Talk:Pharmacogenomics

message: Please merge - To begin with, present definition of Pharmacogenetics as “genetic differences in metabolic pathways” does not make any sense, because metabolic pathways represent proteins/enzymes, not genes.  — Preceding unsigned comment added by Biology editor (talk • contribs) 19:29, 28 February 2013 (UTC)
replies: text: OK, but now, what was the previous page which was merged? 65.102.40.110 (talk) 00:25, 24 May 2008 (UTC)

text: *  Сolleagues, you're absolutely wrong, there's only a close vicinity of words, but pharmacogenetics does not deal whith genetics at all, it studies methabolical pathways and interdrug relations whithout any genetic considerations. The genetic stuff is added into article just by resemblance of words. Akim Dubrow (talk) 08:42, 5 July 2012 (UTC)
replies: text:  Huh??? Pharmacogenetics: A branch of genetics which deals with the genetic variability in individual responses to drugs and drug metabolism.  Boghog (talk) 10:40, 5 July 2012 (UTC)
replies: text:  Ah, it all mixed. Okay, merge them! =) Akim Dubrow (talk) 18:39, 9 July 2012 (UTC)
thread_title:  Merge with pharmacogenetics? 

message: Genetics and genomics are very closely related fields and they usually speak the same language and address the same issues. Many people do both, or migrate between the two over their career.  They are, however, different in their application, tools, and objectives.  Many (most?) people in pharmacogenomics would have a very tough time just extracting the DNA from a tissue sample, let alone cutting out genes, splicing them into some other expression platform (really, that is more genetic engineering, but it is a handy skill for scientists too!) or doing the sequence.  Some geneticists struggle with basic desktop software, let alone tools like bioconductor. 
*Pharmacogenomics has substantial overlap with bioinformatics, as well as genetics. 
**'Keep both entries and cross reference them as much as possible.  In addition, there is a lot of detail work needed for this page:
***What is the paradigm of pharmacogenomics?
***What methods are used to address which kinds of questions (i.e. the science part) or issues (i.e. the clinical applicability part).
****How is the genetic information acquired, represented, stored, analyzed?
*****Discuss bioinformatics applications, e.g. heat maps, GWAS, etc.
****What is the overlap and use of computational biology?
****What sort of study designs are used?
****What resources are used (PharmGKP, KEGG, SwissProt/UniProt, EC, PDB, etc.)
***Provide an overview of the applications, e.g. not just for selection of chemotherapy, but also in avoiding drug-drug interactions for hundreds-thousands of drugs, predicting anticoagulation results, detecting individuals at increased risk of ADR for reasons other than drug metabolism polymorphisms (e.g. sodium/potassium channelopathies).
*Summarize the key genes, proteins, and pathways.  It does not need to be comprehensive on this page, but some good examples are very helpful.  Then a comprehensive listing, with links to relevant WikiPedia articles is required.  
**Need to get all the individual listings done, obviously, but they also need to be put into a WikiPedia category for Pharmacogenomics just to make life easy.  The page for the category should also list the major external references people like (talk page for that could collect recommendations & reviews of such)
**E.g. A row for each of the major CYP450 genes (e.g. 3A4, 2D6, 2C19, etc. and list all of them in another spot w/ links to WikiPedia entry for the gene, KEGG, PharmGKB, etc.), with the polymorphisms/mutations, the protein (including links to the protein's WikiPedia entry and references to SwissProt/UniProt, EC, etc. etc.), the pathway (and links/references), the substrates/inducers/inhibitors of clinical importance (they can find the total list else where, for example Pharmacology Weekly has a nice set of tables to link to).
**List major pathways in a similar fashion, preferably with a graphic, link to WikiPathways, etc.)
**List major clinical scenarios
***Potential role as newborn screening test to provide a life-long (with liver transplant exception noted!) guide to prescribing
***Use in anticoagulation
***Multiple applications in cancer chemotherapy (both in terms of therapy selection--e.g. specific neoplasm mutation/upregulation which predicts response to small-molecule TKase inhibitor) and avoidance of adverse effects (e.g. TPMT when using thiopurine immunosuppressant/chemotherapeutic agents).
--DrKC MD (talk) 18:38, 20 July 2013 (UTC)
thread_title: '''Do NOT concur with merge'''

