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Pharmaceutical Genomics glossary & taxonomy
Evolving terminologies for emerging technologies
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mchitty@healthtech.com
Last revised November 14, 2013 
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Guide to terms in these glossaries  Genomic applications map    Site Map
Basic genetics & genomics starts with a brief explanation of differences between genetics and genomics Other related glossaries include Cancer genomics   Genomic categories   Molecular diagnostics, Genetic & genomic testing   Pharmacogenomics
Applications: Ultimately Drug discovery & Development   Molecular diagnostics & genetic testing  and  Molecular Medicine are the end applications of both genomic and proteomic technologies, data and understanding
Informatics  Bioinformatics   Genomic Informatics   Technologies  Genomic Technologies   Microarrays  PCR and Gene Amplification   Sequencing
Biology  Functional Genomics   Maps   SNPs & genetic variations 
ultimately, Proteins   Protein structures and Proteomics  are all important  

behavior genetics,  behavior genomics: Molecular Medicine 
biochemical genomics: Chemistry & biology

biocomplexity: is concerned with the complex behavioral, biological, social, chemical, and physical interactions of living organisms with their environment. Both the term and the research field are relatively new and encompass other domains like biodiversity, ecology etc.. The aim of biocomplexity research is to discover, access, interpret, integrate and analyze complex ecological data.  Wikipedia http://en.wikipedia.org/wiki/Biocomplexity   Broader terms: complex, complexity

cancer genomics: Cancer genomics 
chemical genomics, chemogenomics: Chemistry
 
comparative genome mapping: Maps genetic & genomic
comparative genomics: Functional genomics

completed genomes: This depends to an extent on how you define "complete". Portions of the human genome are unsequenceable with today's technology.   Related term: Human Genome Project HGP- completion Sequences, DNA & beyond finished sequence

Completed genomes links
Completed Genomes European Bioinformatics Institute, UK http://www.ebi.ac.uk/genomes/ 
Entrez  Genome
, Entrez, NCBI, US  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome 
Special issues [completed genomes], Functional genomics,
Science Magazine http://www.sciencemag.org/feature/plus/sfg/special/index.shtml

complex phenotypes: Those that exhibit familial clustering, which may mean that there is some genetic component, but that do not occur in Mendelian proportions in pedigrees. 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 one cannot accurately predict the expression of the phenotype from knowledge of the individual effects of individual factors considered alone, no matter how well understood each separate component may be. Genetic Architecture, Biological Variation and Complex Phenotypes, PA-02-110, May 29, 2002- June 5, 2005 http://grants1.nih.gov/grants/guide/pa-files/PA-02-110.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 

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] 

Complexity Science comprises a toolset that examines large scale behaviors of complex systems by looking at how individual components of those systems interact with each other and their environment. From these interactions novel behaviors emerge. Stuart Kauffman http://www.santafe.edu/sfi/People/kauffman/

An ill- defined term that means many things to many people. Complex things are neither random nor regular, but hover somewhere in between. Intuitively, complexity is a measure of  how interesting something is. Other types of complexity may be well defined. [Gary William Flake, Computational Beauty of Nature: Computer Explorations of Fractals, Chaos, Complex Systems, and Adaptation, MIT Press, 1998] http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-C.html#complexity  Related term: complex    Narrower terms: biocomplexity, biological complexity
Complexity resources
http://www.comdig.org/ 

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
Genome Project: Why the DOE?
, Oak Ridge National Lab, US, 1997] http://www.ornl.gov/hgmis/publicat/tko/02_why.html

deductive genomics: Functional Genomics
druggable genome: Drug discovery & development
ecotoxicogenomics: Pharmacogenomics

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/

evolutionary genomics: Functional Genomics
expression genomics: Expression gene & protein

function, functional genomics:  Functional Genomics

genetic architecture:
Refers to the full range of genetic effects on a trait; however, when studying variation on such a large [genomic] scale, it is especially important to consider the context or environments in which genetic variation arises, is selected, and is maintained. Genetic architecture is less a fixed property of the phenotype than a characteristic of a phenotype in a particular population. Genetic architecture is a moving target that changes according to gene and genotype frequencies, distributions of environmental factors, and such biological properties as age and sex. Genetic Architecture, Biological Variation and Complex Phenotypes, PA-02-110, May 29, 2002- June 5, 2005 http://grants1.nih.gov/grants/guide/pa-files/PA-02-110.html

genetic variations, human: SNPs & Genetic variations
genetics: Molecular Medicine  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].

