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<%end if%> 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     Genomics categories     Maps     SNPs & genetic variations  ultimately, Proteins     Protein structures and    Proteomics  are all important  

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

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 

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 https://books.google.com/books/about/The_Computational_Beauty_of_Nature.html?id=0aUhuv7fjxMC&printsec=frontcover&source=kp_read_button#v=onepage&q&f=false
Related term: complex    Narrower terms: biocomplexity, biological complexity

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/

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

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    
Personal Genome Project https://pgp.med.harvard.edu/about 

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

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 

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 of Genomics 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 2019 https://www.genome.gov/about-genomics/fact-sheets/A-Brief-Guide-to-Genomics

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,  combinatorial, environmental, food,  forward genetics, forward genomics, genome transplantation, genomics, high- throughput, industrial, intergenomics,  metagenome, metagenomics,  microbial genome,  paleogenomics, phage, quantitative, subtractive 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 

The Genome Project (HGP) was an international scientific research project with the goal of determining the sequence of nucleotide base pairs that make up human DNA, and of identifying and mapping all of the genesof the human genome from both a physical and a functional standpoint.[1] It remains the world's largest collaborative biological project.[2] After the idea was picked up in 1984 by the US government when the planning started, the project formally launched in 1990 and was declared complete on April 14, 2003[3]. Funding came from the US government through the National Institutes of Health (NIH) as well as numerous other groups from around the world. A parallel project was conducted outside government by the Celera Corporation, or Celera Genomics, which was formally launched in 1998. Most of the government-sponsored sequencing was performed in twenty universities and research centers in the United States, the United Kingdom, Japan, France, Germany, Spain and China.[4] Wikipedia accessed 2018 Nov 8 https://en.wikipedia.org/wiki/Human_Genome_Project

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.

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.  Compare multifactorial, polygenic.

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

NHGRI  National Human Genome Research Institute: began as the National Center for Human Genome Research (NCHGR), which was established in 1989 to carry out the role of the National Institutes of Health (NIH) in the International Human Genome Project (HGP). The HGP was developed in collaboration with the United States Department of Energy and begun in 1990 to map the human genome. In 1993, NCHGR expanded its role on the NIH campus by establishing the Division of Intramural Research to apply genome technologies to the study of specific diseases. In 1996, the Center for Inherited Disease Research (CIDR) was also established (co-funded by eight NIH institutes and centers) to study the genetic components of complex disorders. In 1997 the United States Department of Health and Human Services renamed NCHGR the National Human Genome Research Institute (NHGRI), officially elevating it to the status of research institute - one of 27 institutes and centers that make up the NIH. With the human genome sequence complete since April 2003, scientists around the world have access to a database that greatly facilitates and accelerates the pace of biomedical research. The history of the HGP, the history of genomics, and the history of NHGRI, are inextricably intertwined. https://www.genome.gov/27534788/about-the-institute/

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, 

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:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266495/

"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]

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

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

phenotyping:  The process of assigning phenotypes to people or other organisms. Narrower terms: Clinical informatics: computable phenotypes Pharmacogenomics immunophenotyping, molecular phenotyping; : Microscopy image- based phenotyping

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.