message: This article was shot through with discussion of fears about race-based medicine.  I have no idea where all that came from (except perhaps concerns arising from the one-off BiDil controversy - but even that had nothing to do with pharmacogenomics as there was no mention of genetic variants in the BiDil labelling).  So I pulled all that into one section and condensed it.  Deleted a bunch of stuff that was giving the topic way too much WP:WEIGHT, when there is neglible relevance to phamacogenomics as it is practiced. Jytdog (talk) 19:49, 7 December 2013 (UTC)
thread_title:  discussion of race overwhelming the article 

message: Deleted this section.  Sources were all like ten years, and discussion had nothing to do with pharmacogenomics as it is practiced today, when  - as the article says - there are about 120 drugs on the market that refer to genetic testing in their label;  this is routine and well integrated into medical practice today.  Very strange addition to the article.  Some kind of time-lapse happened, as though it were 2004 again. Jytdog (talk) 19:51, 7 December 2013 (UTC)
thread_title:  section on "Incorporating pharmacogenomics into practice" 

message: Although the proposed merge of this article into pharmacogenetics was closed as "no consensus", I would like to note that there was just one oppose !vote. In fact, a lot is to be said in favor of the merge. For example, as currently stated, both fields are simply identital: Pharmacogenomics is "the technology that analyses how genetic makeup affects an individual's response to drugs" and pharmacogenetics is the study of " genetic differences in metabolic pathways which can affect individual responses to drugs, both in terms of therapeutic effect as well as adverse effects". Seems pretty much synonymous to me (with the exception that this is, of course, not a "technology" but a field of study). --Randykitty (talk) 16:09, 9 January 2014 (UTC)
replies: text: agreed; the separation is pedantic and makes no sense for a general purpose encyclopedia. Jytdog (talk) 16:35, 9 January 2014 (UTC)

text: *Note that most thihngs discussed in the current article actually concern single genes ... --Randykitty (talk) 12:56, 12 September 2014 (UTC)
replies: text: * That is true. Sorry about not being clear--I was speaking based on my expertise in the field, rather than the current state of the articles. --Mark viking (talk) 15:00, 12 September 2014 (UTC)
replies: text:   does have a point. I mention the CYPs individually. I probably should modify the article to clarify that those CYPs are used collectively to evaluate a patient's overall response to their treatment. So, for example, they can be on 10 medications. You would then look at the CYPs I mentioned to give a comprehensive report on how a patient will respond to those 10 medications based on all their CYP results. My favourite example is fluoxetine. That medication is metabolized by 2D6, 2C9, 2C19, and 3A4. At the same time fluoxetine also strongly inhibits 2D6, so it's a contradictory little drug. In terms of whether the terms should be merged, I am partial to not merging them. Someone earlier did make some incredibly valid points (titled: do NOT concur). To add to that further, a pharmacogenetic example could be something like TPMT genotype and azathioprine response (I say genotype specifically, because there is another test for TPMT levels, which is separate). You look at the TPMT genotype, and essentially assess the risk of myelosuppression. However, the example I gave before with the 10 drugs and CYPs is an example of pharmacogenomics in practice. You review multiple pathways, take into consideration inhibitors, inducers, drug-drug interactions, drug-gene interactions, etc. So, in practice, there is a considerable contrast between the two. That's my perspective. But then you have other brilliant experts like Kirchheiner and Swen, who do prefer merging the two definitions for simplicity.Jarslan (talk) 00:40, 13 September 2014 (UTC)

text: *It's not just simplicity. To me, "genetics" is not confined to studying single genes. When does something start to be "genomics"? When we study 3 genes? 4? 5? If a field like genomics exists, it is in the realm of comparing, say, the human and the Neanderthal genomes. "Genomics" is on the level of a complete "genome". Anything else is just genetics. Of course, nowadays many people feel more important saying they're doing "genomics" than just simple old-fashioned "genetics"... I myself have been doing genetics for about 40 years now and am involved in identifying genes using whole genome scans, followed by system genetics analyses. But I'd never say that I am doing genomics, even though I work with large sets of genes. Most of the current "omics" are just fashionable terms for things that have been around for decades... --Randykitty (talk) 10:47, 13 September 2014 (UTC)
replies: text: *Of course, genetics isn't confined to studying single genes. However, a majority of the publications in this field over the past 50 years has been on candidate drug-gene interactions. I think GWAS studies only really kicked in for pharmacogenomics around 2007 if I remember correctly (really late here, so +/- a couple of years to be on the safe side). So 'genomics' research has been relatively new compared to pharmacogenetics. Which is interesting, when you think about it. In research we have more pharmacogenetics data, but in practice this information is primarily used for pharmacogenomics. I agree that 'omics' is taking over. Maybe we should follow AAPS' definition of both these terms and design the Wiki pages to better reflect their distinctions (AAPS Focus Group definitions: Pharmacogenetics: “the study of genetic causes of individual variations in drug response”; Pharmacogenomics:“more broadly involves genome-wide analysis of the genetic determinant of drug efficacy and toxicity”). Not sure. Let me sleep on it and get back to you :)Jarslan (talk) 13:02, 13 September 2014 (UTC)
thread_title:  Merge revisited 

