Terminology

Arabidopsis thaliana

Arabidopsis thaliana, thale cress, mouse-ear cress or arabidopsis is a small flowering plant native to Eurasia. A. thaliana is edible by humans and, as with other mustard greens, is used in salads or sautéed, like many species in the Brassicacea. A. thaliana is considered a weed; it is found by roadsides and in disturbed lands. A winter annual with a relatively short life cycle, Arabidopsis is a popular model organism in plant biology and genetics. 

Assembly

Assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 30000 bases, depending on the technology used.

Automated sequencing

Automated sequencing refers to the technique that was invented by Leroy Hood and Lloyd M. Smith and introduced by the Applied Biosystems Model 370A DNA Sequencing System in 1987. This sequencer utilized the Sanger sequencing method and a then-novel fluorescent labeling technique which enabled all four dideoxynucleotides to be identified in a single lane simultaneously. This technology formed the basis of the “first generation” of DNA sequencers and enabled the completion of the Human Genome Proj

BAC library

A BAC library is a series of Bacterial Artificial Chromosomes (BACs) grouped together to store fragments of target DNA to create a "library" containing the target genome.

Bacterial artificial chromosome (BAC)

A Bacterial Artificial Chromosome (BAC) is a DNA construct, based on a functional fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually E. coli. BACs are often used to sequence the genomes of organisms in genome projects, such as in the Human Genome Project.

Bacteriophage

A bacteriophage (also known simply as a phage) is a bacterial virus, that is, a virus that targets and infects bacterial cells. Bacteriophages have been important to molecular biology. During the field's early years, phages were used as a model organism in order to study basic biological processes such as DNA replication.

Base

A base is a single unit of DNA, composed of one of the four nucleotides that make up the molecule.

Behavioral genetics

Behavioral genetics is the study of of the genetic basis of behavioral traits. This field must tease apart the impact of both genetic and environmental influences. Common approaches include twin and adoption studies. Despite considerable technological progress, the genetic influences in most complex behavioral traits are still difficult to pin down.

Bioinformatics

Bioinformatics is a subfield of biology that focuses on analyzing biological data sets.

Biosecurity

Biosecurity refers to procedures designed to protect humans or animals against biological threats or agents.

Biotechnology

Biotechnology is an industry that arose from the genetic engineering revolution of the 1970s focusing largely on drug development. Biotech companies were initially focused on monoclonal antibodies rather than small-molecule drugs, but lines have since blurred.

Caenorhabditis elegans (C. elegans)

C. elegans is a small worm (specifically a nematode) whose size and simplicity have made it a popular model organism for several decades.

Cancer virus

A cancer virus is any virus that can cause cancer by inducing tumor growth. It is also known as a tumor virus or oncovirus.

Capillary DNA sequencer

A capillary DNA sequencer uses capillary electrophoresis as its method of sequencing. The DNA goes through a very thin fiber called a capillary, which separates the molecule by size. The development of capillary DNA sequencing represented an improvement over older, gel-based sequencing processes, significantly increasing the speed of the work.

Capillary electrophoresis (method)

Capillary electrophoresis is an efficient method by which large molecules such as DNA are separated by size, aiding in their analysis. For DNA sequencing, the fluorescently tagged molecule is fed through a long, thin capillary and separated using a conducting medium and and electric field. Capillary electrophoresis is an improvement upon earlier methods of gel electrophoresis, which were slower and required much more manual work from researchers.

Carcinogen

A carcinogen is any substance or agent that has the potential to cause cancer.

Centimorgan (cM)

A centimorgan (also written "centiMorgan" and abbreviated "cM") is a unit of genetic recombination, named in honor of the Drosophila geneticist Thomas Hunt Morgan. It is not a set physical distance, as it is a measurement of recombinant frequency. One centimorgan, however, is on average about 1 million base pairs.

Chromosome

Chromosomes are the threadlike packages containing DNA that are inside all living cells.

