Talk:CDK13-related disorder/GA1
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Reviewer: Canada Hky (talk · contribs) 00:11, 3 January 2020 (UTC)
Hello! I am happy to review this article for GA status. Typically, when I review - I will go through and make general comments as they come up, and then after we work through that, I run through the GA checklist to make sure nothing has been missed. Canada Hky (talk) 00:11, 3 January 2020 (UTC)
- @Canada Hky – initial response below. Thanks for reviewing. SUM1 (talk) 04:06, 4 January 2020 (UTC)
Initial comments
[edit]- Throughout the article - "mutation" should be replaced with "variant".
- This isn't standard on genetics articles. Good articles like Noonan syndrome with multiple lentigines, Birt–Hogg–Dubé syndrome, Lujan–Fryns syndrome and Nasodigitoacoustic syndrome along with all other genetics articles describe mutations as mutations. I see that PeaBrainC complied to get your review of Andersen–Tawil syndrome to pass, though I'd like to see where in the standard you see this as necessary. On that article, it actually added confusion by implying that there's "a variant of the KCNJ2 gene which encodes an ion channel that transports potassium out of cardiac muscle cells", when actually a mutation in that gene breaks its functionality. SUM1 (talk) 03:59, 4 January 2020 (UTC)
- It is standard in clinical genetics. There is no confusion in the article you mention - variant = mutation. Nomenclature has changed. Wikipedia policy may not have kept up, however the secondary sources used for this article are an even split - Gene reviews exclusively uses "variant" and "pathogenic variant". "Mutation" is not used in most reputable journals, per style guides and peer review.Canada Hky (talk) 22:08, 4 January 2020 (UTC)
- @Canada Hky: More of the GeneReview's cited articles (3) use "mutation" than "variant" (2). I would say allow it to remain on Wikipedia for consistency with the article mutation and all other genetics articles, at least until a site-wide decision is made to change this. This is still Wikipedia and not a clinical journal, and that choice of word doesn't serve to take it down from good article criteria (at least in my and some others' view). "Mutation" still represents the common usage word and is also non-contextual and encompasses the pathogenicity of the phenomenon. In order to turn every syndromic instance of "mutation" into "variant", you'd have to also specify that it's a pathogenic variant. The clinical guideline that recommended changing it was referring to it clinically in the context of it being misinterpreted as pathogenic when it isn't – that isn't a problem here. That same guideline also contains numerous uses of "mutation" in its common usage. If this is what ends up failing this review, then I'm happy to accept that, though I'd appeal for you to accept this state of affairs. SUM1 (talk) 03:43, 5 January 2020 (UTC)
- The point of a secondary source is to synthesize primary sources. There are plenty of primary sources out there with clinical language that is now considered offensive, which secondary sources now eschew, and which are reflected in Wikipedia. I think the specific nomenclature issue isn't likely to be clarified on Wikipedia anytime soon, and will get muddied due to the blending of human and animal genetics. Accurately reflecting what is used in a source is very clearly established, though. Canada Hky (talk) 13:14, 6 January 2020 (UTC)
- @Canada Hky: "Mutation" is not an offensive term. You do not have to use the exact same words that are used in a secondary source when other, more common and readily comprehensible ones will suffice; that is encompassed in basic Wikipedia policy. I referred to several Wikipedia policies and standards that establish that there is nothing wrong with using the word "mutation" on Wikipedia. Your statement that "Wikipedia policy may not have kept up" was rather concerning, considering you are reviewing based on Wikipedia policy, standards and criteria. Again, if this brings this review down to failure, then I'm happy to accept that, though if it does you might want to consider nominating for re-assessment all the other articles that use that word. SUM1 (talk) 21:15, 10 January 2020 (UTC)
- Mutation is absolutely an offensive term when referring to a person, as this article is. That's why clinically focused entities are not using it anymore. We disagree on Wikipedia policy here. A high quality secondary source has made a conscious and obvious decision as to how they are using the term, and not using "mutation", and you are ignoring that. I do not think you have accurately represented the source you are citing, which IS Wikipedia policy.