message: and  - you are both new users, and both are part of Wikipedia:WikiProject Computational Biology/ISCB competition entries 2014.  I have to tell you that in my view, the edits you are making are turning this into a textbook or manual, which is a violation of the policy page WP:NOTHOW.  You should seek guidance so you can turn this around.  Jytdog (talk) 09:15, 12 September 2014 (UTC)
replies: text: I believe that should be , just to make sure they get notified. --Mark viking (talk) 09:57, 12 September 2014 (UTC)
replies: text: thanks! Jytdog (talk) 10:51, 12 September 2014 (UTC)

text: Thank you to  and  for bringing this to my attention. I'm not entirely too certain how this is turning into a textbook (I work in this area, and this wouldn't even make half a chapter). Could you possibly elaborate further so we can make the necessary amendments? Jarslan (talk) 10:22, 12 September 2014 (UTC)

text: Just to add to the above further, I've had a look at the policy and the definitions of a textbook and manual, and from my perspective the edits don't fit those descriptions. For example, the manual refers guiding readers on how to do something, and as far as I can tell my edits don't do that. And the textbook thing is about the same.  I can appreciate where you may be coming from, but I need you to detail it further as to me I've included bits of Pharmacogenomics.Jarslan (talk) 10:22, 12 September 2014 (UTC)
replies: text:  I too have concerns about the recent additions.  There is a distinct difference between and encyclopedia (simply state facts) and a text book (whose purpose is to teach).  An example of a text bookish section is A Practical Example In Pharmacogenomic Analysis.  This section also suffers from WP:NOTRECIPE. Other sections of this article are starting to read like a journal article (e.g., example case studies). Phrases like "We can now perform clustering" have absolutely no place in an encyclopedia (see MOS:NOTED).  Boghog (talk) 10:36, 12 September 2014 (UTC)

text:  For what it is worth, , as far as I can see you are new here, and you would do much better to ask questions and learn, rather than arguing.  It can be really hard for new users to understand how WP works.  We love experts and always want to attract more, but when experts are new, they can be extra hard to work with; when they are new, they are ignorant of WP and its complexities, they are often even unaware that they are ignorant of WP (they don't know what they don't know), and too often they are resistant and combative due to their expertise and status in the real world and won't listen, and we end up with really bad WP:IDHT situations.  Sometimes.  I am hoping you will be open to learning.   The content being added is, to me, somewhat instructive - trying to teach people what PGX is, like a lecturer would, and also trying to teach people how to use PGX.   The "like a lecturer would" aspect is leading to stylistic problems, like:  "For example, we have two patients whom are taking codeine for pain relief."  {besides the bad grammar :) } this is what a teacher standing in front of a classroom would say; it is not (in my view) how an encyclopedia article, describing a topic, describes it.  The How-to problems are more clearly content based - there are now two "example" sections doing just that (one of which starts out very textbook/manual like,  with "In this section, a written example of how a micro-array experiment can be designed and analysed are given step-by-step".  This is not encyclopedic - it is "how to".  Those are just some examples.   Summarizing - some of the issues in my view are tone and style (encyclopedia articles don't sound like teachers; they don't say "we have" anything); some are actual content.  I do very much appreciate the efforts to improve the article and to keep this in plain English as much as possible, btw!  I think the intentions are good; it is just going a bit awry, in my view. Jytdog (talk) 10:51, 12 September 2014 (UTC)
replies: text: following up on this, Jarslan above you wrote " this wouldn't even make half a chapter" - and what we are trying to tell you is that you are working in the wrong paradigm or genre; WP is not like a textbook  and not like a journal article in which research is published.  WP is ~kind of ~ like a review article, but without the authors' opinions.  The key difference from a review article, is that what we editors do here (we are called "editors" not "authors") is read the secondary literature - review articles - and paraphrase and summarize them here, citing the review articles as sources.   WP is a strange beast.  You may want to see our manual of style for health-related content, specifically the section on writing style. Jytdog (talk) 11:10, 12 September 2014 (UTC)

