Talk:Genomics

message: word
The National Office of Public Health Genomics, CDC <http://www.cdc.gov/genomics/>
This US government site provides updated information on how human genomic discoveries can be used to improve health and prevent disease.  It provides insight into important segments of genomics such as Family History, Population Research, and Genetic Testing. 
Lid6 17:31, 5 February 2007 (UTC)
thread_title: External Link

message: The comments about identity by descent (twins and other family members) should probably be moved to the "Genetics" article. —Preceding unsigned comment added by 136.152.196.157 (talk) 15:09, 27 September 2002
:Note: There are two completely different ways that the similarity of genes of two individuals can be measured; identity by descent and identity by sequence.  Identity by descent is determined by pedigree, while the other measures of similarity are based upon sequence similarity.  Sequence similarity can be measured in a variety of ways, which will produce very different results.  While I can't say how genomic similarities were measured for those examples in the article, it does seem that they were all measured in the same way...except that Gorilla should be closer to Human than Mouse.  If I get around to it, I could make a table with different measurements of how "close" we are to various species.  However, I'd probably ditch most of the data that already exists because most of these species have not had their genomes sequenced.  I'll definitely keep Chimps. adam
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I added a link to the PLOS primer on Comparative Genomics. Should that link be in the Comparative Genomics section, or at the end of the article with "External Links"? adam
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A brief statement of how genomics differs from genetics might be helpful for people who have heard of genetics, but not genomics, and might otherwise assume they are synonyms. —Preceding unsigned comment added by 66.102.74.128 (talk) 00:45, 22 June 2004 
Some figures in the table with relative genetic similarities of different species to humans are suspect.  In general, the numbers sourced to "Americans for Medical Progress" are suspiciously high.  Mouse should not be as similar to human as gorilla, etc.  Given that this is an organization that promotes and defends animal-based research, their tendancy is probably toward inflated similarity between animals and humans.  Someone who knows more about genomics than I do should find a more definitive source. —Preceding unsigned comment added by Cfs14 (talk • contribs) 02:29, 28 March 2006
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In 1987, McKusick and Ruddle, distinguished geneticists, introduced a new journal bearing the name Genomics.  The name is an irregular hybrid of gene and chromosome, which the authors tell us was first used in 1920 but died aborning.  The ultimate map of the genome was analogized to the Rosetta Stone, which would permit the translation of the complexities of gene expression in development and disease.  Five years later, when Collins and Guttmacher (2002) provided a primer of genomic medicine for the physicians who read the New England Journal of Medicine, they offered a broader definition: “The study of the functions and interactions of all the genes in the chromosome, including their interactions within environmental factors.” Maynard S. Clark 16:53, 20 June 2007 (UTC)
thread_title:  Misc 

message: Should Clinton be considered a reliable scientific soure? How many articles did he published in Nature? How may lies did he mixed in his declarations? —Preceding unsigned comment added by 69.141.56.231 (talk) 20:28, 4 October 2005
:This whole table is on questionable standing, since it invites one to compare numbers that are really not comparable. Nonetheless, the statement that the DNA all humans is 99.9% alike is accurate, subject to certain definitions (see Talk:Human genome which includes what Clinton actually said). --Mike Lin 20:54, 4 October 2005 (UTC)
replies: text:  The table has gotten enough critizism - I removed the section for now. // habj 07:58, 10 October 2006 (UTC)
thread_title:  The comparison table 

message: The opening of the article was unclear, and things had been added to it that was not really genomics. I rewrote the beginning of the article, based on two long articles in my encyclopaedia - which unfortunately is in Swedish. I use the web edition so I could link directly to the articles, but since it is in Swedish I am not sure that will be any good. It should be pretty easy to support the content with a source in English, then we maybe can replace it. // habj 09:51, 6 October 2006 (UTC)
thread_title:  Rewrite of start of article 