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]  

Narrower terms: Gene Definitions chromosomal genome, mitochondrial genome, nuclear genome
Wikipedia http://en.wikipedia.org/wiki/Genome    
Genome databases: Databases & software directory

Personal Genome Project http://arep.med.harvard.edu/PGP/   George Church Lab, Harvard Medical School 

genome components: The parts of a GENOME sequence that carry out the different functions of genomes. MeSH, 2003 

genome properties: An emerging area of research focuses on how properties of genomes arise in evolutionary history. Such research has important consequences for understanding genome organization and for interpreting data on genetic and phenotypic variation. Such research could include the evolution of haplotypes, selection for genetic interactions, and the evolution of recombination and methylation patterns. Genetic Architecture, Biological Variation and Complex Phenotypes, PA-02-110, May 29, 2002- June 5, 2005 http://grants1.nih.gov/grants/guide/pa-files/PA-02-110.html

genome sequencing proposals - prioritization: Status of Organisms in the Prioritization Process for Genome Sequencing and their ‘White Paper’ Proposals. Links to proposals. NHGRI, National Human Genome Research Institute, US  http://www.genome.gov/page.cfm?pageID=10002154

genomic DNA: DNA

genomic instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.  MeSH, 2004

genomic  research: The definition of genomics is not precise. Tom Roderick coined the term, and Victor McKusick and Frank Ruddle used it to launch Genomics the journal in 1987. We follow their definition here, but leave interpretation to your discretion. We intend to include research that addresses all or a substantial portion of an organism’s genome (including a chromosome or chromosome segment, but not a localized gene or gene family). This definition includes positional cloning if it starts from genome- wide (or chromosome- specific) marker scans. We include physical mapping and sequencing of all or a large part of a genome or chromosome. We also include array technologies that monitor expression of very large numbers of genes (hundreds or thousands), and informatic tools primarily intended to interpret DNA sequence or map information on a genomic or chromosomal scale. Software for melding high- throughput sequencing information into contigs would be included, for example, but not software for pedigree construction alone, or translation to protein sequence or simple homology comparison. We include techniques for high- throughput sequencing or genome- scale mapping, but not research directed at one or a few alleles (e.g., a single- locus diagnostic test would be excluded, even if based on DNA sequencing). We acknowledge broad gray zones, and accept therefore that genomics research is what you say it is. [Robert Cooke- Deegan et. al., World Survey of Funding for Genomics Research: Final Report to the Global Forum for Health Research and the World Health Organization,  September 2000]  http://www.stanford.edu/class/siw198q/websites/genomics/finalrpt.htm  Related term: funding of genomic research: Finances

genomics:  The systematic study of the complete DNA sequences (GENOME) of organisms. MeSH, 2001

Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation. Topics within the scope ofGenomics include, but are not limited to:
 Genomics including genome projects, genome sequencing, and genomic technologies and novel strategies.
 Functional genomics including transcriptional profiling, mRNA analysis, microRNA analysis, and analysis of noncoding and other RNAs using established and newly-emerging technologies (such as digital gene expression).
 Evolutionary and comparative genomics, including phylogenomics
 Genomic technology and methodology development, with a focus on new and exciting applications with potential for significant impact in the field and emerging technologies
 Computational biology, bioinformatics and biostatistics, including integrative methods, network biology, and the development of novel tools and techniques
 Modern genetics on a genomic scale, including complex gene studies, population genomics, association studies, structural variation, and gene-environment interactions
 Epigenomics, including DNA methylation, histone modification, chromatin structure, imprinting, and chromatin remodeling
 Genomic regulatory analysis, including DNA elements, locus control regions, insulators, enhancers, silencers, and mechanisms of gene regulation
• Genomic approaches to understanding the mechanism of disease pathogenesis and its relationship to genetic factors, including meta-genomic and the mode and tempo of gene and genome sequence evolution.
 Medical Genomics, Personal Genomics, and other applications to human health
• Application of Genomic techniques in model organisms that may be of interest to a wide audience.  About this journal, Genomics, Elsevier
http://www.journals.elsevier.com/genomics 

The border between genomics and the rest of molecular biology has been stretched thin and has become porous. The term remains useful, but interpreting findings from this and other surveys needs to take definition creep and the changing meaning of genomics in capital markets into account.  . [Robert Cooke- Deegan et. al., World Survey of Funding for Genomics Research: Final Report to the Global Forum for Health Research and the World Health Organization,  September 2000]  http://www.stanford.edu/class/siw198q/websites/genomics/finalrpt.htm

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]  

Brief Guide to Genomics, NHGRI 2011 http://www.genome.gov/18016863

Basic genetics & genomics  (tries to) answer the question of what the difference between genetics and genomics is.

