections that emphasize advantages and disadvantages of the various PCR techniques.

All important terms and concepts are linked to their respective Wikipedia pages for further reference and the highlighted examples are appropriate in that they give non-experts further information on the subject that they might not understand. In addition, the content is unique and doesn't seem to duplicative of any other content already on Wikipedia.

The group did not add any figures to the page and there are no currently existing figures on the page.

The group also did not add any additional references (they are not listed compared to the original entry).

Overall, the draft can be improved by better organization of the advantages and limitations of both traditional PCR and dPCR. In addition, there should be more details on the applications portion of the page because briefly mentioning the applications to genetics does not give a very clear or full picture of how the advantages of this novel technique can be used. Lastly, the development section can be improved by taking out some points in the "timeline" that do not contribute much to the technique it is known as today and replacing that information by adding in more details about the points in the "timeline" that do have a significant impact upon the development of the technique. The draft still needs to include figures that could show the steps of dPCR visually or a visual that compares the advantages and disadvantages of traditional PCR and dPCR. Lastly, the draft needs to add an additional 5 sources, inclusive of non-journal sources.

BY SAMUEL KANG ---

 Introduction: The intro did a great job comparing traditional PCR against digital PCR, but it is too vague for anyone to understand. More explanations on how "PCR carries out one reaction per single sample..." is needed. That section is hard for anyone who is not 100% familiar with how PCR works to understand.  PCR basic I feel this section talks more about the limitation of PRC rather than the basic functions of PCR. It can definitely be revised to explain how PRC works or change the header to PRC limitations. Better yet, I feel this whole section is rather unnecessary as it describes the broad version of PCR rather than dPCR specifically.

Double Droplet PCR you guys never finished the last sentence of the first paragraph. Also, it would be a good idea if you guys explained how fluorescence-quencher probe and PCR mastermix works since they are listed as the main component of double droplet PCR.

More information can be added into this section as well. Since double droplet PCR is considered a type of dPCR, you guys can talk about how it differs from other dPCR, and how this type of dPCR is used in a more research applications.

Comparison of Traditional PCR One minor issue is that you guys never explained what qPCR is. A single sentence could be added to explain that to the readers.

In this section, you guys switched off between ddPCR and qPCR with ever new sentence making it rather confusing and difficult to follow. If a reader does not have full knowledge of PCR, they would have a hard time reading about the characteristics of ddPCR and how it compares with qPCR. A suggestion will be to talk about one aspect of ddPCR and then compare with qPCR in the same sentence. For instance, :ddPCR makes discrete digital measurement... whereas qPCR makes..."

Overall, this topic needs more information and organization. The paragraphs are too broad and can potentially turn off readers from making any attempts of understanding how ddPCR works. I also believe the "comparison of traditional" is unnecessary at this moment. This is because there should be more topics and concepts on how ddPCR works over how it compares againsts/with traditional PCR. The wiki page also failed to mention the various applications of ddPCR, which I believe will only make people more interested in traditional PCR. Lastly, there is enough information on traditional PCR on its own wiki page, so I think it is redundant to list them here.

--XIANG WU — Preceding unsigned comment added by 75.114.205.120 (talk) 01:15, 20 October 2016 (UTC)

--- The introduction is accessible and captivating for non-experts. This section could be improved by clarifying the term “clonal” in the last sentence. The contents of the introduction justify its length.

The PCR Basics section provided a brief overview of PCR. The first sentence in this section is duplicative of information about PCR already on Wikipedia. The section also discusses limitations of PCR. The limitations can be moved to the Comparison to Traditional PCR section for better organization.

Currently, there is only one type of dPCR, double-digital PCR, under the Types section, and the editors could further expand upon the various types of digital PCR. Also, the second paragraph explaining the benefits of dPCR does not flow well within this section and could be moved to Comparison to Traditional PCR section to compare with traditional PCR. Inline citation should be added to this section.

The dPCR Working Principle section explains how dPCR works. This section can be improved with inline citations. Additionally, the page will flow better if this section is placed after PCR Basics section and before Types section. A figure could be added in this section to help visualize the process of dPCR.

The Application section mentions short examples of ddPCR applications such as identifying alleles in developed heterogenous tumors and genetic prenatal diagnostics, but does not include specific details about those examples. The Application section also needs inline citations. Some important concepts are not linked to their respective Wikipedia pages for further reference. Examples include heterogenous tumor and microRNA.

The Development section discusses the origins of dPCR and improvements since conception. This section should primarily focus on dPCR development rather than applications. Some useful applications are discussed such as in surveying for cancer. The last paragraph of this section further explains the applications of dPCR, which can be moved to the Application section.

The Comparison to Traditional PCR directly compares ddPCR to qPCR, providing valuable insight. Limitations of PCR discussed in PCR Basics can be moved to this section for organization. qPCR should be linked to its respective Wikipedia page. Inline citation is needed as well. Limitations of dPCR can be included in this section.

The MIQE (Minimum Information for Publication of Quantitative Digital PCR Experiments) section briefly describes the existence of guidelines for best practices in using dPCR. The contents of this section justify its length.

The editors did not add any figures to supplement the text. Figures showing double-digital PCR and/or the general process of dPCR would be beneficial.