message: I find it strange we have two separate articles for Genomics and Computational genomics. Perhaps they could be merged? At the very least, I'd like to see these articles reference each other, and provide a succinct explaination of why these two articles are (notably) different. JetheroTalk 22:53, 8 July 2007 (UTC)
replies: text: Egad. I'd suggest Computational genomics be merged with the appropriate topic Bioinformatics.--ZayZayEM 08:00, 6 November 2007 (UTC)
thread_title:  [[Computational genomics]] 

message: It seems the scientific community did not reach consensus on the definition of Genomics and the different application specific derivatives like Toxicogenomics and Pharmacogenomics. There seem to be at least three different schools:
* Restriction to DNA sequence analysis
* Inclusion of RNA expression profiles (Transcriptomics), exclusion of other 'omics
For the purposes of this guidance, the term pharmacogenomics is defined as the use of a pharmacogenomic or pharmacogenetic test (see glossary for definitions) in conjunction with drug therapy. Pharmacogenomics does not include the use of genetic or genomic techniques for the purposes of biological product characterization or quality control (e.g., cell bank characterization, bioassays). The FDA plans to provide guidance on those uses at a future time. Pharmacogenomics also does not refer to data resulting from proteomic or metabolomic techniques.
 
(...)
 
Pharmacogenomic test: An assay intended to study interindividual variations in whole-genome or candidate gene, single-nucleotide polymorphism (SNP) maps, haplotype markers, or alterations in gene expression or inactivation that may be correlated with pharmacological function and therapeutic response. In some cases, the pattern or profile of change is the relevant biomarker, rather than changes in individual markers.
* Inclusion of all 'omics
the term "genomics" encompasses a broader scope of scientific inquiry and associated technologies than when genomics was initially considered. A genome is the sum total of all an individual organism's genes. Thus, genomics is the study of all the genes of a cell, or tissue, at the DNA (genotype), mRNA (transcriptome), or protein (proteome) levels. 
Any ideas how to tackle this for the article? Any concensus should also be reflected in the other  -genomics articles.  --Oleginger (talk) 07:39, 27 August 2008 (UTC)
thread_title:  Consensus on Definition 

message: Gave it a "High" importance in WP: Genetics RE: Assessment factors.  Hope this spurs activity. ~ Amory (talk) 04:31, 4 May 2009 (UTC)
thread_title:  Rating 

message: I'm a layman and the introduction does not make it clear how these two are different.  —Preceding unsigned comment added by 98.194.244.143 (talk) 04:06, 18 June 2009 (UTC)
thread_title:  Genomics versus Genetics 

message: I'm proposing a partial merger of full genome sequencing (FGS) with genomics. Specifically, FGS has several sections (full genome sequencing#Societal_impact, full genome sequencing) that I believe would be better included here. FGS also has several sections (Commercialization) that would be better included in History of genomics. Finally, FGS should be moved to Whole genome sequencing, which appears to me to be the preferred term. —Estevezj (talk) 10:42, 29 January 2012 (UTC)
replies: text: I am moving to Whole genome sequencing because that is the preferred term. As supporting evidence, "Whole genome sequencing" gets about 10 times as many ghits as "Full genome sequencing" on both Google and Google scholar. What you say about the migration of information from WGS to genomics sounds like a good idea, because that information has applicability in many genomics subtopics and not just in WGS.  Blue Rasberry (talk) 18:44, 18 March 2012 (UTC)
replies: text: I just found WGS very useful as I feel I know about genomics and genetics and wanted to get straight to the point of the reality and commercial availability of WGS. Don't merge, duplication is fine. Lindosland (talk) 17:02, 12 June 2012 (UTC)
replies: text: Very well. I intend to put some work in to bring genomics up to snuff. As part of that process I'll include some information from whole genome sequencing but leave it in place in that article. I will remove the merger template shortly. —James Estevez (talk) 04:57, 15 June 2012 (UTC)
thread_title:  Merger and splitting proposal 

message: I've begun moving some material that has been staged into on my sandbox draft of the long-promised overhaul of this article, so there'll be some churn over the next few weeks. Also, if there are no objections I also intend to convert this article's references to list-defined format WP:LDR.
Let me know if I inadvertently break anything, or if there any issues. James Estevez (talk) 09:13, 21 December 2012 (UTC)
thread_title:  Article overhaul underway 

