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Basic genetics & genomics starts with a brief explanation of differences between genetics and genomics.

Genetic Variations  is closely intertwined with this glossary. Other related glossaries are Applications Functional Genomics, Sequencing, Biology Gene Definitions,  Maps Sequences, DNA & beyond, and ultimately, Proteins, Protein structure.  Additional references to organizations appear in the In-depth glossary, after the Bibliography.

agricultural genomics: See crop genomics

annotation: Bioinformatics glossary

applied genomics: Applications are at varying stages of development and include clinical genomics, pharmacogenomics, plant and animal breeding, drug discovery and development and microbial genomics.

biochemical genomics: Functional genomics glossary  

biocomplexity: The investigation of complex adaptive systems in all disciplines of biology. The ubiquity in nature of complex non- linear systems has already driven the search for unifying mathematical principles that can be applied to the different branches of life sciences. This effort will be of foremost importance for developing a fundamental understanding of life, and it will have great integrative power because the very same tools will be applicable to a range of problems and disciplines. The study of biocomplexity is (1) driven by theory and quantitative modeling that is explicitly linked to empirical studies and experiments, (2) interdisciplinary in nature within the life sciences, and (3) will engage researchers in bioinformatics, mathematics, physics, and computer science. We are making progress in understanding complex biological systems, but it requires a strong departure from the more familiar reductionist approach - this approach examines the parts while assuming that the behavior of the whole is simply the sum of their individual actions. To understand the whole one must understand the complex integration of these interactions, and in this sense the whole is more than the sum of the  parts. [Office of the President, Univ. of Michigan "Challenges and Opportunities in Understanding the Complexity of Living Systems: The Biocomplexity Initiative, 2000]  http://www.umich.edu/pres/committees/commreport/Biocomplexity_overview.html  Related terms complex, complexity

chemical genomics, chemogenomics: Drug discovery and development glossary.

combinatorial genomics: Similar in concept to required for recognition of all items in long- term memory combinatorial chemistry, this technology shuffles portions of genes to give a vast number of new combinations, which are then screened for a desired function. Enhanced function, or even new functions, can be generated by repeating the cycle circuits many times to "evolve" optimized recombinants in vitro. [Department of Defense Critical  Technologies Part III: Developing Critical Technologies Section 3: Biological Technology, July 1999]  http://www.dtic.mil/mctl/data3/p3sec03.pdf

comparative genomics: Functional genomics glossary.

complex: It has become common to use complicated and complex interchangeably … The essence of ‘complicated’ is hard to figure out. ..Complex, on the other hand is a term reserved for systems that display properties that are not predictable from a complete description of their components, and that are generally considered to be qualitatively different from the sum of their parts. [Editorial, "Complicated is not complex" Nature Biotechnology 17: 511 June 1999] Would it be fair to say that Mendelian genetics is linear, while genomics and polygenic diseases/traits are nonlinear?

According to the Oxford English Dictionary one of the meanings of complicated is complex, though it also means not easy to unravel or separate. Both complex and complicated are contrasted with simple. Whatever the original senses of these two words, the above distinction seems a useful one now. Related term complexity. Narrower terms complex diseases, complex genomes; In-depth complex phenotypes, complex traits.

complex diseases: Diseases characterized by risk to relatives of an affected individual which is greater than the incidence of the disorder in the population. [NHLBI] Are complex diseases essentially the same as polygenic diseases?

Genome scans for other complex diseases have met with limited success, in part because of the difficulty in detecting the small individual contribution to phenotype made by many different genes. Recent theoretical work suggests that this problem may be circumvented by performing association tests with a large number of markers (on the order of 30,000) spread across the genome. To make such a large number of tests feasible, one needs markers that can be scored without resorting to gel- based techniques, and this has led to intense interest in developing methods to identify and detect single- nucleotide polymorphism markers or SNPs. SNPs are typically biallelic markers that differ from each other by one nucleotide (this difference can be a transition, transversion or even a deletion). There are several techniques available to score SNPs, and we are exploring the use of the 5' nuclease- detection system or TaqMan to score SNPs. ["Human genetics" David Botstein Lab, Stanford Univ.] http://genome-www.stanford.edu/group/botlab/humans.html

Related terms Genetic variations glossary Omes & omics phenome, phenomics

complex genomes: Is there a specific definition of complex genomes?  Or is it a more general category (beyond viral, bacterial,  microbial?)

complex phenotypes: Those that exhibit familial clustering, which suggests at least some genetic component, but they do not occur in Mendelian proportions in pedigrees. Such phenotypes may have relatively simple underlying genetics, but their transmission appears complex because of its context, including interactions with other loci and with the environment. Alternatively, complex phenotypes may have multiple genetic and environmental causes. Most chronic, common diseases are complex by this definition. Complex phenotypes may be continuous in distribution, like height or blood pressure, or they may be dichotomous, like affected and not affected. The complexity arises from the fact that many genetic and environmental factors may interact with each other in unpredictable ways, such that the association between the phenotype and any single factor taken by itself may be imperceptible. Nonlinear interactions, including epistasis and genotype by environment interactions, mean that the expression of the phenotype may not accurately predicted from knowledge of the individual effects of each of the component factors considered alone, no matter how well understood the separate components may be. 