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.

Narrower terms include: Genomics categories: agricultural genomics, applied genomics, Beowulf Genomics, combinatorial genomics, crop genomics, environmental genomics, high throughput genomics, industrial genomics, intergenomics, inverse genomics, microbial genomics, network genomics, plant genomics, translational genomics; Clinical genomics & Molecular Medicine behavioral genomics,  cancer genomics, clinical genomics, oncogenomics, predictive genomics; Computers & computing: computational genomics, post- genomic, post- genomics; Drug discovery & development chemical genomics, chemogenomics; Functional genomics: biochemical genomics, comparative genomics, deductive genomics, forward genomics, functional genomics, lateral genomics, phylogenomics, physiological genomics, reverse genomics; SNPs & other Genetic variations: population genomics; Nanoscience & Miniaturization: nanogenomics, Pharmacogenomics: ecotoxicogenomics,  toxicogenomics

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.hugo-international.org/ 

Human Genome Project HGP: 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. 

A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human genome. MeSH, 1990 Related terms: DDBJ, DOE, EMBL, GenBank, NCBI, NHGRI, RIKEN, Sanger Centre; Maps genetic & genomic   Sequencing  resequencing

Human Genome Project HGP- completion:  The completion of the draft human genome sequence has both symbolic and real implications for this next stage. The symbolic nature of the accomplishment is primarily the fact that people have been claiming for the past 15 or 16 years that the Human Genome Project is biology’s moon shot. The fact that it has been accomplished during the past year or so is very important since it connects with the policy makers and decision makers who control and govern the future of public funding for biological and other research in this country.

The real accomplishment for the life sciences has been the transition to big science, as illustrated by the dramatic decrease in the range of cost per sequence (Figure 2.1). In a way, the real transition to big- time science is evidenced by the large- scale sequencing centers that have cropped up over the last few years and accomplished sequencing the human genome in so timely a manner in both the public and private sector. The public has a conservatively estimated sequencing capacity of eight to ten million lanes per month (75- 80% pass rate, 450- 500 Phred20 bases). The private sector effort is much more difficult to estimate, but the capacity is roughly in ten to twenty million lanes per month. For reference, seven million lanes represent approximately one mammalian genome. These figures demonstrate that this country has a very powerful engine in place to deal with the genomes that will need to be sequenced in the months and years ahead. Ari Patrinos, US DOE CHI's GenomeLink 9.2 

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 2002]  http://www.ornl.gov/hgmis/faq/faqs1.html 

When will the human genome project be complete? Jared Roach, Strategic Genomics,  2002  http://www.strategicgenomics.com/Genome/wager_with_Trey.htm

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

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/

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.

Minorities, race and Genetics: Human Genome Project Information, DOE, US http://www.ornl.gov/TechResources/Human_Genome/elsi/minorities.html

monogenic: Diseases caused by alterations in single genes. Single -gene disorders are also sometimes called Mendelian disorders since they  are usually transmitted in a manner such as that described by Mendel as simple recessive or dominant traits. CHA Cambridge Healthtech Advisors, Clinical Genomics: The Impact of Genomics on Clinical Trials and Medical Practice report, 2004 Compare multifactorial, polygenic.

multifactorial diseases: SNPs & other genetic variations
NCBI National Center for Biotechnology Information Bioinformatics

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 

nanogenomics: Nanoscience & Miniaturization 
network genomics: Functional genomics

nonlinear: Advances in genomic technologies are a mix of incremental improvements to existing technologies (linear) and occasionally, a truly new paradigm or breakthrough.  Related terms  complex; Business of biotechnology disruptive technologies, emerging technologies, 

oncogenomics: Cancer genomics 

OpenHelix blog: PLOS http://www.openhelix.com/blog/ Genomics data, databases and tools.

