Talk:Frameshift mutation

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"A frameshift mutation will in general cause the reading of the codons after the mutation to code for different amino acids, but there may be exceptions resulting from the redundancy in the genetic code. Furthermore, the stop codon ("UAA", "UGA" or "UAG") in the original sequence will not be read, and a stop codon could result at an earlier or later site. The protein being created could be abnormally short or abnormally long, and will most likely not be functional."

The "there may be exception resulting for the redundancy in the genetic code" is quite wrong. The protection of codon reading through redundancy is only present in point mutations not frame shift mutations. For example if you look at the article titled DNA Codon Table a +1 frameshift would only preserve Proline and Glycine. When you add on the complexities involved in protein folding one also has to consider that without Cystine disulfide bonds would be unable to form correctly. Bottom line is that one would be more than hard pressed to find a frameshift mutation with no effect.

Daviwrng (talk) 22:20, 13 July 2011 (UTC)[reply]

As stated above, this Wikipedia page is subject for an assignment in 410.602 Molecular Biology, Spring, 2013, at JHU. Group 82G will be working on this article. Group 82G selected frameshift mutation because this topic has limited information and few references. There are more key points, or concepts that will help develop this article from a Stub status. To improve this article we are looking to broaden the basic ideas already highlighted. We would like to add in information regarding the formation of frameshift mutations and how they effect the reading frame/proteins. We would also like to look into the mechanism of the mutation, i.e. genetic or environmental causes, and also how it differs from other point mutations. From there we would like to expand into research on the cause of frame mutations. This will lead into the clinical relevancy of frame mutations, such as role in disease. Finally we would like to talk about frameshift mutations as a positive factor in dealing with improving treatments, and the role frameshift mutations play/have played in evolution, i.e. nylonase.DougCovert (talk) 19:00, 13 March 2013 (UTC)[reply]

Greetings! I was assigned to do the first peer-review of frameshift mutation. Fortunately, my team, 82D, also chooses an article with a topic of missense mutation that is a closely related to frameshift mutation. I will read over a few times with each different focuses, including wiki suitable format and style, overall balance in the content, references and their accuracy, and depth of each section. /Mhk5600 (talk) 21:59, 7 April 2013 (UTC)[reply]

• Wiki suitable format and style

At a glance, this page looks great. Overall partitions among sections are well planned. The following note may be too extreme to say. It is about number of paragraphs in the lead section. It has five paragraphs. While Wikipedia:Manual_of_Style said it is not an absolute rule, but a general guideline, 5 paragraphs for 2273 characters long of the lead section are questionable. Aren’t 5 paragraphs able to be reduced into 1 or 2 paragraphs? It is one of things to think about during Unit 11-12.

The lead section also contains disease specific frame mutation information. They are Tay-Sachs disease, CCR5 HIV, and hypercholesterolemia. How about reduce them into one sentence, like “A frame mutation is responsible for genetic diseases, Tay-Sachs disease, the disabling of the CCR5 HIV receptor, and hypercholesterolemia. Please see the Diseases-Research section in this article for further information.” I see a typo, “indicatee” in Genetic and Environment section.

• References and their accuracy

Reference links that are pointing to the internal Wikipedia and external weblink are all valid and working. I suggest creating a link with in a group of words. For instance, the first sentence in the lead section has “a genetic mutation”. There are 2 separate links that are pointing “genetic” and “mutation”. I assume that authors wants to treat “a genetic mutation” in one meaning, not combining of “genetic” and “mutation”.

In Transcription and translation section, I read, “... aminoacyl-tRNA binding to the start codon (AUG)...” AUG has an internal link to the article, start codon. I think “start codon” needs to have an internal link to the article, start codon, not “AUG”. The same question goes to “stop codon”, not “(UAG, UGA or UAA)”

One of figures that used in this article may not be able to use. It is about ‘Example of amino acid changes in frameshift mutation”. From a description of this figure, “This file is missing evidence of permission...the image will be deleted after Wednesday, 17 April 2013...” I am sure you can find other excellent quality of figures from other websites. From my quick search, there is other good one from NIH webpage. Please double check a permission of each figure, when you get a new figure from outside, just in case. Overall, this is very good work. I am only able to check links, if such links do exist. I cannot read all of listed references to crosscheck with articles at this time. I hope 82G team would do that diligently.

• Depth of each section and overall

Overall depth of content is suitable, except Disease-Research section. I am having a hard to follow a flow of content. It may be due to either a nature of contend or lack of my knowledge in each of those topics. If a public who want to know about what a frameshift mutation is would read this wiki article, I am not sure they could understand this kind of detail and technical. It is purely my opinion.