Genetic Architecture of Complex Phenotypes Initiative, NIGMS, NIH, US (part of its Initiative Supporting Quantitative Approaches to Complex Biological Problems, June 9,1998] http://www.nigms.nih.gov/news/announcements/complexity.html

complex trait: Has a genetic component that is not strictly Mendelian (dominant, recessive, or sex linked) and may involve the interaction of two or more genes to produce a phenotype, or may involve gene environment interactions." [NHLBI] Related term genetic architecture Genetic variations glossary

complexity:: Currently there are more than 30 different mathematical descriptions of complexity. However we have yet to understand the mathematical dependency relating the number of genes with organism complexity. [J. Craig Venter et. al. "The sequence of the Human Genome" Science 291 (5507): 1347, Feb. 16, 2001] Related term biocomplexity, complex.

crop genomics: Agricultural biotechnology continues to benefit from the insights being developed during the era of the Human Genome Project. The proliferation of mapping, genotyping, and diagnostic methodologies has rapidly expanded the analytical tools available to crop scientists for the analysis and utilization of plant genomes. Related terms  environmental genomics;  Model & other organisms glossary Arabidopsis

ARS [Agricultural Research Service] Genome Database, Cornell Univ. US http://ars-genome.cornell.edu/

FAO Glossary of Biotechnology and Genetic Engineering, Food and Agricultural Organization, United Nations, 2000.  About 5000 terms. http://www.fao.org/DOCREP/003/X3910E/X3910E00.HTM#Toc

DNA Forensics: DNA evidence takes an ever- increasing profile in criminal investigation and trials. The goal of this program is to provide an integrated examination of evidence available from DNA and the prospects for further enhancements in technology, databases, and procedures that may address issues of current controversy. DNA Forensics: Profiling PCR June 27- 28, 2002 Washington DC  

The primary forensic technology is Gene amplification & PCR.  Related terms Genetic variations glossary DNA fingerprinting, markers, microsatellites, VNTR.

DNA forensics, Oak Ridge National Laboratory, US http://www.ornl.gov/hgmis/elsi/forensics.html

DNA fingerprinting - Recombinant DNA chapter of MIT's Biology Hypertextbook http://esg-www.mit.edu:8001/esgbio/rdna/rdnadir.html

deductive genomics: Functional Genomics glossary.

environmental genomics: This programme will apply genomics to the natural environment, using sequence data to advance and test evolutionary and ecological theory, and so provide a better understanding of ecosystem function in the context of biodiversity (intraspecific genetic variation, species richness and perceived redundancy). 

The programme aims to advance our understanding of how organisms perceive change (at the molecular and genetic level) and make functional responses within their local environment, and to what extent variation in these responses is adaptive. These measures may be short- term adaptations, quorum sensing, regulated gene expression, survival, reproduction etc. Alternatively, they may be longer- term adaptations in respect to horizontal gene flow, community diversity, species abundance and the evolution of speciation. Genomics also allows investigation of adaptation at the level of individual versus community diversity. Current advances in molecular techniques allow the development of predictive studies of evolutionary biology and ecology. As we enter the post- genomics era, sequence data and technological advances in genomics will facilitate the direct interrogation of habitat diversity and specific cellular activity, and in particular patterns of gene expression in different habitats and in response to environmental change. [Natural Environmental Research Council UK, Environmental Genomics Programme Summary 2001] http://www.nerc.ac.uk/funding/thematics/envgen/

evolutionary genomics: Functional Genomics glossary.

forensics: See DNA forensics

function, functional genomics:  Functional Genomics glossary.

gene: Gene definitions

genetic architecture: Genetic variations glossary

genetic variations, human: Genetic variations glossary

genetics: Clinical genomics  See also Basic genetics & genomics

genome: The complete set of chromosomal and extrachromosomal genes of an organism, a cell, an organelle or a virus; the complete DNA component of an organism. [IUPAC Biotech]