text: , for your information, I wasn't arguing with you. If you note, I offered a thanks and requested clarification on your suggestion. It's quite simple. In the future, may I suggest not jumping the gun, because that is where true ignorance can be found. Now, I will also point out that there are many wonderful resources here that are just as extensive as mine. May I suggest you dabble in Algorithms and Complexities Wiki pages to see what I mean. Personally, the extensiveness of those pages is what I found useful when I first began learning about algorithms. The detail, the tables, they were fantastic, and I am hoping here the basic information I have provided will be of use to others out there. There is some contradiction in what you are telling me. On one hand your discrediting the simplicity of my writing, yet on the other hand you are saying keep it simple. Wiki also does suggest that the articles remain as objective as possible, not subjective, and I've tried to maintain that in my edits as much as possible. I appreciate your view. Jarslan (talk) 11:07, 12 September 2014 (UTC)

text:  The half a chapter thing was a jest. Get a copy of the World Guide for Pharmacogenomics, and you'll see exactly what I mean. I have tried to maintain as much objectivity in this as possible. I appreciate the additional information, though, and thank you for your time in clarifying a few things. Jarslan (talk) 11:07, 12 September 2014 (UTC)

text:  I can only speak for the Example case studies, as that is my edit, not the other parts you mentioned (oh, by the way, , some of the things you have mentioned earlier are not my work). I'll give you my thinking, and we can see if that section still fits. Usually, from my own experience, there is interest in this topic from both patients AND healthcare professionals. And I thought examples in the article would be a good way to illustrate how pharmacogenomics works. Case examples, again from my experience (your experience may be different, I don't know) just make it easier for people to get a concept.Jarslan (talk) 11:30, 12 September 2014 (UTC)
replies: text: Happy that you are willing to discuss but please don't be defensive - please really try to hear us and please don't waste your time and ours arguing that what you have done is just fine.  It is most likely not.   I am sorry you find a contradiction in what I wrote.  There is a difference between using plain English (see WP:TECHNICAL) and essentially transcribing a lecture or writing a textbook.  Going further into the example... the paragraph starting with:  "For example, we have two patients whom are taking codeine for pain relief" appears to be something you created to help teach the point.  Here in WP, this paragraph is WP:OR and probably needs to be deleted.  This kind of goes to what we are trying to tell you.  You are trying to teach, and you created a simple example to teach with, like a good lecturer would.  But that is not what WP is about - WP is not a public lecture by an expert in the topic.  Wikiversity is exactly where something like that belongs -- not here.  And really, please know that I am not questioning your intentions at all - you are clearly trying to make information available to the public, in a clear, NPOV way, which is a great thing. You just seem to be writing the wrong genre.  Jytdog (talk) 11:33, 12 September 2014 (UTC)

text:  Hmm, I thought you also mentioned the Practical Example Case Analysis, which is not my addition. Maybe when I was looking back at what you said, I saw Boghog's paragraph instead. But the codeine example is mine. The original version before my edits had an example, but it was incomplete, so I added more to it. So the example existed prior to my edit, I just clarified it more. And perhaps, but as you said, I want to make this information publicly available. And that is because I have worked in a clinical setting, and I know many people are curious about this topic. But anyway, I do need to leave this here, as I do have work to attend to. Jarslan (talk) 11:52, 12 September 2014 (UTC)
replies: text: Have a great day. i have to get to work too.  Please do reflect on what we're trying to communicate so you can use your WP time well going forward.   Thanks Jytdog (talk) 11:56, 12 September 2014 (UTC)
replies: text: Cheers, I appreciate that. Have a great day too. Jarslan (talk) 12:01, 12 September 2014 (UTC)
thread_title:  Turning into a textbook 