Thanks for having me on your article review. Happy editing! /Mhk5600 (talk) 03:59, 12 April 2013 (UTC)[reply]

Hi There, Thank you for the feedback. To address your suggestions I'll do so under your specific headings.Wiki suitable format and style: Good point; we will probably reformat our paragraphs and combine sentences that are related in topic. References and their accuracy: Yes, we've been having trouble with some of our images. I believe we have solved the problem with this one in particular. Also, we did do early corrections on the links used. We'll revisit this again. Depth of each section and overall: Great find. As I reread this section, I could see where a simple sentence that gives basic background/information will lead the reader into the topic better.DougCovert (talk) 19:08, 15 April 2013 (UTC)[reply]

I love to see this article. I enjoyed this read. The lead section is well-formatted in 2 paragraphs long. I like the background section. It is a good overview with a bit of history. I think public including me would say thanks on those 2 sections. I see many updates and better wording. Overall, I cannot think of any new subtopic to add other than what I can see. In this time, I took a closer look on links and reference links. I think you’d better add a link to Human Genome Mutation Database (HGMD). From my search, it is http://www.hgmd.cf.ac.uk/ac/index.php. If someone reads in this far, he/she wants to know what it is. For reference links, some of those cited references require a membership to view a full article. I am not sure if it is free to join to view article or paid-membership required. Here are list of articles (6 of them) I cannot read other than abstract. Is that possible you could get a public domain article or similar article from internet? What is a policy from Wiki on this kind of case? Please check with them.

• “Production of UV-induced Frameshift Mutations in Vitro by DNA Polymerases Deficient in 3′ → 5′ Exonuclease Activity”
• "Polyalanine and polyserine frameshift products in Huntington's disease"
• "Identification of somatic mutations in human prostate cancer by RNA-Seq"
• "Tay-Sachs disease-causing mutations and neutral polymorphisms in the Hex A gene."
• "Novel frameshift mutation in Troponin C ( TNNC1) associated with hypertrophic cardiomyopathy and sudden death"
• "New approaches to treatment of primary immunodeficiencies: fixing mutations with chemicals"

The following article may be moved or link is missing. Can you generate a reftag again for this article?

• "Digitoxin metabolism by rat liver microsomes."

Happy Wiki writing and Happy editing! /Mhk5600 (talk) 06:43, 28 April 2013 (UTC)[reply]

There's no policy that says that references have to be open access. Some of the best references are, unfortunately, behind pay-walls. The requirement is that any content (such as images, etc.) that is actually included in Wikipedia must have liberal, open licenses. Klortho (talk) 16:52, 2 May 2013 (UTC)[reply]

Thanks for your reply. I learned one fineline of Wiki rule. Yes, I agree that some good reference materials could be blocked by pay-walls. I will consider this rule from the next time. Frameshift mutation is in a good shape from my point of view. /Mhk5600 (talk) 17:52, 2 May 2013 (UTC)[reply]

Hello fellow wiki editors! I was randomly assigned to peer review your wiki page, so here goes. In my opinion, your article so far is very well structured and thought out with a lot of coherent and pertinant information. The one thing that I see as an issue it that this comment pops up at the top of your article from wikipedia: "This article currently links to a large number of disambiguation pages (or back to itself) (check | fix). Please help direct these ambiguous links to articles dealing with the specific meaning intended. Read the FAQ. (April 2013)" This seems like an issue that wikipedia would like you guys to sort out, and would therefore, not be entirely in-line with their style guideline. Happy editing! PJCollettJHU (talk) 22:10, 8 April 2013 (UTC)[reply]

Thanks for that feedback, I think we have worked to make sure all of the links to articles function properly now!Sharkeyr (talk) 18:41, 9 April 2013 (UTC)[reply]

• (grammar) In the first sentence, "from a DNA sequence": the referent is not clear.
• The last sentence in the lead, starting with "However, ..." is too specific. Maybe it could be replaced, by adding a phrase, "however, this interpretation is controversial" to the preceding sentence.
• The heading, "Frameshift Mutation Causes-Research" -- could that be renamed to simply, "Causes"? Similarly, "Diseases-Research" → "Diseases"?
• In the section "Frameshift Mutation Causes-Research", you have one and only one subsection, "Finding Frameshift Mutations". In general, when that's the case, they should be collapsed into one.
• "Flourescence" - headings should not be linked; see Wikipedia:Manual_of_Style/Linking#General_points_on_linking_style.
• The heading "Molecular Biology and Biochemistry Background": could that be changed to simply, "Background"?
• Add "Main page" links under the subsection headings, whenever there is a dedicated Wikipedia article on that topic. See Wikipedia:Summary_style
• I think there is too much detail under "Transcription and translation". This should just be giving enough information to explain why it is important to maintain the proper reading frame. Details about the mechanism of tRNA action (for example) are irrelevant.
• That is, UNLESS you are using this to describe other sources of frameshifting -- that it can actually occur during transcription. I get that impression from reading the second para there, starting "Frameshifting may also occur ...". But if so, it is not clear, and it needs to be resolved.
• Also, if that's the case, then you need to mention it in the lead. Right now, the lead only talks about mutations in the DNA. (And, when I think about it, that seems to be appropriate, given the page title.)
• " How does a mutation alter the genetic code. " is a question, and should have a question-mark. That said, I think that such a rhetorical question isn't really the right tone for an encyclopedia article.
• The section, "The Mutation" is not good. You don't need to talk about other types of mutations here, we've already established that there are other types. The only sentence here that is worth keeping is the last one, regarding the statistics. I'd suggest removing the subsection header, and maybe expanding on the information regarding the frequency of occurance of the various types of frameshift mutations.
• Remove qualifiers like "obviously" and "interestingly".