The fundamental concepts of genome, genotype and phenotype are not defined in a satisfactory manner within the biological literature. Not only are there inconsistencies in usage between various authors, but even individual authors do not use these concepts in a consistent manner within their own writings. We have found at least five different notions of genome, seven of genotype, and five of phenotype current in the literature. Our goal is to clarify this situation by (a) defining clearly and precisely the notions of genetic complement, genome, genotype, phenetic complement, and phenotype; (b) examining that of phenome; and (c) analysing the logical structure of this family of concepts. [M. Mahner, M. Kary "What exactly are genomes, genotypes and phenotypes? And what about phenomes?" Journal of  Theoretical Biology 186 (1): 55- 63, May 1997]

All the DNA contained in an organism or a cell, which includes both the chromosomes within the nucleus and the DNA in mitochondria. [NHGRI] Size expressed by the number of base pairs. [DOE].

Narrower terms: Gene Definitions chromosomal genome, mitochondrial genome

First used by H. Winkler in 1920, was created by elision of the words GENes and chromosOMEs, and that is what the term signifies: the complete set of chromosomes and their genes. [V McKusick "Genomics: Structural and Functional studies of genomes" Genomics 45:244-249 Oct. 15 1997]  

Genome databases: See Databases & software directory.

genomic DNA: The entire length of DNA, including non coding regions. (Sometimes called gDNA.) [CHI Bioinformatics]

DNA which includes exons and introns, coding and noncoding regions. Compare with cDNA.  Gene definitions 

genomic data: [Genomic datasets] are best used to identify "outlier" genes that are particularly highly expressed or have especially many interactions rather than to focus on the individual measurements for a particular gene. A gene that makes a particularly large number of interactions may indicate that it is a key component of the cell. One numerical technique that is particularly useful with regard to dealing with this information is expressing results through ranks - i.e. not giving the number of interactions of a particular gene product, but how it ranks when compared with others.  Furthermore, it provides a powerful way to combine many different heterogeneous sources of information into a common and statistically robust numerical framework (Gerstein & Levitt 1997; Gerstein & Hegyi 1998; Qian et. al. 2001). ... Many websites focus on providing a lot of information for a single gene sequence or protein, in a "non- genomic" fashion. Rather, such sites should be designed to simultaneously display and manipulation large populations of genes. In the absence of such an 'omic interface, it is important that information resources at least accommodate bulk downloading of standardized data.  [Dov Greenbaum, Mark Gerstein et. al. "Interrelating Different Types of  Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001] http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf.

Related terms: Expression glossary; Omes & Omics glossary interactome; Proteomics glossary

genomics: Generation of information about living things by systematic approaches that can be performed on an industrial scale. [Roger Brent "Genomic biology" Cell 100: 169-183 Jan 2, 2000]  http://www.molsci.org/htdocs/publications/omicbio/brentcell.html

If there were any questions previously, the publication of the draft sequence for the human genome has made it very clear that genomics is going to play an increasingly critical role in the development of pharmaceuticals in the years to come. Such specialties as bioinformatics, gene expression monitoring, functional genomics, proteomics, and pharmacogenomics will all need to be melded into efficient strategies to accelerate drug discovery and development. These tools are being brought to bear on the key applied tasks of target identification and validation, as well as clinical evaluation of compounds being developed. Impact of Genomics on Medicine  May 13- 14, 2002, Munich, Germany

Q: After combining all the biological and medical data resulting from different technologies, you end up with much more than the raw genetic sequence. Do we call the sum of these multiple data types genomics, or is there a better word for it? Dr. [Charles] Cantor: People have been inventing terms like "functional genomics," "physiological genomics," and "physiomics." Genomics itself is just a parts list: A car has four tires, two axles, and so on. How well you can predict what will go wrong, knowing the parts list, is arguable. It has some predictive value, but it doesn't have fully predictive value. We need to integrate the parts list with all the other information. To me, that integration is not genomics, it's medicine. It's biology.  [Incyte Genomics "Inside Genomics Archives" Interview with Charles Cantor, 2001] http://www.incyte.com/insidegenomics/int/int/int_int_0003/int_int_0003_8.shtml

Coined by Thomas H. Roderick [of the Jackson Laboratory, Maine, US] in 1986 in Bethesda, MD during a discussion of a name for a planned new journal (Genomics) that was to include sequencing data, discovery of new genes, gene mapping, and new genetic technologies. According to Roderick, the term genomics "also had the comparative aspect of genomes of various species, their evolution, and how they related to each other. Although we didn’t come up with the term ‘functional genomics’ we thought of the genome as a functioning whole beyond just single genes of sequences spread around a chromosome." [B Kuska "Beer, Bethesda, and Biology" JNCI 90(2): 93 Jan 21, 1998]

