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Note: the familiar statement that humans differ from each other by only about 0.1 % seems inaccurate because the two haplotypes of a diploid human genome differ by about 0.5 %, and that was shown for an individual with European ancestry through both parents (PMID: 17803354). Differences might be greater with greater geographical variation in ancestry. Daniel haft ( talk) 19:39, 22 April 2009 (UTC)
The statement seems correct for SNPs only and is also true for comparisons between a Han Chinese and the two European genomes (Nature 456, 60-65 (6 November 2008) | doi:10.1038/nature07484, see supplementary figure 2)
while the 0.5% is a more complex measure (all heterozygous bases, i.e., SNP, multi-nucleotide polymorphisms [MNP], indels, [complex variants + putative alternate alleles + CNV]/genome size; [2,894,929 + 939,799 + 10,000,000]/2,809,547,336) 192.38.114.138 ( talk) 13:14, 20 July 2009 (UTC)
I'm concerned about the statement that GWAS are "hypothesis-free." It's quite the opposite: every SNP tested is a hypothesis, and any analysis must be subject to corrections for multiple-hypothesis testing. —Preceding unsigned comment added by Uri.laserson ( talk • contribs) 05:01, 15 October 2009 (UTC)
I reverted the recent edit that claims that noncoding are almost certainly NOT causal. That is not true. I agree that most GWAS hits still are not complete clear on which particular SNP in a block is the actual causal variant, but for the ones where it is known (e.g. SORT1-locus) it is noncoding SNPs that are ultimately causal. -- LasseFolkersen ( talk) 09:31, 22 November 2011 (UTC)
I'm starting up a major revision of this article. So far I expanded the backgrounds and methods. Will get back to "genes identified" and "limitations". Help and suggestions welcome!-- LasseFolkersen ( talk) 14:40, 6 December 2011 (UTC)
I have tried to keep all the good bits that were already in the text (even though I rewrote some of them). One exception however: "...these [ARMD] genes can predict half the risk of ARMD between siblings, and it is among the most successful examples of GWAS.". I think this sentence is highly useful, but the wording of prediction of half the risk between siblings is a bit confusing in comparison to the more commonly used proportion of heritability explained (which I also use later on). So apologies for removing a good bit - I just think the article will be less confusing without it -- LasseFolkersen ( talk) 08:38, 7 December 2011 (UTC)
Ok, I'm pretty much done with the expansions I planned. Only need to clear up the citations. CitationBot has problems, but I'll try it later again. Then some grammar and prose check-ups, and then I'll have a couple of colleagues read it through. Other comments welcome! -- LasseFolkersen ( talk) 12:16, 7 December 2011 (UTC)
I now had time to go through the reviews as found in the request for peer review page. The changes to the main text have already been comitted, and here is the point-by-point response.
From
User:Cryptic C62
1) Except for the introduction sentence, all "GWAS" have now been replaced with GWA study/ies. This choice was made for easier pluralization.
2) "From 2005" was changed to "published in 2005"
3) Today was replaced with the As of year [update] template, as this is definetly a statement that will age quickly.
4) Surprisingly was deleted
5) I have added the following summary of limitations section to the lead section "Several GWA studies have received criticism for omitting important quality control steps, rendering the findings invalid. Largely this type of criticism can and is overcome in more modern publications. However, the fundamental methodology still have opponents."
1) ok, I have changed the caption to follow the correct way of captioning things here.
2) ok, I have removed the full stop after the caption
3) ok, the User:Cryptic C62 suggestions have been included
4) I think anybody who reads an article called genome-wide association study will think less of it, if it expands DNA to deoxyribonucleic acid. "DNA" is so routinely used that the whole spectrum from science journals to popular newspaper articles assumes knowledge of it and leaves it out of acronym lists.
5) The SNP acronym is already expanded to single-nucleotide polymorphisms at first occurence. Could you perhaps be more specific on where you are aiming.
6) ok - I use the Schena 1995 reference because that's the landmark microarray publication.
7) you might be right that "unity" is a more formal way. I didn't change it now though, because my aim was to loose as few readers to formality as possible. Feel free to change yourself if you think it is important.
8) ok. I have moved it. It's a pity that the article doesn't have a lead figure though.
9) ok, I have now used the correct format for dashes.
Apologies for the lateness, but I was invited to contribute to the peer review through my talkpage.