Chromosome map

A chromosome map is a map of the position of genes on an individual chromosome. It is typically the prelude to determining the complete sequence of that chromosome.

Chromosome mapping (method)

Chromosome mapping is the process of finding the position or location of specific genes on a chromosome.

Chromosome paint

Chromosome paint is a fluorescent probe used to distinguish and identify individual chromosome in in situ hybridization experiments.

Chromosome sequencing

Chromosome sequencing is the determination of the full nucleotide sequence of an individual chromosome. The Human Genome Project could therefore be divided into 24 discrete chapters, as the draft sequence of each human chromosome was published.

Cloning (glossary)

Cloning is the isolation of a particular DNA sequence and the replication of it using vectors and recombinant DNA methods.

Comma-free code

A comma-free code was an early, elegant but flawed model for the genetic code proposed in the mid-1950s by Francis Crick.

Commercial instrument

Commercial instruments are those tools manufactured and distributed by for-profit companies. Although technology often has its roots in academic labs, commercial companies play a vital role in developing, improving, and optimizing those technologies. The Human Genome Project was only made possible through the participation of such firms and the use of their products.

Communicative disorder

A communicative disorder is any disorder that affects a person's ability to communicate with others, either because of partial or full impairment of the ability to speak, hear, or process language and speech information.

Complementary deoxyribonucleic acid (cDNA)

Complementary DNA is a DNA strand that is artificially created from a strand of messenger RNA. Complementary DNA is a key tool in cloning genes.

Complementary DNA (cDNA) probe

A cDNA probe is a probe (i.e. a fragment of DNA) consisting of the DNA copy of an active, transcribed gene.

Complete sequence

A complete sequence is the full, entire sequence of a gene, chromosome, or genome. Determining the complete sequence of a chromosome or genome is hampered by repetitive DNA, heterochromatin and structures such as centromeres.

Deoxyribonucleic acid (DNA)

DNA is the molecule that encodes all organisms' genetic "blueprint."

Designer baby

A designer baby is the concept of a child that has been selected for desirable traits. The concept raises important ethical concerns about eugenics and the future of genetic screening and personalized medicine.

DNA chip

The DNA chip, also known as a DNA microarray, was developed in the 1990s to measure gene expression and variation.

DNA clone

A DNA clone is an isolated fragment of DNA propagated in a vector such as a plasmid or artificial chromosome.

DNA clone (cosmid) library

A DNA clone library is a collection of fragments of DNA used to

DNA fingerprinting

DNA fingerprinting was discovered by SIr Alec Jeffreys (Leicester, UK) in 1983 and published in 1984. It is the use of repetitive DNA elements to provide a genetic "fingerprint." It began to be used in criminal cases and transformed forensic science and also paternity cases.

DNA forensics

DNA forensics refers to the use of DNA as a forensic tool. This was made possible by the discovery of DNA fingerprinting.

DNA methylation

DNA methylation refers to the presence of methyl groups on the DNA molecule. Methyl groups modify the expression of genes and the function of DNA in general.

DNA sequencing instrument

These are lab instruments used to determine the sequence of nucleotides in a DNA strand. The first commercial automated DNA sequencing machine was produced by Applied Biosystems in 1986. Subsequent machines provided the technology for the Human Genome Project.

Double helix

The double helix is the "winding staircase" structure of DNA, discovered by James Watson and Francis Crick in 1953.

Draft sequence

A draft sequence refers to a "rough draft" of a complete genome sequence that needs more work for refinement and accuracy. The draft sequence of the human genome was completed in 2001, two years before the final sequence was published.

Epigenome

The epigenome is a genomic map of epigenetic modifications.

EST (expressed sequence tag) strategy

The use of expressed sequence tags, or fragments of active genes, was championed by J. Craig Venter and colleagues as a rapid means to acquire sequence information on the most important regions of the human genome. The strategy was published in Science (Adams et. al.) in 1991.