Although I haven't found any references to "genomics" prior to 1987, "genomic" is easily found in Medline from 1966 on, and probably could be located in journals earlier than that.

genomics- commercialization: Commercialization of Genomics report, August 2001 Cambridge Healthtech Institute http://www.chireports.com/upcoming-reports.asp

genotype: The genetic constitution of an organism as revealed by genetic or molecular analysis, i.e. the complete set of genes, both dominant and recessive, possessed by a particular cell or organism. [IUPAC Biotech]

The observed alleles at a genetic locus for an individual. [NHLBI] 

An organism’s genetic makeup, as revealed through molecular analysis. [CHI SNPs Update]

May refer to identifying one or more, up to the entire gene sequence of an organism. Compare phenotype.

genotyping: The determination of relevant nucleotide- base sequences in each of the two parental chromosomes. [CHI SNPs Update]

genotyping technologies: Sequencing glossary

haplotype: A particular pattern of sequential SNPs found on a single chromosome. These SNPs tend to be inherited together over time and can serve as disease- gene markers. The examination of single chromosome sets (haploid sets), as opposed to the usual chromosome pairings (diploid sets), is important because mutations in one copy of a chromosome pair can be masked by normal sequences present on the other copy. [CHI SNP Update]

The linear, ordered arrangement of alleles on a chromosome.  Haplotype analysis is useful in identifying recombination events. [NHLBI]  

The resulting genotype for a chromosomal locus constructed by combining the allele assignments from two or more genetically linked allele systems. Each individual will have two haplotypes for the 'megalocus', representing the markers on the two homologous chromosomes, and the haplotypes will segregate in a pedigree following Mendelian inheritance. [C. Helms, Washington Univ. St. Louis, US "Haplotyping" Nov. 1990] http://hdklab.wustl.edu/lab_manual/14/14_4.html

From  “haploid genotype.”  

Related terms  Cell biology glossary diploid, haploid, ploidy; Sequencing glossary haplotyping, haplotyping technologies. Narrower term: Genetic variations glossary SNP haplotype

high throughput genomics: Genomic studies are now approaching "industrial" speed and scale, thanks to advances in gene sequencing and the increasing availability of high- throughput methods for studying genes, the proteins they encode, and the pathways in which they are involved. Data can now be acquired on many genes at once, either sequentially or in parallel. It is also possible to expand the range of genomic effects being examined. The abundance of new data available means that more targets should now be identifiable, but the key to finding such new targets will be to use the right combination of technologies and have them ideally integrated. [CHI High Throughput Genomics] Related terms Bioinformatics high throughput Drug discovery & development target validation.

Human Genome Project HGP : An international effort formally begun in October 1990. The project was planned to last 15 years, but rapid technological advances have accelerated the expected completion date to 2003. Project goals are to discover all the approximate 30,000 human genes (the human genome) and make them accessible for further biological study ..  Another project goal is to determine the complete sequence of the 3 billion DNA bases in the human genome. As part of the HGP, parallel studies are being carried out on selected model organisms such as the bacterium E. coli to help develop the technology and interpret human gene function. The Department of Energy's Human Genome Program and the National Institutes of Health's National Human Genome Research Institute (NHGRI) together make up the U.S. Human Genome Project. [Oak Ridge National Lab, HGP "FAQ"  About the Human Genome Project 2001]  http://www.ornl.gov/hgmis/faq/faqs1.html  http://www.ornl.gov/hgmis/project/about.html

The total human genome, contained in a set of 23 chromosomes, is now estimated to contain 3,164.7 million letters (or nucleotides). In humans the actual part of the genome that codes for proteins makes up less than 2% of the genome Compared with the organisms whose genomes have been sequenced before, humans have a particular abundance of proteins involved in cell structure, defense and immunity, DNA copying, the synthesis of RNA and proteins, and communication between cells. Humans have an unusually high number of complex proteins that fit into more than one functional category and many proteins that are embedded in the surface of cells. [NHGRI "Summary of the Initial Sequencing and Analysis of the Human Genome" press release, Feb. 11, 2001] http://www.nhgri.nih.gov/NEWS/summary_of_sequence.html

Horace Freeland Judson writes in "Talking about the genome" (Nature 409:769, 15 Feb. 2001) "The language we use about genetics and the genome project at times limits and distorts our own understanding, and the public understanding. Look at the phrase - or marketing slogan - 'the human-genome project'. In reality, of course we have not just one human genome but billions. ... Then, too, the entire phrase - the human- genome project: singular, definite, with a fixed end- point, completed by 2000, packaged so it could be sold to legislative bodies, to the people, to venture capitalists. But we knew from the start the genome project would never be complete. The maps, or the sequences, are just the start of many lines of research, polyphiloprogenitive, multiply multiple genome projects."