Lead:
Body: (Prelim)
Overall, the citations are mostly present when needed (I have not investigated the references themselves yet), the blue-linking is about right and the language is not overly technical. My criticisms are that sometimes the language could be tighter and I feel this article is missing some content, I suggest there are additional examples which convey the power and findings of these studies (failing that a CC-licensed publisher could add some nice diagrams, e.g. PLoS Genet.). Jebus989 ✰ 23:43, 4 January 2012 (UTC)
Point-by-point response for lead:
1) Could you come with more suggestions on what is unclear? Is it the use of the word trait? Or association? Instead of trait I could use "property" or "characteristic" or something like that. Association is more difficult to get around, but not impossible if I just use more words. How about "(WGA study, or WGAS), is an examination of many common genetic variants in different individuals to see if they are more or less common depending on the characteristics of the individuals."
2) Changed genetic variants to point to genetic variants (thanks for pointing out). About the focus of the article on SNPs and/or "other variant types" (CNVs, etc) - a CNV study is also a GWA study, but I the vast majority of all GWA studies are on SNPs. So I kept focus on that, while still mentioning the more general genetic variants. Hence "Typically SNPs are investigated".
3) Sure. I moved the sample size info to results.
4) Ok. I removed a lot of it. The bits about risk-SNPs being outside coding regions were not even in the main text so I removed it also. I could probably fill in a little about that in the main later. TODO
5) The variants-variants is the same sentence you comment on in 1). See there. The typical-typical... I would argue for keeping it this way. The reason is that it is not only SNPs and it is not only majory diseases. Only the vast majority of studies are. But if we don't write it with a "typical"-disclaimer all the people in the non-major-disease/other-phenotype/CNV groups will conclude that the text is wrong.
Point-by-point response for prelim body:
1) yes, 'GWAS' is a bit more widely used historically but I feel this is turning towards GWA study/ies, because it is so much easier for the writer to indicate pluralization. And so it also makes for more readable wikipedia article.
2) I think I understand what you mean - how about "In addition to the conceptual framework, the following technological factors enabled GWA studies: One was the advent...." then it is more connected, and by writing technological it's emphasized that it is requirements apart from just the idea to test for many associations. Or did I understand this comment correctly?
3) you are right - it is not very noteworthy yet. I think their manuscript for it must still be in review (I'm not associated with that group by the way). In contrast the most noteworthy attempt (the PNAS article reference, with http://www.genome.gov/gwastudies) is just so horribly in lack of updates that it seems wrong to let it stand as the sole source. How would you think about just removing the web-page reference but leaving the sentence "however, more updated resources might be found...".
4)I'll extend this SORT1 example rather than leave it. The bioessays-article was just a review covering all the research on it, which is much more heavy-weight. I'll do better and expand that, because I think this is one of the most notable examples at least of cardiovascular GWA studies. Certainly more than the Peginterferon-link which was here previously, but which I've heard very little about outside of wikipedia. TODO
5) Ok I added the reference from the lead that was already used for the same. For now. You are undoubtly right that several of these are of less than strong significance, but finding out exactly how many is probably original research.
6) I reworded it to "Ignoring these correctible issues has been cited as contributing to a general sense of problems with the GWA methodology", because I think it is important comments from some of the heavy weighters in the field (Joe Pickrell etc. in the reference). Did this address your concern?
7) I don't know. This factory-science-sentence was here before I started so I left it, to not upset previous authors. I'll just contract it into the cousin-frankel reference which was definetly a verifiable and much discussed opionion piece.
That's it for now. I know I left some to-do loose ends, but it's getting late so I'll get back to them later. --
LasseFolkersen (
talk)
16:40, 5 January 2012 (UTC)
After some research I reverted the changes on first GWA study to the 2005 CFH study by Klein et al. In addition I added "the first successful GWA study". As far as I could see, the results from earlier studies such as the one by Ozaki et al were never reproduced successfully.-- LasseFolkersen ( talk) 11:17, 7 August 2012 (UTC)
GA toolbox |
---|
Reviewing |
Reviewer: Estevezj ( talk · contribs) 02:48, 9 January 2013 (UTC)
I've started my first read-through and will update this review as I proceed. — James Estevez ( talk) 02:48, 9 January 2013 (UTC)
A good article is—
Criteria | Notes | Result |
---|---|---|
(a) (prose) |
|
![]() |
(b) (MoS) | The article complies with the five WP:MOS sections required by the GAC. |
![]() |
Criteria | Notes | Result |
---|---|---|
(a) (references) | The References section contains a properly formatted list of references used in the article. [7] |
![]() |
(b) (citations to reliable sources) |
|
![]() |
(c) (original research) | Besides the tagged exceptions, statments in the article are supported by the sources and contain no original research. |
![]() |
Criteria | Notes | Result |
---|---|---|
(a) (major aspects) | The article offers a good overview of the main aspects of GWAS. |
![]() |
(b) (focused) | The article is concise and adheres to summary style. |
![]() |
Notes | Result |
---|---|
The article fairly represents different significant viewpoints on the topic. |
![]() |
Notes | Result |
---|---|
Stable. Article had fewer than 20 edits in the last six months of 2012. |
![]() |
Criteria | Notes | Result |
---|---|---|
(a) (images are tagged and non-free images have fair use rationales) | Images are available under free licenses and are appropriately cited where necessary. |
![]() |
(b) (appropriate use with suitable captions) | The images are appropriate for the article and the captions are accurate and informative. [9] |
![]() |
Again, fine work on the article. In the course of the review I've made some minor changes to the article to correct for usage, style, and to add a handful of references. I've tagged several statements that require in-line citations under the Good Article criteria.
