Genetic Research: scientific study of nature that sometimes includes processes involved in health and disease. (NCIt) Techniques for the targeted, specific modification of the genome of living organisms. (HGPIA) Research into the cause, transmission, amelioration, elimination, or enhancement of inherited disorders and traits. (Includes) the systematic study of the complete DNA sequences of organisms. (MeSH)

Bioreactor: container where “proteins” are grown. Nutrients are sent in and wastes are removed. (Lewis, 377) Tools or devices for generating "products" using the synthetic or chemical conversion capacity of a biological system. They can be classical ‘fermentors,’ cell culture systems, or “enzyme” bioreactors. For production of proteins or enzymes, “recombinant” microorganisms such as “bacteria,” mammalian cells, or insect or plant cells are usually chosen. (MeSH)

Breeding: the production of offspring by selective mating in animals or plants. (MeSH) The production of animals or plants by selective pairing. (NCIt)

Dihybrid Cross: cross fertilization focusing on two characteristics. (Norman, 7/21/09) Cross in which the parents different in two distinct characters. (Lawrence) A genetic cross between individuals in which "genes" at two different “loci” are considered. (Indge, 80)

Genetic Hybridization: crossbreeding between genetically dissimilar parents to produce a hybrid. (MeSH)

Monohybrid Cross: cross fertilization focusing on one characteristic only. (Norman, 7/21/09) A genetic cross between individuals in which a single gene is being considered. (Indge, 177) Also referred to as ‘single-trait hybrids.’ Editor's note - when the “true-breeding” parents differ with regard to a single trait, their first generation offspring are called 'monohybrids.'

Test Cross: the researcher crosses the individual of interest to a “homozygous recessive” individual and observes the “phenotypes” of the offspring. (Brooker, 330)

True-Breeding: an organism which has the same "genotype" as its parents. (Indge, 277) A variety that continues to exhibit the same "trait" after several generations of self-fertilization. To ‘breed true’ is to continue a trait that does not vary from generation to generation. (Brooker, 327) Also referred to as ‘true-breeding line’ and ‘purebred.’

Direct DNA Analysis: the use of 'mutation analysis,' 'mutation scanning,' 'sequence analysis,' or other means of molecular genetic testing to detect a genetic alteration associated with a specific disorder; direct DNA analysis is possible only when the genes or genomic region associated with a disorder is known. (GeneReviews)

DNA Amplification: mass-producing a DNA sequence from a small sample. (Lewis, 373) Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template. (MeSH) This technique refers to selectively replicate DNA sequence of interest to multiple extra copies that meet the need of research or health care activity. Polymerase chain reaction (PCR), can be considered a type of man-made gene amplification process. (NCIt) Also referred to as ‘nucleic acid amplification.’

DNA Microarray Analysis: an experiment in which “probes” representing genes that one wants to study are affixed to a glass slide and then exposed to target molecules (sometimes referred to as ‘the sample’). The level of “hybridization” between a specific probe and a target indicates the level of the gene corresponding to that probe in a test solution. (NCIt) Used to study the expression of many genes at once. Involves placing thousands of gene sequences in known locations on a glass slide called a ‘gene chip.' A sample containing DNA or RNA is placed in contact with the gene chip. Complementary base pairing between the sample and the gene sequences on the chip produces light that is measured. Areas on the chip producing light identify genes that are expressed in the sample. (NHGRI) Cancer cells can look alike under a microscope, but DNA microarrays show that they are distinct. Researchers examined what cancer cells do, rather than what they look like. They used DNA microarrays to compare 12,000 genes in cancer cells from two types of “leukemia” patients. (They) found that cancer cells made too little of 1000 proteins and too little of 200 proteins. Increasingly, cancer diagnosis utilizes DNA microarrays that scan the genome for cancer-associated mutations as well as gene expression patterns. (Lewis, 366-367)

DNA Replication in Vitro: involves the isolation of DNA from a specimen, the identification of the DNA sequence of interest, and finally the "PCR" process. If there is a single strand of DNA floating about in “solution,” under the right environmental conditions it will replicate by forming “chemical bonds” between the correct “base pairs.” This according to "Chargaff’s Rules," providing that the bases, the “nucleic acid,” “deoxyribose,” and “phosphates” are present. (Norman Labs, 81) 