- @Canada Hky: "Mutation" is not an offensive term. You do not have to use the exact same words that are used in a secondary source when other, more common and readily comprehensible ones will suffice; that is encompassed in basic Wikipedia policy. I referred to several Wikipedia policies and standards that establish that there is nothing wrong with using the word "mutation" on Wikipedia. Your statement that "Wikipedia policy may not have kept up" was rather concerning, considering you are reviewing based on Wikipedia policy, standards and criteria. Again, if this brings this review down to failure, then I'm happy to accept that, though if it does you might want to consider nominating for re-assessment all the other articles that use that word. SUM1 (talk) 21:15, 10 January 2020 (UTC)
- The point of a secondary source is to synthesize primary sources. There are plenty of primary sources out there with clinical language that is now considered offensive, which secondary sources now eschew, and which are reflected in Wikipedia. I think the specific nomenclature issue isn't likely to be clarified on Wikipedia anytime soon, and will get muddied due to the blending of human and animal genetics. Accurately reflecting what is used in a source is very clearly established, though. Canada Hky (talk) 13:14, 6 January 2020 (UTC)
- @Canada Hky: More of the GeneReview's cited articles (3) use "mutation" than "variant" (2). I would say allow it to remain on Wikipedia for consistency with the article mutation and all other genetics articles, at least until a site-wide decision is made to change this. This is still Wikipedia and not a clinical journal, and that choice of word doesn't serve to take it down from good article criteria (at least in my and some others' view). "Mutation" still represents the common usage word and is also non-contextual and encompasses the pathogenicity of the phenomenon. In order to turn every syndromic instance of "mutation" into "variant", you'd have to also specify that it's a pathogenic variant. The clinical guideline that recommended changing it was referring to it clinically in the context of it being misinterpreted as pathogenic when it isn't – that isn't a problem here. That same guideline also contains numerous uses of "mutation" in its common usage. If this is what ends up failing this review, then I'm happy to accept that, though I'd appeal for you to accept this state of affairs. SUM1 (talk) 03:43, 5 January 2020 (UTC)
- It is standard in clinical genetics. There is no confusion in the article you mention - variant = mutation. Nomenclature has changed. Wikipedia policy may not have kept up, however the secondary sources used for this article are an even split - Gene reviews exclusively uses "variant" and "pathogenic variant". "Mutation" is not used in most reputable journals, per style guides and peer review.Canada Hky (talk) 22:08, 4 January 2020 (UTC)
- This isn't standard on genetics articles. Good articles like Noonan syndrome with multiple lentigines, Birt–Hogg–Dubé syndrome, Lujan–Fryns syndrome and Nasodigitoacoustic syndrome along with all other genetics articles describe mutations as mutations. I see that PeaBrainC complied to get your review of Andersen–Tawil syndrome to pass, though I'd like to see where in the standard you see this as necessary. On that article, it actually added confusion by implying that there's "a variant of the KCNJ2 gene which encodes an ion channel that transports potassium out of cardiac muscle cells", when actually a mutation in that gene breaks its functionality. SUM1 (talk) 03:59, 4 January 2020 (UTC)
- When multiple references are used for a single sentence, they should be in numerical order.
Done. This was difficult because the citations appear in order in VisualEditor but not after publishing, and in the source editor, the ref numbers don't correlate with the order. SUM1 (talk) 03:59, 4 January 2020 (UTC)
- The signs and symptoms section is very disjointed. Rather than having 6 very short sections, they could be combined in "Signs and symptoms" as two or three paragraphs. This would clean up the referencing as well.
- Done. I'd recently switched it from no subheadings to subheadings on the basis of my other, larger articles. I agree that it's disjointed; I'll switch it back. SUM1 (talk) 03:59, 4 January 2020 (UTC)
- This article relies very heavily on two primary sources. Where possible these should be minimized, in favor of the secondary sources, such as refs 3 and 4. I'd consider using the primary sources for dates, and initial findings, and Gene Reviews for most other information.
- In fact it relies very heavily on two secondary sources, the GeneReview and Hamilton (2019). There are hardly any sentences not cited with those two existing secondary sources; I'd already attempted to maximise their spread. All info is sourced in the secondary sources, the primary sources are appended to represent the source of the original finding and the extra detail not included. WP:MEDREV: "Primary sources may be presented together with secondary sources." SUM1 (talk) 03:59, 4 January 2020 (UTC)
- Under "Causes" - is there a reference for CDK13 being embryonic lethal in humans? It likely is, but a mouse study can't be used to prove that.