Ethical, legal, and social implications (ELSI)

ELSI refers to the study of the possible effects of genetics and genomics research on individuals, communities, and broader society. It was an important component of the Human Genome Project: inaugural director James Watson authorized 3% of HGP funds be directed to the study of ethical, legal, and social issues (ELSI) surrounding genome mapping and screening.

Expressed gene

An expressed gene is a gene that is actively switched on in certain tissues and/or stages of development.

Expressed sequence tag (EST)

EST (expressed sequence tag) was a term coined by J. Craig Venter, Mark Adams and colleagues at the NIH in a landmark 1991 article in Science. As originally defined, an EST was a cDNA fragment selected at random and partially sequenced, prior to searching for sequence homologues in GenBank.

Fetal tissue transplantation

Fetal tissue transplantation is an experimental procedure in which fetal tissue could produce chemicals to treat neurological diseases including Huntington's, Parkinson's, and Alzheimer's.

Fluorescent chain-terminating dideoxynucleotide

The development of fluorescent dideoxynucleotides was a crucial step in the launch of automated capillary electrophoresis, which greatly accelerated the pace of genome sequencing in the latter stages of the Human Genome Project.

Free availability of human genome sequence

A key principle of the public Human Genome Project was the free deposition of data into the public domain every 24 hours.

Free-living organism

A free-living organism is any organism that is able to live on its own and is not dependent on another organism for survival.

Fugu rubripes (pufferfish)

Fugu is a species of pufferfish. The sequencing of the Fugu genome was completed and published in 2002. Its small genome is useful as a reference for finding genes and studying other aspects of genomics.

Functional element

The International ENCODE Project concluded that large tracts of the human genome possessed some biochemical or functional activity.

Functional genomics (discipline)

Functional genomics is a term that arose midway through the Human Genome Project that addressed the need to assay and identify the functional properties of the gene catalogue.

Gene

A gene is a distinct section of DNA that represents the code or "instructions" for a specific protein product. Genes are composed of specific sequences of bases (nucleotides) of varying length.

Gene/genome mapping

Gene/genome mapping is determining the chromosomal location of genes, through either physical or genetic approaches.

Gene-based designer drug

Identification of disease genes gives hope to rationally designed drugs. Gleevec, which counters the BRC-ABL gene fusion in leukemia, is a good example. Gene therapy is showing signs of promise after a major setback in the Gelsinger case.

Gene count

Analysis of the reference genome revealed that human possess about 20,000 genes. This is far fewer than the oft-quoted 100,000 estimate that was widely used until the draft sequence came into view.

Gene expression

Gene expression is the pattern of gene regulation and activity, which varies by cell type and at different stages of development. The advent of DNA microarrays provided a huge leap in our understanding of gene expression in development and diseases such as cancer.

Gene patent

Newly isolated genes were widely patented by biotech companies and non-profit organizations throughout the 1990s, often stirring controversy. A high-profile lawsuit filed by the American Civil Liberties Union against diagnostics company Myriad Genetics led to the U.S. Supreme Court's overturning gene patents in 2013.

Genetic code

The genetic code refers to the rules that determine which codons (triplet sequences of nucleotides) code for which proteins in DNA.

Genetic linkage map

A genetic linkage map shows the position of genes on a chromosome based on their recombination frequency. This is done by identifying close association or linkage to random polymorphic markers of known chromosomal location.

Genetic mapping

Genetic mapping is a method of building a recombination map of DNA markers by performing systematic linkage studies of genes and random polymorphic DNA markers.

Genetics

Genetics is the branch of biology that studies genes, genetic information, and heredity.

Genetic screening

Genetic screening refers to the analysis of human DNA for medical purposes, especially in testing for genetic features or mutations that may bring about disease.

Genome

A genome is the total genetic material of an organism.

Genome maintenance

Genome maintenance refers to biological mechanisms and processes that preserve the genome's integrity. These include mechanisms for preventing cancer like DNA repair and cell division cycle control.