Identification: (DNA replication step that uses) sequencing techniques called ‘blotting methods’ to identify the desired DNA sequence. (Norman Labs, 81)

Isolation: (DNA replication step that includes) destruction of the cell membranes that are protecting the DNA. Accomplished by soaking the cells in various acidic solutions, heating the cells, and finally physically tearing the cells up and separating their parts. (Norman Labs, 81)

DNA Synthesizer: invention by Marvin Caruthers, at the University of Colorado, Boulder. Uses four bottles containing the DNA bases A, T, C, and G, and adds one base to another in a prescribed order. In this way, DNA synthesizers can make short stretches of DNA. (Venter, 61)

Oligonucleotides: short stretches of DNA (made by a DNA synthesizer). An entire industry has been built around synthesizing oligonucleotides and shipping them to researchers because 'synthetic DNA' is used in molecular biology for "DNA sequencing" and "PCR." (Venter, 61)

DNA Transformation: the cellular uptake and  expression of DNA in a "bacterium." (Micklos, 120) A method of acquiring genes. (Norman, 7/1/09) A type of genetic transfer between bacteria in which a a segment of DNA from the environment is taken up by a competent cell and incorporated into the bacterial “chromosome.” (Brooker, G-370) A most unexpected observation was made in 1928 by Fred Griffith, a scientist in the British Ministry of Health. Griffith was interested in “pneumonia” and studied its bacterial agent. It was known that there were two bacterial strains, designated (S) and (R). These strains differed visually but also in their “toxicity.” Inject the ‘S-bacteria’ into a mouse, and within a few days the mouse dies; inject ‘R-bacteria’ and the mouse remains healthy. In his famous experiment Griffith found that ‘something’ had allowed the living ‘R-variant’ in the presence of the heat-killed ‘S-variant’ to transform itself into a living ‘killer-S’ strain of bacteria. In 1944, Oswald Avery and his team set out to duplicate Griffith’s experiment in order to isolate and characterize what it was that had caused those ‘R-cells’ to change to the ‘S-type.’ First the Avery team “degraded” the sugar-like coat of the ‘S-cells.’ Transformation still occurred: the coat was not the ‘transforming  principle.’  Next, they used a mixture of two protein-destroying enzymes to degrade virtually all the proteins in the ‘S-cells.’ Transformation was again unaffected. Next, they tried an enzyme that breaks down “RNA.” Again transformation occurred. Finally, they came to DNA, exposing the ‘S-bacteria’ to a DNA-destroying enzyme. This time they hit a ‘home run!’  All ‘S-inducing’ activity ceased completely. The transforming  factor was DNA. (Watson, 37-39) The phenomena of transformation, which provided a key clue to understanding the molecular basis of the gene, also provided a tool for manipulating the genetic makeup of living things. (Micklos, 122) Important to genetic engineers because it allows for the introduction of an engineered or naturally occurring gene into a bacterial cell. (Norman, 83)

Transformation Efficiency: expressed as the number of ‘antibiotic-resistant colonies’ per microgram of “plasmid” DNA. (Micklos, 396) Elements for efficient transformation include: a suitable “host” organism in which to insert the gene; a self-replication "vector" to carry the gene into the host organism; and a means of selecting for host cells that have taken up the gene. (Micklos, 120)

Genealogy: an account of a person's descent from an ancestor or ancestors, by enumeration of the intermediate people; a "pedigree." (Oxford) (Written record) of relationships, but not traits. (Lewis, 2)

Gene Library: any well-defined collection of genetic material used to identify unknown nucleic acids; classically, a collection of expressed “complementary DNA" "clones” representing the genome of a particular organism, used to identify newly purified genes or mRNAs by hybridization. (NCIt) A large collection of "DNA fragments" cloned from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (“genomic library”) or complementary DNA sequences, the latter being formed from messenger RNA and lacking “introns.” (MeSH) Also referred to as ‘genetic library.'

DNA Bank: a service that stores DNA extracted from blood samples or other human tissue. (HGPIA) 

DNA Banking: the process through which DNA is extracted from any of a number of possible cell sources and stored indefinitely by freezing or refrigerating for future testing; done when a specific test is not presently available or when the decision to have testing has not been made. (GeneReviews) Also referred to as ‘DNA storage.’