- Done. It is, but will change it to "in mice" then. SUM1 (talk) 03:59, 4 January 2020 (UTC)
- Consider combining some of the shorter sections - this article isn't going to get much longer for several years, and the phenotype is pretty well delineated based on the initial patients. This is likely close to the steady state. Cause and Diagnosis. Prognosis and Treatment. And Epidemiology can be combined with History.
- I see what you mean about the latter sections. Though, good articles Noonan syndrome with multiple lentigines, Lujan–Fryns syndrome and Birt–Hogg–Dubé syndrome have similar-length distinct Epidemiology or Prognosis sections. Even Andersen–Tawil syndrome, which you reviewed, has single-line-long Epidemiology and History sections. The MOS aims for consistency in the section titles. If you permitted it there, can you permit it here? SUM1 (talk) 03:59, 4 January 2020 (UTC)
- Not going to argue this one. Canada Hky (talk) 18:23, 11 January 2020 (UTC)
- I see what you mean about the latter sections. Though, good articles Noonan syndrome with multiple lentigines, Lujan–Fryns syndrome and Birt–Hogg–Dubé syndrome have similar-length distinct Epidemiology or Prognosis sections. Even Andersen–Tawil syndrome, which you reviewed, has single-line-long Epidemiology and History sections. The MOS aims for consistency in the section titles. If you permitted it there, can you permit it here? SUM1 (talk) 03:59, 4 January 2020 (UTC)
- In "diagnosis" - you have two testing strategies and one testing method, which is confusing. It should either be "NGS + Sanger" or "WES / single gene / panel" for consistency.
- Done.
I'm going to put this on hold. If you have any questions, or anything is unclear, just drop me a note.
- The caption for the Gallery figure should be expanded. What facial features should everyone be looking at?
- Done. Fair enough, will do. SUM1 (talk) 03:59, 4 January 2020 (UTC)
- No copyvio issues. No disambiguation links found. No external link issues.
- I'm going to request a second opinion and step back. This is counter productive, and your willingness to die on this hill is not something I wish to further engage in. Misrepresenting a source as you insist on doing for arguably the best source for clinical genetics online is clear grounds for failure, in my opinion and interpretation of policy. To the second opinion provider: please feel free to close this as you see fit based on your review. Canada Hky (talk) 18:23, 11 January 2020 (UTC)
- Is this over mutation vs variant? AIRcorn (talk) 18:48, 16 January 2020 (UTC)
Second opinion
[edit]- @SUM1: my opinion is that the eighteen instances of the word "mutation" should indeed be replaced with "variant" as has been mandatory practice for half a decade per the American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines for interpretation of sequence variants.[1] However, I see no need to combine short sections, which is contrary to the style guide for good reasons. I am happy to provide the customary seven day hold for this to happen. Please ping me on my talk page when the article is ready for promotion. EllenCT (talk) 10:19, 30 January 2020 (UTC)
- Just to muddy the waters a bit I was going to go a different way. The language may be changing, but I don't think it is part of the Good Article criteria to force that change when both words are still in use in reliable sources.[2] This feels like something better decided at the article talk page than here. AIRcorn (talk) 22:02, 30 January 2020 (UTC)
- I think the post I liked to makes a convincing case that "mutation" is imprecise, which bears on the clear prose requirement of criterion 1(a). The connotation of the word may have some impact on whether it is at least perceived as a neutral term when applied to human conditions that patients and their parents might be researching. EllenCT (talk) 01:43, 31 January 2020 (UTC)
- That link is to blog post and is specific to epilepsy genetics, which often involves multiple genetic factors. Here a paper that discusses definitions of SNPs and mutations highlights the conventional definition of mutation as DNA variants detectable in <1 % of the population. That fits with this article and is actually more precise than just using variant. A NCBI search with both terms tied to the last five years uses both at a relatively similar frequency.[3] Heres a 2016 cancer one that says variant and mutation can be used interchangeably. Even our own Genetic variant article is a DAB to SNPS, mutations and CNV. I feel that insisting on variant over mutation goes more into personal preference over any actual criteria or even policy and it would be unfair to fail it on that regard. Anyway, it is up to SUM1 I guess to decide how they want to proceed, this is just my opinion on the issue. AIRcorn (talk) 08:53, 31 January 2020 (UTC)