Genome project

A genome project is the research effort to sequence the entire DNA of any organism.

Genomics

Genomics is the study of whole genomes. This includes sequencing and mapping as well as analysis of their structure and function.

Germline

Germline refers to cells that pass the genetic information from generation to generation.

Haemophilus influenzae (glossary)

Heamophilus influenzae is a bacterium that was the first free-living organism to have its genome sequenced. The sequence was published in 1995 and demonstrated the viability of the then-new whole-genome shotgun sequencing method.

HeLa (definition)

HeLa is the cancer cell line derived from the African-American woman Henrietta Lacks (also known by the pseudonym Helen Lane) without her knowledge in the 1950s. It is now the most widely used cancer cell line in research.

Heritable mutations

Heritable mutations are mutations that are passed down from generation to generation, rather than acquired spontaneously or somatically.

High throughput biology

The term "high throughput" refers to using automation to conduct large numbers of experiments and therefore produce large quantities of data. For instance, in drug discovery, high-throughput screening means the use of automation to assess the biological activity of many different compounds. High-throughput sequencing refers to sequencing large amounts of DNA in short amounts of time.

Hybridization

Hybridization is a method by which complementary DNA strands can anneal together. It is a critical component of gene mapping, linkage mapping, and DNA amplification through the polymerase chain reaction.

Informatics

Informatics is the computational analysis of information. It includes sub-specialties such as bioinformatics and cheminformatics.

Junk DNA (glossary)

Junk DNA is the nickname given to DNA that does not code for proteins. The term "junk" was used for many years to imply the DNA had no function; now, many scientists believe it may serve to regulate the coding regions.

Marker

A marker is a genetic landmark representing a specific location on a chromosome. Markers in the Human Genome Project were typically polymorphic DNA sequences such as RFLPs and STSs.

Marker spacing

Marker spacing is the interval between adjacent DNA markers. The shorter the average distance between markers, the higher the resolution of the genetic map.

Megabase (Mb)

A megabase (Mb) is a unit of measurement for DNA length. It is equal to 1 million bases or nucleotides.

Mendelian inheritance

Mendelian inheritance refers to genes or traits that follow the rules of classical genetics, established by Gregor Mendel in the 1860s.

Messenger RNA (mRNA)

Messenger RNA is the intermediary molecule on which the DNA code is "transcribed" and then brought from the cell nucleus to the ribosome for protein synthesis.

Microarray

A microarray is a genetic profiling technique used to analyze gene expression – that is, which genes are turned on and which are turned off.

Microbial genome

A microbial genome is a bacterial genome sequence. The first was sequenced and published in 1995 by J. Craig Venter and colleagues at The Institute for Genomic Research (TIGR).

Microbiome

The microbiome is the collection of microbial life in a particular ecosystem. This could refer to a location or a part of the human body, such as the gut microbiome or the skin microbiome. It is a rapidly growing aspect of genomic research, given growing evidence of the sheer volume of microbes that live in and on humans and their positive and negative role in human health.

Mitochondrial DNA

Mitochondrial DNA is DNA found within a cell's mitochondria. Mitochondria take the energy from food and make it usable to the cell.

Model organism

A model organism is a relatively simple organism scientists study to understand biological processes in more complex living things.

Molecular biology (discipline)

Molecular biology is the study of biology and biological processes at the molecular level by examining the structure and function of essential molecules such as DNA and RNA.

Molecular genetics

Molecular genetics is a term referring to the modern study of genetics at the molecular level. The term is redundant since there is no field of contemporary research using a non-molecular approach to genetics.

Moore's Law

In technology, Moore's Law refers to the doubling of the number of transistors on integrated circuits every two or so years, pointing to the increasing complexity of computer processors. The law's logic has been applied to molecular biology both in the analysis of the complexity of life and in the area of genome sequencing. For instance, as sequencing technology has become "miniaturized" (that is, as the working parts of automated sequencers have shrunk) the process has become cheaper.