message: The existing lede ends:
 Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genomes networks.
The first reference for this statement reads:
 Genetics is a term that refers to the study of genes and their roles in inheritance
and
 Genomics is a more recent term that describes the study of all of a person's genes (the genome)
Consequently I have deleted the reference cited incorrectly for the closing para (leaving the other one and asking for more specifics), and have added the definitions given in the citations into the opening sentence of the lede. Hopefully this will clarify the issue e.g for Maina zacharia who posted above. LookingGlass (talk) 17:58, 28 October 2016 (UTC)
thread_title:  Lede confusion 

message: This article has been rated B-class for a while and is Top/High importance in three WikiProjects. It seems worthy of Good Article status, so I suggest nominating it for Good Article review. As I'm not a significant contributor, I'm opening this discussion before nomination, as recommended at WP:GAI. Pinging  and  as two contributors with recent wiki activity and  who did some great work on this article for WikiProject Computational Biology a while back - what are your thoughts? Comments from anyone else are also welcomed, of course. Thanks! Amkilpatrick (talk) 15:27, 22 June 2017 (UTC)
replies: text: This article clearly needs some work.  I simplified the lead to hopefully make it more accessible. Further work on the lead is needed so that better summarizes the article. In addition, some of the sections are too specialized or sound like advertisements.  I don't think I am capable of bringing this article to GA status all by myself, but I would be willing to help.  Boghog (talk) 19:50, 22 June 2017 (UTC)
replies: text: Thanks for that improvement! Jytdog (talk) 20:24, 22 June 2017 (UTC)

text: Thanks . I've thought this could make GA with a moderate lift but I've not had the time since leaving school. I'm willing to chip in if it's a team effort. I'll defer  to the more recent contributors as to coordination. To put that in more concrete terms, I can commit to about 4 hours of work per week for the next 3 weeks. — James Estevez (talk) 20:38, 22 June 2017 (UTC)
replies: text: Sounds good, it's not my direct area of expertise but I'm willing to help out also. , thanks for working on the lead, what other sections do you think need worked on? To me, the section on sequencing seems a bit long compared to the assembly and annotation sections. I might try and recruit some more people from relevant WikiProjects, hopefully we can improve what we already have. Amkilpatrick (talk) 06:09, 23 June 2017 (UTC)
replies: text:  Thanks Amkilpatrick and James for volunteering to help.  I agree with Amkilpatrick that the assembly and annotation sections should be expanded.  Another section that should be fleshed out is the application section, especially with respect to biomedical research.  Finally, several of the sequencing sections in my opinion focus too much on the companies.  If it is OK with everyone, I plan to start with the application section. Boghog (talk) 07:06, 23 June 2017 (UTC)
replies: text:  I've just made some revisions to the sequencing sections, to focus more on the methods and less on the companies, also attempting to clarify on shotgun methods/Sanger sequencing. Any improvements welcomed as always, I should have some time to look at the assembly section in the next few days. Amkilpatrick (talk) 14:51, 25 June 2017 (UTC)
thread_title:  Proposed Good Article nomination 

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thread_title:  External links modified 

message: The definitions in the respective Wikipedia pages do not appear to differ between genotype and genome. This is also evident in most definitions I found. Is there a difference? Clarification would help - and perhaps a mention in the Introduction to Genetics article (https://en.m.wikipedia.org/wiki/Introduction_to_genetics).
“The genotype of an organism is its complete set of genetic material”(https://en.m.wikipedia.org/wiki/Genotype). There is a somewhat different definition of genotype from the NHGRI at NIH (https://www.genome.gov/genetics-glossary/genotype).
“a genome is all the genetic information of an organism” (https://en.m.wikipedia.org/wiki/Genome)
It would also be informative to discuss the genetic information of the entire population of an organism. Does it have a name? How many more genes are present in the population of an organism than in a single individual? Presumably unknown but the current academic thoughts (or lack of) would be interesting. QuietJohn (talk) 16:49, 14 June 2023 (UTC)
thread_title:  Genome, genotype and genes of an entire population