Moving forward, as work on the article continues I would like to bring to your attention the article available at PLoS Computational Biology. [10] This article is available under the Wikipedia compatible CC-BY license, meaning that figures and text from it can be incorporated in this article. This resource may prove valuable should editors decide to work towards FA status.
Best regards, — James Estevez ( talk) 02:26, 18 January 2013 (UTC)
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An editor has asked for a discussion to address the redirect Phenome-wide association study. Please participate in the redirect discussion if you wish to do so. Pam D 19:58, 18 February 2020 (UTC)
I added another application of GWAS, its Agricultural Application. I cited two articles to support the idea that GWAS is useful for developing new pathogen-resisted cultivars and improving yields. Would anybody be willing to review it for me? MaggieKKK ( talk) 00:27, 10 December 2020 (UTC)KKK
I added a new section called Conservation applications to provide information about GWA studies as a tool for genetic diversity research and conservation. Aharveypdx ( talk) 02:58, 21 March 2023 (UTC)
![]() | Genome-wide association study has been listed as one of the Natural sciences good articles under the good article criteria. If you can improve it further, please do so. If it no longer meets these criteria, you can reassess it. | |||||||||||||||
| ||||||||||||||||
Current status: Good article |
![]() | This article is rated GA-class on Wikipedia's
content assessment scale. It is of interest to the following WikiProjects: | |||||||||||||||||||||||||||||
|
Note: the familiar statement that humans differ from each other by only about 0.1 % seems inaccurate because the two haplotypes of a diploid human genome differ by about 0.5 %, and that was shown for an individual with European ancestry through both parents (PMID: 17803354). Differences might be greater with greater geographical variation in ancestry. Daniel haft ( talk) 19:39, 22 April 2009 (UTC)
The statement seems correct for SNPs only and is also true for comparisons between a Han Chinese and the two European genomes (Nature 456, 60-65 (6 November 2008) | doi:10.1038/nature07484, see supplementary figure 2)
while the 0.5% is a more complex measure (all heterozygous bases, i.e., SNP, multi-nucleotide polymorphisms [MNP], indels, [complex variants + putative alternate alleles + CNV]/genome size; [2,894,929 + 939,799 + 10,000,000]/2,809,547,336) 192.38.114.138 ( talk) 13:14, 20 July 2009 (UTC)
I'm concerned about the statement that GWAS are "hypothesis-free." It's quite the opposite: every SNP tested is a hypothesis, and any analysis must be subject to corrections for multiple-hypothesis testing. —Preceding unsigned comment added by Uri.laserson ( talk • contribs) 05:01, 15 October 2009 (UTC)
I reverted the recent edit that claims that noncoding are almost certainly NOT causal. That is not true. I agree that most GWAS hits still are not complete clear on which particular SNP in a block is the actual causal variant, but for the ones where it is known (e.g. SORT1-locus) it is noncoding SNPs that are ultimately causal. -- LasseFolkersen ( talk) 09:31, 22 November 2011 (UTC)
I'm starting up a major revision of this article. So far I expanded the backgrounds and methods. Will get back to "genes identified" and "limitations". Help and suggestions welcome!-- LasseFolkersen ( talk) 14:40, 6 December 2011 (UTC)
I have tried to keep all the good bits that were already in the text (even though I rewrote some of them). One exception however: "...these [ARMD] genes can predict half the risk of ARMD between siblings, and it is among the most successful examples of GWAS.". I think this sentence is highly useful, but the wording of prediction of half the risk between siblings is a bit confusing in comparison to the more commonly used proportion of heritability explained (which I also use later on). So apologies for removing a good bit - I just think the article will be less confusing without it -- LasseFolkersen ( talk) 08:38, 7 December 2011 (UTC)
Ok, I'm pretty much done with the expansions I planned. Only need to clear up the citations. CitationBot has problems, but I'll try it later again. Then some grammar and prose check-ups, and then I'll have a couple of colleagues read it through. Other comments welcome! -- LasseFolkersen ( talk) 12:16, 7 December 2011 (UTC)
I now had time to go through the reviews as found in the request for peer review page. The changes to the main text have already been comitted, and here is the point-by-point response.