Mouse genetics

Mouse genetics is the study of genetics in inbred strains of mice, providing crucial discoveries and understanding of genetic phenomena. The mouse is an important model organism, with close genetic similarilty to humans but significant advantages in the ability to cross, develop inbred strains, etc. The mouse genome was mapped and sequenced in parallel with the human genome.

Mutagen

A mutagen is any compound that causes mutations in DNA.

Naturally occurring DNA

Naturally occurring DNA is DNA that occurs in nature, as opposed to that which is synthesized or assembled artificially.

Next-generation sequencing (definition)

Next-generation sequencing refers to methods of DNA sequencing developed in the early 2000s that replaced Sanger sequencing for high-throughput genome sequencing. This was commercially developed by companies like Solexa, 454 Life Sciences, and Pacific Biosciences.

Oncogene

An oncogene is a gene that has the potential to convert normal cells into cancerous ones.

Personal genome

Personal genome is a term for the partial or full sequencing and analysis of individual genomes, made possible by rapid advances in DNA sequencing technology. The first published personal genomes were those of J. Craig Venter and James Watson in 2007-08.

Personalized medicine

Personalized medicine is an approach to medicine that seeks to individualize a patient's treatment based on his or her genetic information.

Phenome

The phenome is the set of all observable properties of an organism.

Physical map

A physical map is a structural map of genes and other DNA landmarks using physical mapping techniques, such as fluorescence in situ hybridization or radiation hybrid mapping, in contrast to genetic mapping approaches.

Plant genome

A plant genome is the total genetic material of a plant. Arabidopsis thaliana was the first model plant organism to be sequenced. The rice genome is perhaps the best known and arguably the most important plant genome sequenced to date.

Polymerase

Polymerase is an enzyme used to synthesize polymers, specifically chains of nucleic acids such as DNA and RNA. DNA polymerases specifically create DNA molecules and are an essential tool of molecular biology.

Polymerase chain reaction (PCR) (method)

Polymerase chain reaction is a revolutionary laboratory technique in which a piece of DNA can be amplified many times over, creating thousands or even millions of copies.

Population-scale sequencing

Population-scale sequencing is the ability to sequence large communities, or even entire populations or countries, thanks to the plummeting price of next-generation sequencing.

Positional cloning

Positional cloning refers to a method for identifying genes, especially disease genes.

Post-genomic world

Post-genomic world is a disputed term sometimes used to refer to the era of biology and medicine following the completion of the Human Genome Project. Some argue, however, that this is merely the genomic era.

Prenatal genetic testing

Prenatal genetic testing is genetic screening and testing before birth. Screening is increasingly being performed non-invasively using new methods to detect small quantities of fetal DNA in the maternal blood.

Protein sequencing (glossary)

Protein sequencing is the process of determination the sequence of amino acids that compose a protein molecule.

Pulsed field electrophoresis

Pulsed field electrophoresis was an important gel-based method developed by Charles Cantor and colleagues to separate large fragments of DNA. It was widely used in the early phase of the Human Genome Project.

Recombinant DNA

Recombinant DNA is DNA molecules formed by the splicing together of genetic material from different sources.

Regulatory region

A regulatory region is a section of the genome that contains sequences (such as promoters) that regulate the activity of genes. These genes may be adjacent to the regulatory region or far removed.

Research and development (R&D)

Research and development, or R&D, is the collective term for basic and applied research, as used in corporate and government organizations.

Restriction fragment length polymorphism (RFLP)

A restriction fragment length polymorphism (RFLP) is a DNA fragment produced by restriction enzymes that differs in length across genetically related organisms. As a technique, they are used in the diagnosis of hereditary disorders.

Sanger chain termination method, DNA sequencing

The Sanger method is a manual DNA sequencing method. It was developed by Frederick Sanger and published in 1977. It was one of the earliest sequencing methods devised and soon became the standard in the field.

