Talk:Digital polymerase chain reaction

Subhead change requested: Droplet Digital PCR

Please replace the subhead

Digital-Droplet PCR

with the subhead

Droplet Digital PCR

The reason for this change is that the technology is called droplet digital PCR, as cited in reference 4, which is: http://www.bio-rad.com/en-us/applications-technologies/droplet-digital-pcr-ddpcr-technology

Cg.wikawikawow (talk) 15:18, 2 December 2016 (UTC)Cg.wikawikawow

 Already done Another editor seems to have performed this. st170e 23:34, 31 December 2016 (UTC)

question

Is this the same as emulsion PCR or are they distinct techniques? --Dan|^(talk) 14:07, 22 January 2009 (UTC)

Answer: emulsion PCR (ePCR) is the method for amplifying each template molecule separately. It is used as a first step in high throughput sequencing and also to avoid crossproducts when the DNA template is an heterogeneous mix. Digital PCR uses ePCR and then measures the ratio of positive droplets. — Preceding unsigned comment added by 186.136.104.137 (talk) 17:24, 4 December 2014 (UTC)

Neutrality and Additional Citations

There are several issues with the neutrality of this piece and with some unsubstantiated claims made in the article. I have specifically flagged passages that I thought were in need of adjusting. The last section of this article makes subjective and uncited claims about a particular brand of Digital PCR machine:

• "The QX100 Droplet Digital PCR system is the only instrument currently that can quantify 96 samples in under 4 hours.[citation needed]"
• "Droplet Digital PCR (ddPCR) also has a greater dynamic range than Fluidigm and OpenArray.[citation needed]"
• "No other method provides this information with such accuracy and precision.[neutrality is disputed]."
• "Digital PCR has been shown to be a promising surveillance tool… the human genome. [citation needed]"

These particular sentences (and others flagged and explained in the main text) should be specifically made more neutral and/or linked to valid references. Due to these passages, I am nominating this post to be checked for its neutrality.Tevyeguy (talk) 22:03, 7 June 2012 (UTC)

In exploring the neutrality of the article, we noticed this review already on the page. In regards to at least the third point and possibly the fourth, we might be able to support the claims, as the authors of the review have no immediately visible connection to Dr. Christopher M. Hindson (the pioneer of the technique) or Biorad (the company making money of it). This may or may not rest concerns about neutrality entirely, but it might be able to help. AMF2718 (talk) 23:15, 2 November 2016 (UTC)

I spotted one neutrality issue raised in the article as it stands currently. That was the statement that the technique (not a particular brand) was more accurate and precise. This has been well documented, measured and peer reviewed in the article I added a reference for Pinheiro et al, 2012. I worked for Bio-Rad and specialized in digital PCR for 5 years (AntoBeck (talk) 05:48, 5 July 2018 (UTC)).

Student comment 1

Currently, the wikipedia page is sparse and could benefit from more citations. We will want to incorporate the work of Hindson et. al., which focuses on a new version of the ddPCR technique. We will focus on a specific version of emulsion PCR, wherein 20,000 oil droplets are made to run PCR individually and will thoroughly analyze the positive and negative aspects of this technique. We will also incorporate the aspect of endpoint versus real-time methods and why ddPCR is considered “digital.” Proposed edits will be made here.— Preceding unsigned comment added by AMF2718 (talk • contribs) 14:47, 13 October 2016 (UTC)

I can't imagine anyone is going to be interested in reviewing this entire article and that entire proposed replacement and figuring out how they are different much less if the changes are improvements. Proposing a whole rewrite is rarely successful in WP. Better for everyone if you go bit by bit.

If by "HIndson et al" you mean PMID 22122760 that is a primary source; you need a separate source - ideally a literature review or book, that characterizes the method there and compares it with others and puts it in the context of other methods. You can't do that yourself, as that is WP:OR.