The human genome sequencing effort has enabled researchers to search for genes that encode the proteins that run our cellular machinery and have a role in disease progression in order to identify targets for therapeutic intervention. The emphasis is now shifting from identifying to validating and prioritizing targets and selecting compounds directed against those targets. This conference will explore the world of information technology that is impacting genomics and the life- science industry as a whole, as well as the latest efforts to create operating systems for biology.  Human Genome Discovery: Commercial Implications Feb. 25-27, 2002, Santa Clara, CA

Related terms In-depth DDBJ, DOE, EMBL, GenBank, NCBI, NHGRI, RIKEN, Sanger Centre; Sequencing glossary  resequencing

Human Genome Project Links
International Human Genome Sequencing Consortium special issue: Nature 409 (6822) 15 Feb., 2001   http://www.nature.com/nature/journal/v409/n6822/ http://www.nature.com/genomics/human/papers/analysis.html

Celera Genomics special issue: Science 291 (5507) Feb. 16, 2001 http://www.sciencemag.org/content/vol291/issue5507/index.shtml

Human Genome Project Working Draft Univ. of California Santa Cruz, US, http://genome.ucsc.edu/

GenomeWeb, Medical Research Council, UK.   http://www.hgmp.mrc.ac.uk/GenomeWeb/

Human Genome Project Dept. of Energy (DOE), Oak Ridge National Lab, US http://www.ornl.gov/hgmis/

Human Genome Central, Sanger Centre, UK  http://www.ensembl.org/genome/central/

Human Genome Project, NHGRI, NIH, US http://www.nhgri.nih.gov/HGP/

DOE’s Primer on Molecular Genetics is a useful introduction to the HGP,  the concepts and technologies underlying genomics. http://www.ornl.gov/hgmis/publicat/primer/intro.html

industrial genomics: Related term: high throughput genomics

integrative genomics: The journal Functional & Integrative Genomics is devoted to large- scale studies of genomes and their functions, including systems analyses of biological processes. Topics covered include: – Whole genome analysis, – Comparative genomics, – Genetic variation, – Human disease genes and loci, – Proteomics, – Bioinformatics, – Expression profiling, – Behavioral genomics, – Structural genomics, – Chemical genomics, – Pharmacogenomics, – Integrative genomics, – Large- scale analysis of biological systems. [Springer website, Functional & Integrative Genomics - Aims & scope, 1999] http://link.springer.de/link/service/journals/10142/aims.htm

Mendelian genetics: Classical genetics, focuses on monogenic genes with high penetrance, the tip of the iceberg of genetics. It is useful to remember that Mendelian genetics itself was a true paradigm shift, and not at all intuitively obvious.

This is poignantly described in Robin Henig's artfully crafted biography of Gregor Mendel The Monk in the Garden. Mendel was not recognized by scientists until 1900 --  35 years after his initial publication and 16 years after his death.  Those who heard his talks did not seem to understand them.  Some of the reprints he sent out have vanished.  Others were found (years later) with leaves uncut and unread.

It is also instructive to remember that Mendelian genetics were quite applicable to the breeding of plants and animals (including racehorses) with serious economic implications. This may well have encouraged Mendel's superiors to let him pursue his work with peas.

Mendelian genetics from MIT's Biology Hypertextbook http://esg-www.mit.edu:8001/esgbio/mg/mgdir.html

microbial genomics: Includes microbial sequencing projects and post- sequencing, functional  genomic projects, plant or animal pathogens, environmentally interesting microbes, and related technology development. [Interagency Report on the Federal Investment in Microbial Genomics, White House, 2000] http://www.ostp.gov/html/microbial/start.htm   

Related terms In-depth Beowulf Genomics; Omes & omics glossary microbiome

nanogenomics: The overall objective of this meeting is to bring together investigators who have a common interest in the development and use of nanotechnology for understanding genome organization and function. This meeting provides a unique opportunity for established investigators and students to interact and exchange ideas regarding the use of new and developing technologies to study the nanostructural aspects of the genome, nuclear architecture and biomolecular machinery required for genome- scale management of gene expression. This meeting is particularly relevant in light of the availability of complete model genome sequence data and the implications that sequence elements, both known and unknown, may have on genome structure and organization within the nucleus. It is especially important that scientific communication keep pace with discovery, particularly with respect to advances across disciplines which may have profound impact on the pace of breakthrough discovery. [Jackson Laboratory, US Genomics Meets Nanoscience, October 9 - 12, 2001, Bar Harbor Maine] http://www.jax.org/courses/documents/nano_0901.html