The editors did not add new references. All additional information added to the page should be supported with references, and references should be inclusive of non-journals sources.

-James Rhee Rnagger (talk) 02:11, 20 October 2016 (UTC)

dPCR Peer Review
As noted by Sam, this draft lacks many of the components that were required for the assignment. There was no additional image and no added citations. The original page lacks any images and thus, the addition of an images would greatly aid the general public in understanding much of the information presented. Simply having an image makes a wiki page seem more accessible and user-friendly. There is also a problem that no citations were added to support the paragraphs of information that were written on the subject matter. Without citations, it seems as if the information that is presented is being plagiarized. This information must have come from somewhere and it is extremely important to give credit where it is due. On another point, the lack of citations makes it difficult to judge the biases of the information presented. Adding more sources bolsters the credibility of the information and makes it not seem as if the information is being pulled out of thin air. Please add images and citations to this page.

Aside from improvements that can be made by following the class assignment, there are a few other points that could be improved upon. It must be recognized that the wikipage that is being edited is first and foremost about digital PCR (dPCR). The massive addition of information regarding ddPCR overwhelms the initial intent of the page. I believe that the best thing would be to simply create a new page titled "Double droplet PCR" and move all of the information added about ddPCR to the new page. Another (less satisfactory) route that can be taken is to delete the header titled "Types" and simply have a header titled "Double droplet PCR". The information in the "applications" section and "comparison to traditional PCR" should be added to this new section because they focus on ddPCR instead of dPCR. These headers should rather include information about dPCR, its applications and its comparison to traditional PCR. However, this does not eliminate the issue of the page being taken over by information on ddPCR.

One point that Xiang mentioned that I agree with is the lack of a simple description of qPCR and the confusion that occurs when the sentences continually interchange between ddPCR and qPCR. This needs to be formed into a coherent narrative that does not jump around.

In conclusion, it would be best if the information on ddPCR is moved to a new, separate page. Visual aids should be included in the page to grasp the attention of readers. Finally, citations should be added to verify that the information is indeed valid. Magnus Ma (talk) 02:26, 20 October 2016 (UTC)

Article Edit - MSIYER
I felt that the article edit adequately covered the basics for a non-science user but could use significant improvements on certain areas. The introduction did provide a basic, easy to understand description of dPCR and its distinction from conventional PCR. However, I would either expand on the error prone statement or leave it out to discuss later in the page below (inexperienced users are obviously not going to be very good at a burgeoning research technique, not very informative). The explanation of how dPCR separates a sample into multiple partitions is good. I also think that it would be a good idea to include a short history of how dPCR came (when it was discovered/proposed etc.) by pulling information from your “Development” subheading. In the PCR basics, you do not have to explain the methodology of regular PCR, because that can be hyperlinked to the existent article on PCR. Instead, you can combine the theoretical inadequacies of regular PCR to the “dPCR working principle” subheading.

Double droplet PCR was explained well, but the explanation of how the binary representation of fluorescence improves PCR interpretation could be expanded on. I realize that this was touched on in “dPCR working principle” but I would rearrange the order of the subheadings. Put the working principle first, followed by the different types. I would also explain more about the advantages and disadvantages and how ddPCR proves to be different than other subcategories of digital PCR. I’m assuming from the fact that only one type of dPCR was expanded on, that there are not too many other variations. If there are, I would add more subheadings that address more types of dPCR instead of just ddPCR. If ddPCR is the only existent form of dPCR, is it possible to make the entire article on just ddPCR alone?

The applications tab is pretty sparse and seems to mirror/overlap a lot of the material already covered in “Development”. I would either combine the two topics under one heading and explain each application and provide proper citation.

There are no images in the article revision and could benefit from the use of a graphic representing the dPCR methodology or an example graph of PCR fluorescence data.

Overall, I’m not seeing too many distinct edits from the already existing article. However, the existing article has some noticeable holes that are worth patching (incomplete citations, writing from a biased point of view, etc.). Explanation of ddPCR was very good, but I would avoid using “Types” unless there are other forms of dPCR that are in the works and can be compared to ddPCR. I would remember to review the references already present in the article and add an image to make the methodology of dPCR or ddPCR easy to visualize.

Also, I think the user Jytdog replied to your initial comments with some recommendations. Could you perhaps detail the information of ddPCR vs emulsion PCR, etc.?

Msiyer (talk) 13:03, 20 October 2016 (UTC)Mayuresh Iyer (Msiyer)

Additional comments from the librarians
I second Magnus_Ma's suggestion that something needs to be done with the double droplet PCR section: having a section in the ToC with a single subsection under it is not good practice. Either rename the section, and make it clear how ddPCR relates to dPCR generally, or add more variant dPCR types in that section. Since the "dPCR working principle" section has already been designated by the community as needing additional citations, you should prioritize adding those citations as part of your revision. You might also consider adding the link to the open-source MIQE documentation (http://www.rdml.org/miqe.php) as a reference in the final section. Finally, make sure that you've linked your technical terms to the Wikipedia articles on those terms where they exist. ScottMLibrary (talk) 15:39, 24 October 2016 (UTC)