From
User:Cryptic C62
1) Except for the introduction sentence, all "GWAS" have now been replaced with GWA study/ies. This choice was made for easier pluralization.
2) "From 2005" was changed to "published in 2005"
3) Today was replaced with the As of year [update] template, as this is definetly a statement that will age quickly.
4) Surprisingly was deleted
5) I have added the following summary of limitations section to the lead section "Several GWA studies have received criticism for omitting important quality control steps, rendering the findings invalid. Largely this type of criticism can and is overcome in more modern publications. However, the fundamental methodology still have opponents."
1) ok, I have changed the caption to follow the correct way of captioning things here.
2) ok, I have removed the full stop after the caption
3) ok, the User:Cryptic C62 suggestions have been included
4) I think anybody who reads an article called genome-wide association study will think less of it, if it expands DNA to deoxyribonucleic acid. "DNA" is so routinely used that the whole spectrum from science journals to popular newspaper articles assumes knowledge of it and leaves it out of acronym lists.
5) The SNP acronym is already expanded to single-nucleotide polymorphisms at first occurence. Could you perhaps be more specific on where you are aiming.
6) ok - I use the Schena 1995 reference because that's the landmark microarray publication.
7) you might be right that "unity" is a more formal way. I didn't change it now though, because my aim was to loose as few readers to formality as possible. Feel free to change yourself if you think it is important.
8) ok. I have moved it. It's a pity that the article doesn't have a lead figure though.
9) ok, I have now used the correct format for dashes.
Apologies for the lateness, but I was invited to contribute to the peer review through my talkpage.
Lead:
Body: (Prelim)
Overall, the citations are mostly present when needed (I have not investigated the references themselves yet), the blue-linking is about right and the language is not overly technical. My criticisms are that sometimes the language could be tighter and I feel this article is missing some content, I suggest there are additional examples which convey the power and findings of these studies (failing that a CC-licensed publisher could add some nice diagrams, e.g. PLoS Genet.). Jebus989 ✰ 23:43, 4 January 2012 (UTC)
Point-by-point response for lead:
1) Could you come with more suggestions on what is unclear? Is it the use of the word trait? Or association? Instead of trait I could use "property" or "characteristic" or something like that. Association is more difficult to get around, but not impossible if I just use more words. How about "(WGA study, or WGAS), is an examination of many common genetic variants in different individuals to see if they are more or less common depending on the characteristics of the individuals."
2) Changed genetic variants to point to genetic variants (thanks for pointing out). About the focus of the article on SNPs and/or "other variant types" (CNVs, etc) - a CNV study is also a GWA study, but I the vast majority of all GWA studies are on SNPs. So I kept focus on that, while still mentioning the more general genetic variants. Hence "Typically SNPs are investigated".
3) Sure. I moved the sample size info to results.
4) Ok. I removed a lot of it. The bits about risk-SNPs being outside coding regions were not even in the main text so I removed it also. I could probably fill in a little about that in the main later. TODO
5) The variants-variants is the same sentence you comment on in 1). See there. The typical-typical... I would argue for keeping it this way. The reason is that it is not only SNPs and it is not only majory diseases. Only the vast majority of studies are. But if we don't write it with a "typical"-disclaimer all the people in the non-major-disease/other-phenotype/CNV groups will conclude that the text is wrong.
Point-by-point response for prelim body:
1) yes, 'GWAS' is a bit more widely used historically but I feel this is turning towards GWA study/ies, because it is so much easier for the writer to indicate pluralization. And so it also makes for more readable wikipedia article.
2) I think I understand what you mean - how about "In addition to the conceptual framework, the following technological factors enabled GWA studies: One was the advent...." then it is more connected, and by writing technological it's emphasized that it is requirements apart from just the idea to test for many associations. Or did I understand this comment correctly?