network genomics: The information provided by completely sequenced genomes can yield insights into the multi- level organization of organisms and their evolution. At the lowest level of molecular organization individual enzymes are formed, often through assembly of multiple polypeptides, and at a higher level, sets of enzymes group into metabolic networks. Such context information of metabolic networks combined with genomic context on co- occurrence of genes, fusion of genes or gene- order are powerful approaches in prediction of new functional features and analysis. [Christian Forst "On Network Genomics" CHI's Functional Genomics Oct. 9-10, 2001, Cambridge MA  http://www.functionalgenomics2001.com/fgen.htm

penetrance: The probability of expressing a phenotype given a genotype. Penetrance is described as either "complete" or "incomplete" … .Penetrance may also be dependent on a susceptible individual’s current age… incomplete penetrance is usually a matter of chance or modifiers in the genetic background. [NHLBI] 

Mendelian genetics focuses on genes with high penetrance. These were the easiest genes to identify. Related terms Genetic variations glossary.

phenotype: The observable structural and functional characteristics of an organism determined by its genotype and modulated by its environment. [IUPAC Biotech]

The observed manifestation of a genotype, which may be expressed physically, biochemically or physiologically. [NHLBI]

Refers to all biological consequences from the presence of the mutation in question. Phenotype is logically the subject of functional genomics. In its broadest definition, phenotype includes phenomena at all organizational levels of biology, and is defined as the consequence of mutations in one or more genes relative to an non- mutated or wild type genotype in a given organism. At the molecular level, for example, phenotype includes all temporal and spatial aspects of gene expression as well as related aspects of the expression, structure, function and spatial localization of proteins. The latter has acquired the name "proteomics"   [Univ. of California - Davis "What is Genomics", c. 1999] http://genomics.ucdavis.edu/what.html#compare

Systematic collection and organization of data on phenotypes is still at an early stage.  The International Mouse Mutagenesis Consortium (IMMC), writing in the Human Genome issue of Science notes that improved phenotyping technologies are needed, as are "more efficient and reliable methods for archiving, managing, analyzing, displaying and disseminating the complex phenotype data sets resulting from mutagenesis programs, and that there are no large-scale phenotype databases. Phenotype vocabularies seem to be in the works and a Mouse Phenome Project is based at Jackson Labs, US.  [IMMC JH Nadeau et. al "Functional Annotation of Mouse Genome Sequences" Science 291: 1251-1255 Feb. 16, 2001] 

See note on variant meanings for phenotype, genome and genotype under genome, Journal of Theoretical Biology 1997 article.

Phenotype databases See Databases & software directory

Compare genotype. Related terms genetic architecture; Microarrays glossary phenotype array; Omes & omics glossary phenome, phenomics; Drug discovery & development glossary phenotypic screening; Functional genomics phenotypic profiling; Model & other organisms glossary

phenotypic screen: See under chemical genomics Drug discovery & development glossary

phenotyping: A test that measures some aspect of an organism's functions, for example, the amount of a certain drug needed to inhibit the growth of HIV in a test- tube culture. If HIV has developed resistance to a certain drug, higher- than- normal amounts of that drug will be necessary to inhibit viral activity. Phenotyping assays for HIV test the effect of one drug at a time on the virus in vitro. Results may not correspond to what happens in vivo where the virus is exposed to a combination of antiretroviral agents because marked patient- to- patient variability in the concentrations of the agents may be present and factors such as drugs binding to blood proteins make direct comparison of the in vitro phenotype result and in vivo response incompatible. Phenotyping testing results are expressed as IC50 values [Inhibitory Concentration 50]  the concentration of drug required to reduce the virus' growth in cell culture by 50%. [Visible Genetics NewsRoom Press Kit Glossary of  Terms]  http://www.visgen.com/News_Room/Press_Kit/glossary_of_terms.shtm

phylogenomics: Functional Genomics glossary.

physiological genomics: Functional Genomics glossary.

polygenic: Genetic disorder resulting from the combined action of alleles of more than one gene (e.g. heart disease, diabetes and some cancers). Although such disorders are inherited, they depend on the simultaneous presence of several alleles; thus the hereditary patterns are usually more complex than those of single gene disorders. [DOE] See also multigenic, oligogenic, pleiotropy. Genetic variations glossary