optogenetics: A rapidly evolving field of technology that allows optical control of genetically targeted biological systems at high temporal and spatial resolution. By heterologous expression of light-sensitive microbial membrane proteins, opsins, cell type-specific depolarization or silencing can be optically induced on a millisecond time scale. … Although recent developments in optogenetics have largely focused on neuroscience it has lately been extended to other targets, including stem cell research and regenerative medicine. The optogenetic (r)evolution, Martin L Rein, Jan M. Deussing, Mol Genet Genomics. 2012 February; 287(2): 95–109, Published online 2011 December 20. doi: 

organelle genomes:  Eukaryotic genomes are multicomponent. The majority of genetic information is located in the nucleus and inherited according to Mendel's laws. However, there are small but essential genomes located in the cellular organelles - the plastids and mitochondria. Plant cells, therefore, have three separate genetic systems. Organelle genomes differ from nuclear genomes in a number of important ways. They are small relative to the nuclear genome. There are multiple organelles per cell and each organelle contains from 20 to 20,000 organelle genomes depending upon the cell type. Organelle genomes are organized into structures called nucleoids. Organelles are easily purified from other cell contents by differential centrifugation. The abundance of these organelles and organelle genomes makes it easy to study their biochemistry and molecular biology. Organelle genomes are inherited in a non- Mendelian fashion. Inheritance can be studied using RFLP markers. While inheritance is usually through the maternal parent only, there are a number of interesting exceptions in the higher plants. [Christine Chase, PCB 6528, Institute of Food and Agricultural Sciences, Univ. of Florida, 2001] http://www.hos.ufl.edu/ctdcweb/pcb6528I.htm

Related term: organelles Cell biology  Narrower term: mitochondrial genes Compare nuclear genes

"parts list": Now that the sequencing of the human genome is approaching completion, an important next step is to extract as much of the information contained in the genome as possible. All of the genes encoded in the genome should be enumerated, a task that is not as simple as once thought. Other data sets of high interest include all of the regulatory elements, all forms of structural RNA, recombination and replication signals, and all encoded proteins and their modified forms. In contrast to genomic sequence, which can in principle be determined completely, there are questions about whether any of these other data sets can be compiled with the same degree of completeness. It is not obvious that completeness is even conceivable in the case of some data sets, such as transcripts (given alternative splicing), regulatory elements, proteins (given isoforms), protein- protein and protein- nucleic acid interactions, and protein modifications. The desire for completeness will need to be balanced by cost-benefit considerations.  Beyond the beginning: The Future of Genomics, NHGRI, Dec. 12-14, 2001, Warrenton, VA  http://www.genome.gov/10001650

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: SNPs & Genetic variations

pharmacogenomics: Pharmacogenomics

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, Genome Center "What is Genomics" http://www.genomecenter.ucdavis.edu/what.html

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] 

From a cellular point of view, the phenotype can be divided into two parts – the proteome and the metabolome, the observed phenotype being their summation. Both of these phenotypes are important, but in different ways. The changes observed in the metabolome directly indicate what system changes (i.e. genes or drugs) affect the function of which pathways. As well, the exact point(s) in the pathway affected can be determined. The proteins involved in these pathways may be useful drug or pesticide targets.

See note on variant meanings for phenotype, genome and genotype under genome definition, Journal of Theoretical Biology 1997 article.  Narrower term: human phenotypes

Phenotype databases See Databases & software directory  
Mammalian phenotype ontology:
http://www.obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype 

Mammalian Phenotype Browser, MGI Mouse Genome Informatics, Jackson Laboratory, Compare genotype. Related terms: genetic architecture   immunophenotyping  Microarrays & protein arrays  phenotype array; -Omes & -omics  metabolomics, phenome, phenomics; Drug discovery & development  phenotypic screening; Functional genomics phenotypic profiling; Microarrays  phenotype array; -Omes & -omics  metabolomics, phenome, phenomics;  Model & other organisms   Pharmacogenomics genotype- to- phenotype, phenotype standards, phenotype- to- genotype  Narrower terms: metabolic phenotypes: Metabolic engineering & profiling  molecular phenotyping: Pharmacogenomics  reaction phenotypes: Metabolic engineering & profiling

phenotypic screening: Assays & screening

phenotyping: A major challenge in phenotyping is weighing the need to gather sufficient information on each mutation against the need to screen large numbers of animals to gain broad coverage of the genome. Proper balance of these factors will maximize the eventual recovery of interesting new mutations. Our approach is to devise efficient screens for a series of phenotypic domains, favoring high- throughput, simple tests (and multiple tests where possible), and then to rely on more sophisticated confirmatory testing of suspect mice. [Scientific Overview, Neuroscience Mutagenesis Facility, Jackson Laboratory, US, 2002]  http://www.jax.org/nmf/documents/overview.html Narrower terms: Pharmacogenomics immunophenotyping, molecular phenotyping; : Microscopy image- based phenotyping

phylogenomics, physiological genomics: Phylogenomics

polygenic:  The next scientific frontier, however, will be those polygenic disorders involving a combination of gene polymorphisms, each of which contributes in some small way to pathology. Examples of such conditions include a variety of mental and behavioral problems (alcoholism, schizophrenia, depression), as well as physiological disorders that involve complex interactions between genetics and environment (atherosclerosis, hypertension). These problems will require the ability to look at patterns of gene expression at multiple stages of disease/ disorder progression and under a variety of physiological and environmental conditions. Array technologies will provide just such capabilities. 