3) you are right - it is not very noteworthy yet. I think their manuscript for it must still be in review (I'm not associated with that group by the way). In contrast the most noteworthy attempt (the PNAS article reference, with http://www.genome.gov/gwastudies) is just so horribly in lack of updates that it seems wrong to let it stand as the sole source. How would you think about just removing the web-page reference but leaving the sentence "however, more updated resources might be found...".
4)I'll extend this SORT1 example rather than leave it. The bioessays-article was just a review covering all the research on it, which is much more heavy-weight. I'll do better and expand that, because I think this is one of the most notable examples at least of cardiovascular GWA studies. Certainly more than the Peginterferon-link which was here previously, but which I've heard very little about outside of wikipedia. TODO
5) Ok I added the reference from the lead that was already used for the same. For now. You are undoubtly right that several of these are of less than strong significance, but finding out exactly how many is probably original research.
6) I reworded it to "Ignoring these correctible issues has been cited as contributing to a general sense of problems with the GWA methodology", because I think it is important comments from some of the heavy weighters in the field (Joe Pickrell etc. in the reference). Did this address your concern?
7) I don't know. This factory-science-sentence was here before I started so I left it, to not upset previous authors. I'll just contract it into the cousin-frankel reference which was definetly a verifiable and much discussed opionion piece.
That's it for now. I know I left some to-do loose ends, but it's getting late so I'll get back to them later. --
LasseFolkersen (
talk)
16:40, 5 January 2012 (UTC)
After some research I reverted the changes on first GWA study to the 2005 CFH study by Klein et al. In addition I added "the first successful GWA study". As far as I could see, the results from earlier studies such as the one by Ozaki et al were never reproduced successfully.-- LasseFolkersen ( talk) 11:17, 7 August 2012 (UTC)
GA toolbox |
---|
Reviewing |
Reviewer: Estevezj ( talk · contribs) 02:48, 9 January 2013 (UTC)
I've started my first read-through and will update this review as I proceed. — James Estevez ( talk) 02:48, 9 January 2013 (UTC)
A good article is—
Criteria | Notes | Result |
---|---|---|
(a) (prose) |
|
![]() |
(b) (MoS) | The article complies with the five WP:MOS sections required by the GAC. |
![]() |
Criteria | Notes | Result |
---|---|---|
(a) (references) | The References section contains a properly formatted list of references used in the article. [7] |
![]() |
(b) (citations to reliable sources) |
|
![]() |
(c) (original research) | Besides the tagged exceptions, statments in the article are supported by the sources and contain no original research. |
![]() |
Criteria | Notes | Result |
---|---|---|
(a) (major aspects) | The article offers a good overview of the main aspects of GWAS. |
![]() |
(b) (focused) | The article is concise and adheres to summary style. |
![]() |
Notes | Result |
---|---|
The article fairly represents different significant viewpoints on the topic. |
![]() |
Notes | Result |
---|---|
Stable. Article had fewer than 20 edits in the last six months of 2012. |
![]() |
Criteria | Notes | Result |
---|---|---|
(a) (images are tagged and non-free images have fair use rationales) | Images are available under free licenses and are appropriately cited where necessary. |
![]() |
(b) (appropriate use with suitable captions) | The images are appropriate for the article and the captions are accurate and informative. [9] |
![]() |
Again, fine work on the article. In the course of the review I've made some minor changes to the article to correct for usage, style, and to add a handful of references. I've tagged several statements that require in-line citations under the Good Article criteria.
Moving forward, as work on the article continues I would like to bring to your attention the article available at PLoS Computational Biology. [10] This article is available under the Wikipedia compatible CC-BY license, meaning that figures and text from it can be incorporated in this article. This resource may prove valuable should editors decide to work towards FA status.
Best regards, — James Estevez ( talk) 02:26, 18 January 2013 (UTC)
{{
cite journal}}
: CS1 maint: unflagged free DOI (
link)
Hello fellow Wikipedians,
I have just modified one external link on Genome-wide association study. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
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An editor has asked for a discussion to address the redirect Phenome-wide association study. Please participate in the redirect discussion if you wish to do so. Pam D 19:58, 18 February 2020 (UTC)
I added another application of GWAS, its Agricultural Application. I cited two articles to support the idea that GWAS is useful for developing new pathogen-resisted cultivars and improving yields. Would anybody be willing to review it for me? MaggieKKK ( talk) 00:27, 10 December 2020 (UTC)KKK
I added a new section called Conservation applications to provide information about GWA studies as a tool for genetic diversity research and conservation. Aharveypdx ( talk) 02:58, 21 March 2023 (UTC)