Sequence-tagged site (STS)

A sequence-tagged site (STS) refers to a short DNA sequence that can be easily located and amplified using the polymerase chain reaction (PCR) laboratory technique. The purpose of an STS is to serve as a genetic marker when mapping. They supplanted the use of restriction fragment length polymorphisms (RFLPs) during the Human Genome Project.

Sequencing

Sequencing refers to the process of determining the sequence of nucleotide bases in a DNA strand.

Sequencing dye

Sequencing dyes are dyes, typically fluorescent, that are used to track DNA nucleotides and fragments in sequencing methodologies.

Sequencing strategy

A sequencing strategy is the choice of sequencing system, platform or approach used for a project. For de novo genome sequencing, shotgun sequencing strategies have become almost ubiquitous since the conclusion of the Human Genome Project.

Single nucleotide polymorphism (SNP)

A single nucleotide polymorphism is a point of variation among DNA sequences in which the difference is one nucleotide base.

Somatic cell hybridization

Somatic cell hybridization is a classic method used to map genes using somatic cell hybrids containing varying compositions of human chromosomes on a mouse background.

Structural variation

Structural variation refers to a tier of genetic variation in humans and other organisms involving deletions, duplications and rearrangements of variably sized segments of DNA. Structural variation impacts the copy number of scores of genes, and growing evidence points to the role of structural variation in many genetic disorders. It is also known as copy number variation.

Synthetic biology

Synthetic biology refers to a 21st century version of genetic engineering. Specifically, it is the ability to synthesize long stretches of DNA and to cut and paste DNA modules to engineer new functions and properties into cells and organisms.

Systems biology

Systems biology is a conceptual approach to the study of biology that stresses viewing biological phenomena as part of a larger picture. Specifically it is the computational analysis of complex biological systems, whether molecules, cells, organs, or entire organisms.

Technology transfer

Technology transfer is the process by which products, devices, and technologies developed in universities or non-profit laboratories is licensed and commercialized.

Telomere

A telomere is a DNA fragment that serves as the "tip" or "cap" at the ends of a chromosome. They are made of a repeating sequence of  DNA and are responsible for protecting the chromosome's physical integrity.

Therapeutics

Therapeutics refers to drugs and treatments and their delivery to patients.

Thermostable polymerase

Thermostable polymerase is a heat-stable form of DNA polymerase crucial to the commercial development of polymerase chain reaction (PCR).

Transcriptional regulation

Transcriptional regulation is the regulation of gene activation and RNA transcription by a variety of protein transcription factors, in addition to epigenetic modifications.

Transposon

A transposon, also known as a transposable element, is a small segment of DNA that can transpose, or change position within the genome.

Tumor virus

A tumor virus is any virus that is associated with cellular transformation and cancer.

Vector

Vectors are vehicles used to isolate, propagate and transfer DNA, for example in cloning experiments or in clinical settings using gene therapy.

Viral genome

A viral genome is the total genetic material of a virus. The first genome ever sequence, completed by Fred Sanger and colleagues in the late 1970s, was that of the virus PhiX174.

Whole-genome shotgun method (method)

Whole-genome shotgun sequencing is a sequencing method in which DNA is randomly broken up into smaller pieces, which are sequenced and reassembled by using computer algorithms to look for overlapping regions.

X-ray crystallography

X-ray crystallography is a method of studying the structure of crystals and molecules by measuring the scattering of X-rays through the structure (i.e. X-ray diffraction). Rosalind Franklin's historic Photograph 51, an X-ray of the B form of DNA, was created using the X-ray crystallography method; this was an essential resource in the elucidation of the double helix by James Watson and Francis Crick in 1953.

Y chromosome

The Y chromosome is the male chromosome in humans. It contains only a few dozen functional genes.

Yeast artificial chromosome (YAC)

Yeast artificial chromosomes are chromosomes that have been genetically engineered from yeast DNA. They are an important vehicle for cloning long segments of DNA.