[Axel Kahn] also suggests that the notion of interacting genetic factors in polygenic conditions remains an uncertainty. "Thus far, when we have looked at what we have thought of as multifactorial polygenic conditions, we have only seen diseases with several monogenic causes. Thus for each of a number of conditions we can identify several separate genes, each of which on its own in different patients is associated with diseases which we classify as diabetes or Alzheimer’s disease or obesity. We simply have not really started looking at the additive or multiplicative contributions of several factors to disease inheritance." J. Hodgson "Crystal gazing the new Biotechnologies" Nature Biotechnology 18: 29-31 Jan 2000]

population genetic, population genomics: Genetic variations glossary

post-genomic: The genome era is generally regarded to have started on 28 July 1995, with the publication of the genome of the bacterium Haemophilus influenzae. ["A point of entry into genomics" Nature Genetics 23:273 Nov. 1999]

The "post- genomic era" holds phenomenal promise for identifying the mechanistic bases of organismal development, metabolic  processes, and disease, and we can confidently predict that bioinformatics research will have a dramatic impact on improving  our understanding of such diverse areas as the regulation of gene expression, protein structure determination, comparative  evolution, and drug discovery. The availability of virtually complete data sets also makes negative data informative: by mapping entire pathways, for example, it becomes interesting to ask not only what is present, but also what is absent. [David Roos "Bioinformatics -- Trying to Swim in a Sea of Data" Science 291:1260-1261 Feb. 16, 2001]

Post-genomic can also refer to the increasing emphasis on functional genomics. With an increasing number of organisms for which we have (more or less) complete genomes we are beginning to see glimpses of the power of having fully mapped sequences. Still, in most contexts talk about being "post- genomic" seems a little premature. "Post Mendelian" seems more accurate as we move from an era in which genetics has been rooted in monogenic diseases with high penetrance to a greater awareness (but limited understanding) of polygenic diseases (and traits) often with relatively low penetrance. However with the publication of the draft human sequences in Feb. 2001 we are beginning to be truly "post- genomic".

post-Mendelian: See under post- genomic

structural genomics: Structural genomics glossary.

whole genome: There are several reasons for completely sequencing a genome.  The first and most simple reason is that it provides a basis for the discovery of all the genes. Despite the power of cDNA analysis and the enormous value in interpreting genome sequence, it is now generally recognized that a direct look at the genome is needed to complete the inventory of genes. Second, the sequence shows the long- range relationships between genes and provides the structural and control elements that must lie among them. Third, it provides a set of tools for future experimentation, where any sequence may be valuable and completeness is the key. Fourth, sequencing provides an index to draw in and organize all genetic information about the organism.  Fifth, and most important over time, is that the whole is an archives for the future, containing all the genetic information required to make the organism (the greater part of which is not yet understood). [C. elegans Sequencing Consortium “Genome sequence of the nematode C. elegans; A platform for investigating biology” Science 282: 2013 Dec 11 1998]  Narrower term whole genome index

whole genome index: All the data related to genes, with the information indexed and catalogued in a uniform manner ... [and with] access [to] information about what tissues [those] genes are known to be expressed in, and under what circumstances. The family that the protein encoded by the gene belongs to would be quickly identified, as would valuable information about how genetic variation, or other processes, alter the structure and function of that protein. The active sites on the protein, and the types of compounds that are most likely to interfere with its activity, would be available through a few strokes on a keyboard. ... Without a complete gene index for humans (as well as other medically important organisms), the data- integration problem will be huge, and those researchers who have not adapted their systems to allow for the constant and dramatic changes ahead will spend much of their time just making sure their old data remain usable [CHI Bioinformatics]

Bibliography

[CHI High Throughput Genomics] Genomic Report, Dec. 2001.

Nature “Genome Gateway  http://www.nature.com/genomics/

List of Terms

In-depth Genomics glossary

Beowulf Genomics: The Wellcome Trust established the Beowulf Genomics Initiative in January 1998.  The initiative was established to ensure that the genome sequences of microbial pathogens were available to as wide a range of researchers as is possible.  So far, [Sept. 2000] this initiative has supported the sequencing of 16 bacterial genomes and participated in the funding of two further bacterial genomes, 3 protozoan parasites and one fungus. [Beowulf Genomics, Wellcome Trust, UK, Sept 2000]  http://www.beowulf.org.uk/ Related term microbial genomics.  Any relation to Beowulf computing? Computers & computing

DDBJ: DNA DataBank of Japan Shares information daily with EMBL and GenBank. http://www.ddbj.nig.ac.jp/