The current article is very bad and does need improvement. It needs to be written in language that is less WP:TECHNICAL, it needs to be contextualzeed, and it needs much better sourcing. Jytdog (talk) 17:51, 13 October 2016 (UTC)

Adding other dPCR methods (i.e.: BEAMing)

I think this article would benefit from listing other dPCR methods/options that build off the basic scientific principles section. Specifically, I would like to propose the addition of a short section on BEAMing, which is another emulsion dPCR method, linking back to the main BEAMing page. This is the current draft of the blurb:

BEAMing, or beads, emulsion, amplification, magnetics, is a digital PCR method that combines emulsion PCR and flow cytometry to identify and quantify somatic mutations in DNA. BEAMing creates hundreds of millions of water-in-oil emulsions that serve to compartmentalize individual PCR reactions, enabling a massively parallel process. A bead contained within each droplet is fluorescently labeled and discriminated as mutant or wild-type using a flow cytometer. BEAMing dPCR then provides a digital readout of the quantity of mutant tumor DNA and has been shown to be highly sensitive, detecting rare mutant templates at ratios greater than 1:10,000 (0.001% sensitivity). [Diehl, PNAS 2005 and Diaz & Bardelli review article in 2014]

The article has been flagged to be checked for neutrality and I think it would benefit from including other dPCR methods to help that. Ashley at Sysmex Inostics (talk) 20:27, 2 November 2017 (UTC)

New companies and new instruments I have added 2 new companies and changed a lot of the partition number to read "approximately" because those numbers are never exactly attained. I used to work in the digital PCR industry for Bio-Rad for 5 years. (AntoBeck (talk) 05:53, 5 July 2018 (UTC))

Maintenance template removal requested: History Section

Please remove the advert template form the "History" section.

The reason for this change is that the History section has been rewritten to remove promotional content and to rely on neutral sources.

Cglife.bmarcus (talk) 20:22, 22 July 2019 (UTC)

Reply 23-JUL-2019

  Edit request implemented  

1. The rationale for why this template was originally placed in August of 2013 was not described at the time, and the editor who placed it has not been active since 2017.
2. The COI editor is reminded that new posts on talk pages are always placed at the bottom of the page.
3. The COI editor is also reminded that individuals with a conflict of interest are strongly advised not to directly edit the article. Please see Wikipedia:Conflict of interest for more information. The COI editor is urged to request changes here on the talk page for independent editors to review rather than to directly edit pages themselves.

Regards,  Spintendo  08:21, 23 July 2019 (UTC)

Notes

Maintenance template removal requested: Applications Section

Please remove the advert template form the "Applications" section.

The reason for this change is that the Applications section has been rewritten to remove promotional content and to rely on neutral sources. You will see that I am paid to represent Bio-Rad, but I removed sources written by them and their employees. I know that editors with a COI are urged not to edit Wikipedia themselves, but I hope my edits appear neutral and in accordance with Wikipedia's rules and guidelines. If you have any questions, please refer to my talk page.

Cglife.bmarcus (talk) 17:02, 23 July 2019 (UTC)

Reply 23-JUL-2019

  Please consult assigning editor  

• It is recommended that, as a courtesy, you first try asking the editor who assigned the template — in this case DadOfBeanAndBug — in order to find out from them if it can be removed. Since they placed the template, they are in the best position to know whether or not the issues which caused its placement have been corrected. You may contact them by placing a new message on their talk page. In the unlikely event that you do not hear back from them after a reasonable amount of time, please reopen this request by altering the {{request edit}} template's answer parameter to read from |ans=yes to |ans=no.
  Regards,  Spintendo  18:06, 23 July 2019 (UTC)

Notes

Reply 8-AUG-2019

On July 23, 2019, I requested to the user who initially added the "advert" template to the Applications section, DadOfBeanAndBug, that the template be removed, but this user has not responded to me. Therefore, I kindly request that another user please remove the template.

If you have any questions, please refer to my talk page.

Cglife.bmarcus (talk) 3:10, 8 August 2019 (UTC)

Reply 8-AUG-2019

  Template removed    Spintendo  15:43, 8 August 2019 (UTC)

Reply 25-AUG-2019

Cglife.bmarcus, I apologize, I haven't checked my messages in a while and didn't see your edit request. The rewritten Applications section looks 100% better, and I agree (retroactively) with removing the advert template. Thanks a lot!

DadOfBeanAndBug (talk) 18:46, 25 August 2019 (UTC)

Reply 26-AUG-2019

User:DadOfBeanAndBug, no worries! I appreciate your response, even if it's a tad late ;-). I'm glad I was able to make the sound less biased in more in line with Wikipedia's guidelines.