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] 

[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." John. Hodgson "Crystal gazing the new Biotechnologies" Nature Biotechnology 18: 29- 31 Jan 2000]  Related terms: Clinical genomics: behavior genomics; SNPs & genetic variations  multigenic, oligogenic, Gene definitions: pleiotropy. 

population genetics, population genomics: SNPs &  Genetic variations

post-genomic era: 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]

But the human mitochondrial genome was sequenced in 1981 and published in Nature 290 (5806): 457- 465, Apr. 9, 1981. Sequence and organization of the human mitochondrial genome by S. Anderson et. al.

[Francis Collins] began his presentation by taking issue with the term "post-genomics era." He queries whether his means that from the beginning of the universe until 2001 we were in the "pre-genome era," and then suddenly, "bang" we moved into the past-genome era (leading one to wonder what happened to the genome era). He suggested that it was presumptuous to say that the Human Genome Project is already behind us.  He pointed out that proteomics is a subset of genomics, and genomics is more than sequencing genomes, which will be ongoing for decades to come. Defining the Mandate of Proteomics in the Post- Genomics Era, Board on International Scientific Organizations, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html 

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]  http://www.sciencemag.org/cgi/content/full/291/5507/1260

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-genomics: The general rubric "post- genomics" encompasses an increasingly broad array of topic areas -- essentially, anything connected with teasing higher biological meaning and function out of raw sequence data. [Science Online "Functional genomics research]  http://www.sciencemag.org/feature/plus/sfg/research/index.shtml  Related terms: -Omes & -omics

post-Mendelian: See under post- genomic
predictive genomics: Clinical genomics
Radio Free Genome: DNA 
reference genome: 

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

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/

structural genomics: Protein informatics
toxicogenomics: Drug safety & pharmacovigilance 
virtual genomes: Protein informatics

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 

Bibliography
DOE, Human Genome Project Information, Oak Ridge National Laboratory, Genome Glossary, 2012. 100+ definitions. http://web.ornl.gov/sci/techresources/Human_Genome/glossary.shtml
FAO Glossary of Biotechnology for Food and Agriculture: Revised and augmented edition, Food and Agricultural Organization, 2001  http://www.fao.org/DOCREP/004/Y2775E/Y2775E00.HTM
     Searchable database http://www.fao.org/biotech/index_glossary.asp  Not just for food or agriculture. 
NHGRI (National Human Genome Research Institute), Glossary of Genetic Terms, 100+ definitions. http://www.nhgri.nih.gov/DIR/VIP/Glossary/pub_glossary.cgi   Includes extended audio definitions.
GenomeWeb, Medical Research Council, UK.   http://www.hgmp.mrc.ac.uk/GenomeWeb/
All about the Human Genome Project, NHGRI, NIH, US, 2005  http://www.genome.gov/10001772 
Human Genome Project Working Draft Univ. of California Santa Cruz, US, http://genome.ucsc.edu/
Users guide to the Human Genome, Nature Genetics, 2002 http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v32/n1s/index.html#Editorial
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
Supplemental Celera Public Information http://publication.celera.com/cds/login.cfm
Human Genome Working Draft Sequence published February 15 & 16, 2001 Science and Nature, HGMIS, Oak Ridge National Lab, http://www.ornl.gov/hgmis/project/journals/journals.html  
Nature “Genome Gateway  http://www.nature.com/genomics/

Genomics Conferences http://www.healthtech.com/Conferences/Search.aspx?k=&r=&s=GENS
Genomics CDs, DVDs http://www.healthtech.com/Conferences/CompactDiscSearch.aspx?k=&r=&s=GENS 
Genomics Short courses http://www.healthtech.com/Conferences_Upcoming_ShortCourses.aspx?s=GENS

Insight Pharma Reports Genomics series http://www.insightpharmareports.com/Genomics-Reports/

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