- Thank you for that clarification, but be that as it may, I am still persuaded that the term can be seen as "offensive or shaming by patients and families" and thereby can be considered non-neutral. EllenCT (talk) 00:51, 1 February 2020 (UTC)
- Lots of articles are offensive to different people (just pick any religious topic). Neutrality for the purpose of whether an article meets the GA criteria should be decided through a balanced look at the sources not what we consider offensive. Changing mutation to variant has implications for quite a few articles on medical conditions. I think this needs a wider discussion so have started a one at Wikipedia talk:WikiProject Medicine#Mutation vs Variant. AIRcorn (talk) 02:12, 1 February 2020 (UTC)
- Offensive doesn't come under non-neutral. @EllenCT, may I point you to WP:CENSORED. The only other thing I have left to say about this issue is just consider how vastly many articles you'd need to change in order to enforce this practice. Clearly a vast majority of editors who've created these articles and continue to add to them seamlessly use "mutation" with no issue. · • SUM1 • · (talk) 02:42, 1 February 2020 (UTC)
- Mutation is not an offensive term. The use of this word cannot bar the article from being passed User:Dunkleosteus77 |push to talk 19:09, 3 February 2020 (UTC)
- Thank you for that clarification, but be that as it may, I am still persuaded that the term can be seen as "offensive or shaming by patients and families" and thereby can be considered non-neutral. EllenCT (talk) 00:51, 1 February 2020 (UTC)
- Hmmm, terminology is important, and using a term that could make someone feel marginalized just because it's the term we're accustomed to using is pretty lousy. The link EllenCT shared is interesting and I wasn't previously aware that this was a push in the clinical genetics world. But if we want to guide encyclopedia editors to use "variant" instead of "mutant" let's have a discussion at some noticeboard about it, and not at the GA review for an on article on a particular genetic disease. If we want to only have a limited discussion as to the use on CDK13-related disorder, then I'd say in general I prefer variant, but for this article I don't think it matters (the disease is caused by a single variant that is obviously pathogenic). SUM1 prefers mutation. There has been no larger discussion on the topic I'm aware of. I'd vote it's fine as is and move on. Ajpolino (talk) 19:49, 3 February 2020 (UTC)
Status query
[edit]This review has been sitting in limbo for nearly two months. The discussion Aircorn started at WikiProject Medicine over "mutation" vs. "variant" has since been archived. Can someone review it to see what the consensus may have been (or if not a consensus, whether there were points relevant to this discussion), and take this review onto the next stage? I'm putting this back on "second opinion" in the hopes of moving this nomination forward. Thanks to anyone who can help. BlueMoonset (talk) 19:54, 2 April 2020 (UTC)
- I think it's fair to say the discussion was archived with no consensus, though many opined that they personally found "mutation" to be inoffensive. While I think it's clear that we should use terms preferred by practitioners of the field when possible, whether articles must use those terms to pass GA review remains undecided (and was hardly directly addressed at the WT:MED discussion). My opinion is that this article meets the good article criteria, and we should pass this review. For the more important issue of language, those interested could consider a follow-up discussion at Wikipedia talk:Manual of Style/Medicine-related articles (pinging those who participated in the WT:MED discussion) to discuss whether mutation vs. variant should be added as an example at Wikipedia:Manual_of_Style/Medicine-related_articles#Careful_language. Or a discussion at WT:GAN on whether these kinds of issues are part of a GA review. Or someone can just improve the wording at CDK13-related disorder, and if anyone disagrees they can discuss it at the talk page. Either way, I don't think leaving this article in eternal limbo is a preferred situation, and there's no consensus that this kind of non-ideal language is grounds for failing review. If no one voices opposition in a day or two, I'm happy to close this review. Ajpolino (talk) 20:43, 2 April 2020 (UTC)