Talk:Genomics

Wiki Education Foundation-supported course assignment

This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): La15d. Peer reviewers: Tc16e.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 22:13, 16 January 2022 (UTC)

External Link

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)lid6

I'm not at all sure that eliminating all the external links is quite the best way to clean them up. Perhaps we should dig through the history and replace some, eh?Sairen42 02:57, 22 May 2007 (UTC)

Misc

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

---

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

---

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 ____ 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)

Growth of omics - dropping glycome

It is important to back up statements like that made about glycome with facts. Glycobiology is far and away the preferred term over glycomics. Glycome will perhaps gain in popularity over time but it is not a widely used term in the long running field of glycobiology and it's still a buzzword. To back this up with some numbers take a look at List_of_omics_topics_in_biology where I've done some information gathering on the prevalence of these and related terms in the published literature. I'm basing my statement not only on that (incomplete) piece of work, but also on personal scientific experience. Courtland 02:21, 2005 Mar 2 (UTC)

The comparison table

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)

The table has gotten enough critizism - I removed the section for now. // habj 07:58, 10 October 2006 (UTC)

But... I don't quite see where this article is going?

I'm glad someone took the trouble to write an entry for "genomics". But beyond the first two sections, the information in the article seems a bit randomly assembled.

Generally, a lot of the text in this article puzzles me. For instance it sais, regarding conserved sequence: "Experimental investigation of some of these sequences has shown that some are transcribed into small RNA molecules, although the functions of these RNAs were not immediately apparent." I don't get the point. What RNA are we talking about? What sequences? Of course, functional genes are usually transcribed into RNA (since this is what it means to be coding sequence), but I suppose you mean some third subgroup of conserved sequence, which is non-coding and non-regulatory (as far as is known), and which is then transcribed into some type of RNA of unknown function? Could you provide some sort of reference for the type of phenomenon you refer to?

I think you should get rid of the table too. It seems to be more anecdotal than scientific, judging from the sources, and some of the numbers make no sense at all. 35% genetic similarity between humans and daffodils, for instance? But the daffodil genome isn't fully sequenced, and in any case, how would you align those two genomes? Of course some basic pathways are present in both organisms (as in all eukaryotes, or indeed all organisms!) but a huge number of genes wouldn't even have homologues in the two, and then what would you align? I doubt this was intended as more than a snappy way of saying "all organisms are related"... —Preceding unsigned comment added by MetteHHH (talk • contribs) 13:31, 1 June 2006s

Rewrite of start of article

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)

== genomics and nutrition/health == v

Potential use of genomics could include streamlining an individuals nutrient needs by knowing what the genes say.An example would be knowing if a person had a specific single nucleotide polymorphism or SNP the suggests that they may benefit from an increase of a specific vitamin or vitamins to enhance the function of an effected pathway. One of the SNP variants, MTHFR, can plays a role in homocystiene pathway. Elevated homocystiene could be modified by increased (above the RDA) amounts of supplements such as B12,Folate and P-5-P which can assist in overriding the variants SNP and lead to a normal (versus elevated) homocystiene level. This SNP may play a role in Autism as well (Boris).

Computational genomics

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. Jethero^Talk 22:53, 8 July 2007 (UTC)

Egad. I'd suggest Computational genomics be merged with the appropriate topic Bioinformatics.--ZayZayEM 08:00, 6 November 2007 (UTC)

Ok Tapeshwarkumar6 (talk) 15:01, 2 October 2015 (UTC)

Consensus on Definition

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."Guidance for Industry Pharmacogenomic Data Submissions" (PDF). US Food and Drug Administration. March 2005. Retrieved 2008-08-27.

• 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. "EPA Interim Genomics Policy" (PDF).