message: One Non-Free Database I don't have access to: http://www.terveyskirjasto.fi/terveysportti/laake.generx.koti
I just received this list of Free DataBases. Sorry I do not have time to check are these already at Wikipedia:
Pharmacogenomics Knowledge Base: 
Collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. 
http://www.pharmgkb.org/index.jsp   
Pharmacogenetics Research Network: 
A nationwide collaboration of scientists studying the effect of genes on people's responses to a wide variety of medicines. 
http://www.pgrn.org/pgx-tools.html  
The Single Nucleotide Polymorphism (SNP) Database: 
A comprehensive database of identified SNP’s 
http://www.ncbi.nlm.nih.gov/snp   
Database of Genotypes and Phenotypes (NCBI): 
A database developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. 
http://www.ncbi.nlm.nih.gov/gap   
Eudragene:
Eudragene is a European collaboration that established a collection of DNA samples as a resource for studying genes which influence serious or adverse drug reactions (ADRs). The group will study an initial set of six ADRs that are important because they cause serious illness in a small number of those exposed to drugs that are otherwise more effective than any alternative, and that are easily identified because they produce distinctive conditions that are not related to the disease for which the drug was prescribed. The coordinating centre will manage the database, and will make samples freely available to academic and industry-based researchers throughout Europe. The collection will be extended to include more ADRs after the first 1-2 years, based on problems of current concern
https://www.eudragene.uk/ 
U.S. Food and Drug Administration – Genomics: 
FDA site on genomics. 
http://www.fda.gov/Drugs/ScienceResearch/ResearchAreas/Pharmacogenetics/default.htm   
Human Genome Project Information: 
Provides a wide variety of information regarding the Human Genome Project 
http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml   
American Medical Association – Pharmacogenomics: 
AMA site that provides a wealth of information regarding pharmacogenomics and its impact on the practice of medicine. 
http://www.ama-assn.org/ama/pub/physician-resources/medical-science/genetics-molecular-medicine/current-topics/pharmacogenomics.shtml  
International HapMap Project: 
A partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals. 
http://hapmap.ncbi.nlm.nih.gov/   
Environmental Genome Project (NIEHS): 
The long-term goal of the EGP is to characterize how specific human genetic variations, or polymorphisms, contribute to environmentally induced disease susceptibility. 
http://www.niehs.nih.gov/research/supported/programs/egp/ 
The Biomarkers Consortium: 
Collaboration designed to coordinate and accelerate the development of biomarker-based technologies, medicines, and therapies for the prevention, early detection, diagnosis, and treatment of disease. 
http://www.biomarkersconsortium.org/index.php?option=com_content&task=view&id=132&Itemid=184 
National Human Genome Research Institute (NIH): 
Established in 1989 to carry out the role of the National Institutes of Health (NIH) in the International Human Genome Project (HGP). The NHGRI's mission has expanded to encompass a broad range of studies aimed at understanding the structure and function of the human genome and its role in health and disease. 
http://www.genome.gov/ 
Table of Valid Genomic Biomarkers in the Context of Approved Drug Labels (NIH): 
Provides a table of valid genomic biomarkers in the context of FDA-approved drug labels. 
http://www.fda.gov/Drugs/ScienceResearch/ResearchAreas/Pharmacogenetics/ucm083378.htm 
Genetests: 
Provides current, authoritative information on genetic testing and its use in diagnosis, management, and genetic counseling. 
http://www.ncbi.nlm.nih.gov/sites/GeneTests/?db=GeneTests  — Preceding unsigned comment added by Ee1518 (talk • contribs) 09:53, 13 April 2016 (UTC)
thread_title:  Some FREE DataBases 

message: Note for future reference that last year I completed the merge from pharmacogenetics; see https://en.wikipedia.org/w/index.php?title=Pharmacogenetics&type=revision&diff=902289086&oldid=900841074&diffmode=visual. II | (t - c) 02:14, 27 September 2020 (UTC)
thread_title:  Merge completed 

message: Which concepts in this article are "too technical" for readers to understand? Jarble (talk) 18:20, 9 May 2024 (UTC)
replies: text: After reviewing the previous talk page discussions, I'm beginning to understand how this article came to be so overly complicated. I find myself agreeing with a lot of the points brought up in the turning into a textbook section of the talk page, which discusses how the article seems to dive into extensive detail where it should be paraphrasing concepts. I also noted an editor merged two articles together. I suspect this wound up creating one giant overly detailed article that tries to explain two concepts poorly instead of one topic well. To that point, the first sentence of the revision before the merge does a far better job of explaining what pharmacogenomics is to a layperson than the entire lead of the current article. Funnyfarmofdoom (talk to me) 01:53, 10 May 2024 (UTC)
thread_title:  "Too technical"