Klortho (talk) 17:14, 21 April 2013 (UTC)[reply]

Hi Klortho: Wonderful comments, thanks. We'll begin making the changes today.DougCovert (talk) 18:41, 21 April 2013 (UTC)[reply]

Hi Klortho, I'm a little confused on how to set up the "Main page" links. I went into summar_style and reviewed it, but I am still wondering about it. Would you be kind enough to show us a particular need in our article. Many thanks.DougCovert (talk) 18:09, 22 April 2013 (UTC)[reply]

I did one for you, under "Central dogma". Use the edit button to see what it looks like in wikitext. Klortho (talk) 11:48, 25 April 2013 (UTC)[reply]

Hi Klortho, A belated Thank-you!DougCovert (talk) 13:50, 28 April 2013 (UTC)[reply]

Hello! It looks like I have been assigned as your second reviewer. This article has been greatly improved with great added information. The article is neutral without any jargon and is easy to read and understand for a user without a strong background in molecular biology. The information given in each section is coherent and correct and there doesn't seem to be any gaps in the information nor plagiarism. There are some structural changes that I would like to suggest. Under the subheading 'Transcription and Translation' there are two main articles that are listed. Is is possible to list both articles without having 'Main article' listed twice? Also throughout the article, some words are linked to other wiki pages, but you should be careful that you are not over linking some main words. For example, 'insertions' and 'deletions' are linked more than once in the lead section. You should only link something, in general, the first time you use it, not every time. To quote the style guide page: "A term should be linked, generally, at most once in an article's lead, perhaps once again in the main article body, and perhaps once at first occurrence in each infobox, table, caption, and footnote." Also when using headings and subheading, you should think about writing a small introduction under the heading. For example, 'Finding Frameshift Mutations' has multiple subheading but there isn't anything written under the main heading 'Finding Frameshift Mutations'. As a user this was a little confusing when navigating through the article. You should also think about rephrasing the heading 'Cures' just so its more clear. The article could also benefit from more referenced articles and having two columns for your references. In all, this group has greatly improved this article. Great job! Autumn Zack-Taylor (talk) 18:49, 29 April 2013 (UTC)[reply]

Thanks so much for the review. I will check to make sure things aren't over linked. We are definitely looking at adding small introductions for each heading. Sharkeyr (talk) 21:39, 30 April 2013 (UTC)[reply]

Hi guys! For my second peer review, I will be reviewing this article as a participant in the JHU Ambassador program.

• Research and References: All of the references that I was able to double check appeared to have been suitably and appropriately represented. From the several references that I checked, I was not able to find any instances of unacceptably close paraphrasing or misrepresentation of the reference material. However, I do feel that this article should have a little more references considering how much content there is in this article. In fact, I noticed that many paragraphs (especially in the diseases section) have only one or two references despite having quite a bit of content. I think this would be improved if we could include a reference at the end of almost every other sentence. That way, readers can more easily verify the origin of the information used in each section. Furthermore, I think it would be helpful if more than one reference was used for each paragraph or even single sentences, since multiple corroborating sources lend greater credibility. There was one issue that did catch my attention though. I noticed that the Diagnosis section cited a patent. I’m not sure if a patent would be a reliable source of information because the applicant would have an incentive to spin the information one way or another to maximize his chances of getting the patent allowed. In this way, a patent might be considered to be a biased source of information but I could be completely wrong.

• Writing Quality: I have no problems with the writing quality, as it is appropriate in all sections. Language is clear and straightforward with little or no fluff. I still think that there are minor issues that can be corrected though, like cleaner wording and improved diction. This article in general seems to consistently follow the Wikipedia manual of style and I haven’t found any major abnormal deviations. I do not see any problems with too much jargon either for the most part.