Cglife.bmarcus (talk) 13:33, 26 August 2019 (UTC)

Maintenance template removal requested: Applications Section on the Digital Polymerase Chain Reaction Page

Spintendo thank you for removing the neutrality template at the top of the article. Could you please remove the advert template in the "Applications" section, now that it is moot? Thank you! Cglife.bmarcus (talk) 15:49, 19 August 2019 (UTC)

Reply 20-AUG-2019

  Edit request implemented  

1. The advert template has been removed.
2. A COI maintenance template has been added to the article. The large amount of in-depth information about the supposed effectiveness of digital polymerase chain reaction technology, much of it added by an editor with a COI (portions of which were placed without independent review) suggests that this is an appropriate template to place in the article. Readers should be aware that the content which has been added has been done so by an editor with a disclosed connection to the industry which manufactures and uses much of the technology described herein.
3. The COI editor is free to garner other editor opinions on the appropriateness of the placement of this template.

Regards,  Spintendo  22:12, 20 August 2019 (UTC)

28-AUG-2019

Spintendo, Thank you for your concern about maintaining neutrality and avoiding bias on this page. I share the same concern about ensuring Wikipedia remains a neutral source of information for the world. I rewrote two sections of this article that had templates on them suggesting that they were written like advertisements. My goal was to make these sections neutral, and I feel my edits were validated by your removal of these templates. You'll notice that I heavily sourced all the statements regarding dPCR's applications and capabilities, I did not make any unsubstantiated claims about its benefits, and I did not include links to the websites of any companies that have a financial stake in the subject nor any articles written by employees of these companies. Despite my relationship to Bio-Rad, I included information about their competitors in the "History" section. I welcome you or other editors to discuss the validity of the COI template with me on my talk page.

User:cglife.bmarcus (talk) 16:02, 28 August 2019 (UTC)

For the reasons mentioned above, I kindly request that someone remove the COI template from this article. Thank you, Cglife.bmarcus (talk) 19:34, 11 September 2019 (UTC)

I appreciate your response to the template, and I understand your feelings about the content you've added to the article. I don't believe that there was a conscious intent to add items that were promotional. However, a conflict of interest — where your role as a Wikipedia editor comes into conflict with your external role as representative of CG Life — can have deleterious effects on an article which you may not be conscious of. It's for this reason that independent review of items added to the article is a necessity. Since this independent review did not take place on several occassions, the template is warranted. You must understand that it's simply not enough to take your word for it that the items you've added are not promotional, because an editor's "word" may be compromised by their conflict of interest. That conflict of interest has a way of obfuscating an editor's judgement — especially when that editor derives income from having their edits implemented. In order to have the template removed, it would be best if the items which were added by you were submitted for a third party to consider. This would go a long way towards ensuring that the article is free from promotional content. Regards,  Spintendo  06:41, 12 September 2019 (UTC)

Spintendo, Do you have any recommendations for next steps? Are there channels through which I can ethically draw the attention of an independent editor to this page and review it for neutrality? Thank you, Cglife.bmarcus (talk) 14:08, 18 September 2019 (UTC)

ddPCR and UIC reference

In the first sentence of this Article, should this method also be termed "ddPCR" to indicate "digital droplet"? Here is a preprint from UIC: https://www.biorxiv.org/content/10.1101/2020.06.18.159434v1.full Charles Juvon (talk) 12:42, 22 August 2020 (UTC)

Absolute measurement or not?

The subsection "Absolute quantification" is in direct contrast to the text on the principles, where it says: "Different from many peoples's belief that dPCR provides absolute quantification, digital PCR uses statistical power to provide relative quantification." plus example. This does not make sense to a reader unless either the subsection "Absolute quantification" further explains under what conditions or with which limitations absolute quantification by dPCR is possible, or the claim that absolute quantification is not possible is removed or edited. — Preceding unsigned comment added by 134.245.221.67 (talk) 14:30, 17 March 2021 (UTC)

Yes, I was about to write the same thing. This looks like a contradiction in the article.

Marchino61 (talk) 01:13, 19 May 2021 (UTC)

Figure 2 title has a typo

Concetration -> Concentration 61.16.68.170 (talk) 02:11, 21 June 2023 (UTC)