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)

Rating

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

---

This article is very poor in quality. It is strange in its focus (2 sentences on human genomics, a paragraph on phage genomics, and one on cyanobacteria???) and it doesn't really say much about the important things. There are many better ways to divide the article. Very broad categories that can be discussed include comparative genomics, functional genomics, evolutionary genomics, ... (structural genomics, developmental,...) Also, it would be good to include more up-to-date information on genome initiatives (e.g. the 1000 human genomes project, various mammalian genomes, etc). Goals that haven't been reached (e.g. single cell genomics) --I could go on and on, but well, it's just a mess right now —Preceding unsigned comment added by 18.97.6.175 (talk) 21:25, 3 October 2009 (UTC)

Genomics versus Genetics

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)

I am zack and i don't understand the difference of genomics and genetics... The only difference I get is genome.. But not that big difference Maina zacharia (talk) 14:29, 5 July 2016 (UTC)

Merger and splitting proposal

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)

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)

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)

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)

Article overhaul underway

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)

The High-throughput sequencing section currently ends in a truncated sentence that makes no sense. PapayaSF (talk) 19:09, 1 November 2013 (UTC)

Also, I don't know enough about this topic to fix this, but there is something else unclear about the High-throughput section. It mentions pyrosequencing, which has a separate entry, but I can't tell if the two are the same thing, or if one is a subset of the other. PapayaSF (talk) 19:14, 1 November 2013 (UTC)

Sanger

in this article it says Sanger sequenced insulin in 1955 yet in the Sanger article it says 1951 http://en.wikipedia.org/wiki/Fred_Sanger

198.103.184.76 (talk) —Preceding undated comment added 14:42, 11 March 2013 (UTC)

There is some ambiguous wording in the Fred Sanger article, the chronology is:

1951

A chain sequenced: Sanger, F.; Tuppy, H. (1951). "The amino-acid sequence in the phenylalanyl chain of insulin. I. The identification of lower peptides from partial hydrolysates". The Biochemical journal. 49 (4): 463–481. PMC 1197535. PMID 14886310.

1952

B chain sequenced: Sanger, F.; Thompson, E. O. (1953). "The amino-acid sequence in the glycyl chain of insulin. I. The identification of lower peptides from partial hydrolysates". The Biochemical journal. 53 (3): 353–366. PMC 1198157. PMID 13032078.

1955

Disulfide bonds sequenced: Ryle, A. P.; Sanger, F.; Smith, L. F.; Kitai, R. (1955). "The disulphide bonds of insulin". The Biochemical journal. 60 (4): 541–556. PMC 1216151. PMID 13249947.

So the complete sequence would have been obtained in 1955 or 1952, depending on whether or not one includes the -S-S- bonds. This is all reviewed in: Stretton, A. O. (2002). "The first sequence. Fred Sanger and insulin". Genetics. 162 (2): 527–532. PMC 1462286. PMID 12399368.. — James Estevez (talk) 03:42, 16 March 2013 (UTC)

Lede confusion

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)

Proposed Good Article nomination

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 Boghog and Shippleheuser as two contributors with recent wiki activity and Estevezj 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)

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)

Thanks for that improvement! Jytdog (talk) 20:24, 22 June 2017 (UTC)

Thanks Amkilpatrick. 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)

Sounds good, it's not my direct area of expertise but I'm willing to help out also. Boghog, 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)

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)

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)

External links modified

Hello fellow Wikipedians,

I have just modified one external link on Genomics. 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:

• Added archive https://web.archive.org/web/20091115214635/http://www.igs.umaryland.edu/research_topics.php to http://www.igs.umaryland.edu/research_topics.php

When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.

This message was posted before February 2018. After February 2018, "External links modified" talk page sections are no longer generated or monitored by InternetArchiveBot. No special action is required regarding these talk page notices, other than regular verification using the archive tool instructions below. Editors have permission to delete these "External links modified" talk page sections if they want to de-clutter talk pages, but see the RfC before doing mass systematic removals. This message is updated dynamically through the template {{source check}} (last update: 18 January 2022).

• If you have discovered URLs which were erroneously considered dead by the bot, you can report them with this tool.
• If you found an error with any archives or the URLs themselves, you can fix them with this tool.

Cheers.—InternetArchiveBot (Report bug) 14:18, 29 December 2017 (UTC)

Genome, genotype and genes of an entire population

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)