• Coverage and Scope: This article looks pretty solid. I see that most of the essential information is present and I can not think of any blatantly obvious sections that I would be able to add here. The sections also seem to be organized logically as well so as to flow. Comparisons with other types of mutations might be good to talk about if you really want to go into detail.

• Visuals: The images are clear, very straightforward, and represent the subject matter accurately. If anything, I think that the last image may be too small, as I have difficulty making out what that thumbnail is supposed to be. I would enlarge it a little bit.

• Stability: The subject and writing appears to be stable for all practical purposes. The frameshift mutation is a fairly straightforward topic. It has been the subject of many studies and much has already been deduced since it is an important type of mutation. I believe it is unlikely that this writing will become significantly obsolete or outdated anytime in the near future.

• Neutrality: The writing appears neutral for the most part. Much of what we know seems to be well established already so there seems to be little controversy and few opposing views to consider.

Great job and thanks for reading! Bcheon1 (talk) 21:55, 30 April 2013 (UTC)[reply]

Thank you for the detailed review and comments. I'll send a note to double check with the OA regarding the patent. We will also try and include more refs where feasible based on your recommendations.DougCovert (talk) 02:12, 1 May 2013 (UTC)[reply]

I don't see any problem with referencing the patent, in particular because in the article you are merely describing what the patent says, as factual information. However, on re-reading that section, I have another comment, and that is: aren't there other ways of diagnosing frameshift mutations that aren't covered in this patent? Also, the descriptions of the techniques that you do have are lacking in detail. I think this section could be improved by adding more details and some other methods, if you can find them. Cheers! Klortho (talk) 03:29, 1 May 2013 (UTC)[reply]

Thank you for clarifying the issue about whether it is okay to use patents. I actually wasn't sure if patent were okay but now I do. I will be checking to see if there are suitable patent applications that I can reference for the articles that I edit. Bcheon1 (talk) 21:19, 8 May 2013 (UTC)[reply]

Thank you to all our peer reviewers on this article. Your analysis greatly helped my partner and I add to making this a better article. I think we all learned how to increase our writing and editing skills by being involved with this article. As you know the final progress report for the article is in the gruop page.DougCovert (talk) 02:38, 10 May 2013 (UTC)[reply]

))) Мутация сдвига рамки (так-же называется RED-ERROR или orf frameshift (сдвиг рамки считывания)). Представляет собой генетическую мутацию, вызванную индели (инсерция либо делеция) во множестве нуклеотидов кодирующей области ДНК-последовательности, акт которой не делиться на три. В связи с триплетным характером экспрессии генов дробленных на триединици кодонов, вставки или делеции не кратные трём могут изменить рамку считывания (группируемость кодонов), в результате транскрипция принимает совершенно другой перевод с оригенала. Инсерции либо делеции приводят к синтезу совершенно более измененного и структурно и длиной белка. Мутации сдвига рамки считывания совершенно не то же самое что и моно-нуклеотидный полиморфизм линейной эволюционной мутируемости, при котором нуклеотид меняется, а не вставлен либо удален. Мутирование рамки считывания в общем приводит к синтезу биополимера с иным аминокислотным процентом. Мутации сдвига рамки считывания также изменяют протяженность кодирующей области, то есть: позицию первого стоп-кодона («TAA", "TAG" или "TGA"), встречающихся в цепи биополимерной последовательности. Создающийся полипептид будет обычно аномально короток либо аномально удлинен, но скорее всего он не будет нормально работать. А если такая мутация окажется эволюционно актуальна и дарвинистически выгодно закрепленной (по разным источником от десятков до десятков тысяч ген в геноме человека), то тогда часто синтез такого полипептида во многом снижен из-за его конфронтации с естественным имунным ответом в границах той или иной степени приточенности его структуры к иммунным телам организма и конкуренцией с позитивной отсутствующей вакансией его дикого аналога.

Мутации сдвига рамки считывания являются и очевидными факторами при тяжелых генетических нарушениях-мутациях, таких как болезнь Тея-Сакса и кистозный фиброз ; они повышают чувствительность к определенным видам рака и классам семейной гиперхолестеринемии ; в 1997 году [2] обнаружены мутации сдвига рамки считывания, связанные с устойчивостью к инфекции ретровируса иммунодефицита. Рамки считывания были предложены в качестве источника биологической новизны, как предположение о создание nylonase , однако, такая интерпретация является спорной.

С построением алгоритма поиска ген со сдвигом рамок считывания и их известными функциями, 

блокируемыми иммунным ответом, можно более подробно ознакомиться на сайте patternscom.nethouse.ua Дмитрий Полесинский (talk) 06:38, 29 October 2013 (UTC)Dmitrij Polesinskij[reply]