DOE Department of Energy: Human Genome Initiative announced by DOE OHER [Office of Health and Environmental Research] in 1986. Congressionally chartered DOE advisory committee, HERAC [Health and Environmental Research Advisory Committee], recommended a 15 year multidisciplinary, scientific, and technological undertaking to map and sequence the human genome in 1987. DOE and NIH outlined plans for cooperation on genome research in 1988. [Oak Ridge National Laboratory (ORNL), Tennessee, US "Major events in the US Human Genome Project"] http://www.ornl.gov/hgmis/project/timeline.html

EMBL (European Molecular Biology Laboratory: Main laboratory is in Heidelberg, Germany, with outstations in Hamburg, Grenoble, France (access to high powered instruments for structure studies) and Hinxton, UK (bioinformatics). Supported by 14 European countries and Israel, shares data daily with DDBJ and GenBank.  http://www.embl-heidelberg.de/

GenBank: Located at NCBI, shares information daily with DDBJ and EMBL. NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. Currently estimated (early 2000) that over 2 million bases are deposited here each day. This growth will only accelerate in the future.  http://www.ncbi.nlm.nih.gov/Genbank/index.html

Now accommodates >10 ¹⁰ nucleotides and more than doubles in size every year. [David Roos "Bioinformatics -- Trying to Swim in a Sea of Data" Science 291:1260-1261 Feb. 16, 2001]

Genetic Annotation Initiative: Genetic variations glossary

Genome Analysis Pipeline: Purpose: Submit a sequence and get back the results of (1) gene and exon model predictions, (2) GRAIL annotated features, and eventually (3) BLAST analysis. This tool is currently undergoing development and testing. Genome Centers wanting to help us refine the options available through this tool are encouraged to contact us. Hosted by the Computational Biosciences Section, Oak Ridge National Laboratory, Oak Ridge, Tennessee, US. http://grail.lsd.ornl.gov/tools/pipeline/

Genome Catalog, Genome Channel: Functional annotation pipeline is being applied to the genome sequences of human, mouse, and over 23 other organisms. This analysis integrates experimental data and predictions around a genome sequence framework. The data is periodically obtained from the GenBank/ EMBL/ DDBJ collaboration and processed through a large- scale computational framework consisting of several analysis modules. Gene models and other features are predicted. Links are made to other databases and experimental data. The results are stored in the Genome Annotation Data Warehouse. There are two major set of interrelated interfaces to this annotated genomes and the links to external databases: Genome Catalog , an HTML browsing and querying interface with summary and detail data about annotation organized around chromosome, contigs, submitted GenBank clones, GenBank annotated genes, GRAIL- EXP gene models, GENSCAN gene models, STS markers, and other features and Genome Channel. a JAVA interactive browser interface provides a rich graphical view of contigs, clones, genes, and other annotation features. [Oak Ridge National Lab, TN, US] http://genome.ornl.gov/GCat/

Genomes to Life: An ambitious program to achieve the most far-reaching of all biological goals: a fundamental, comprehensive, and systematic understanding of life. DOE's proposed Genomes to Life program would make important contributions in the quest to venture beyond characterizing such individual life components as genes and other DNA sequences toward a more comprehensive, integrated view of biology at a whole- systems level. The DOE offices of Biological and Environmental Research and Advanced Scientific Computing Research have formed a strategic alliance to meet this grand challenge. [US Dept. of Energy 'Genomes to Life"]  http://doegenomestolife.org/

HUGO: Human Genome Organization, an international organization of scientists involved in the Human Genome Project, the global initiative to map and sequence the human genome. Established 1989. http://www.gene.ucl.ac.uk/hugo/

International Human Genome Sequencing Consortium: Published the draft human genome sequence in Nature 15 Feb. 2001 See also Human Genome Project.

International Nucleotide Database: Composed of  DDBJ, EMBL and GenBank.

Joint Genome Initiative: Collaboration between Los Alamos National Lab, Lawrence Livermore National Lab and Oak Ridge National Lab. Organized in 1997. http://www.jgi.doe.gov/

NCBI National Center for Biotechnology Information Bioinformatics glossary

NHGRI  National Human Genome Research Institute http://www.nhgri.nih.gov  The National Center for Human Genome Research (NCHGR) became a NIH Institute in 1997 Original NIH funding of genome projects was through NIGMS (National Institute of General Medical Sciences) in 1985. [Oak Ridge National Laboratory (ORNL), Tennessee, US "Major events in the US Human Genome Project"] http://www.ornl.gov/hgmis/project/timeline.html

RIKEN: Rikagaku Kenkyusy Institute of Physical and Chemical Research, Japan. http://www.riken.go.jp/eng/

Sanger Centre, UK: A genome research centre founded by the Wellcome Trust and the Medical Research Council. Our purpose is to further the knowledge of genomes, particularly through large scale sequencing and analysis.   http://www.sanger.ac.uk/