Genomic Library: a collection of clones made from a set of randomly generated overlapping DNA fragments that represent the entire "genome" of an organism. (HGPIA) For each application, such as using a human protein as a drug, a particular piece of DNA must be identified and isolated from the library. (Lewis, 377) A form of gene library containing the complete DNA sequences present in the genome of a given organism. It contrasts with a 'cDNA library’ which contains only sequences utilized in protein coding (i.e. lacking introns). (MeSH) Also referred to as a ‘genome library’ ‘clone library,’ and ’clone bank.’

Gene Silencing: (laboratory techniques) to diminish or silence the expression of specific genes. (Lewis, 382) The shutdown of gene expression. The term usually refers to cases in which a particular gene or group of genes is inactive by virtue of the state of the chromatin in which they are located. The term is also used to describe the shutdown of gene expression by "RNA interference." (Lawrence)

RNA Interference (RNAi): the suppression of a specific gene expression by an RNA complementary to part of the mRNA This guides RNA-cleaving enzymes to the mRNA, leading to its destruction. (Lawrence) (The process of introducing) short, double-stranded RNAs into a cell (so that they will) bind to their complements in mRNAs, preventing "translation." Involves tRNA, mRNA, and rRNA. (Lewis, 384) Sequence-specific post-transcriptional gene silencing. It is mediated by small interfering RNAs. (NCIt) 

Genetic Analysis: determining the function of a particular gene by altering a genome so the normal product is not made and then seeing the effect of this change on the organism. (Batista, 179) The study of a sample of DNA to look for mutations that may increase risk of disease or affect the way a person responds to treatment. (NCI1)

Genetic Mapping: determination of the relative positions of genes on a DNA molecule (chromosome or plasmid) and of the distance, in linkage units or physical units, between them. (HGPIA) Any method used for determining the location of and relative distances between genes on a chromosome. (MeSH) Early gene maps used “linkage” analysis. The closer two genes are to each other on the chromosome, the more likely it is that they will be "inherited" together. By following inheritance patterns, the relative positions of genes can be determined. More recently, scientists have used “recombinant DNA” techniques to establish the actual physical locations of genes on the chromosomes. (Includes the) process of making a representative diagram cataloging the genes and other features of a chromosome and showing their relative locations. 'Cytogenetic maps' are made using ‘photomicrographs’ of chromosomes stained to reveal structural variations. Genetic maps use the idea of linkage to estimate the relative locations of genes. Physical maps, made using recombinant DNA technology, show the actual physical locations of landmarks along a chromosome. (NHGRI) Also referred to as “gene mapping” and “chromosome mapping.”

Chromosome Ideogram: schematic chromosome map. Divided into arms, numbered regions and subregions. Displays chromosomal bands and features of individual chromosomes. (Lewis, 242-243) Also referred to as ‘ideogram.’

Genetic Marker: an alteration in DNA that may indicate an increased risk of developing a specific disease or disorder. (NCI1) An identifiable segment of DNA (for example a “SNP”) with enough variation between individuals that its inheritance and co-inheritance with alleles of a given gene can be traced. Used in linkage analysis. (NCI3) A gene or other identifiable portion of DNA whose inheritance can be followed. (HGPIA) A DNA sequence with a known physical location on a chromosome. Genetic markers can help link an inherited disease with the responsible gene. DNA segments close to each other on a chromosome tend to be inherited together. Genetic markers are used to track the inheritance of a nearby gene that has not yet been identified, but whose approximate location is known. The genetic marker itself may be a part of a gene or may have no known function. (NHGRI) Also referred to as ‘marker.’

Linkage Maps: genetic maps. (Lawrence) Assign distances to linked genes based on "crossover" frequencies. (Lewis, 107)

Positional Cloning: a (laboratory) technique used to identify genes. (HGPIA) Used to locate the position of a disease-associated gene along the chromosome. Used in conjunction with linkage analysis. (NHGRI) The cloning or identification of a gene for a particular disease based on its location in the genome. Determined by a collection of methods including linkage analysis, genomic (physical) mapping, and “bioinformatics.” Distinguished from the more common strategy of gene cloning beginning with a known protein product, determining its amino acid sequence, and using that information to isolate the gene. (GeneReviews)

SNP Maps: maps of sites in the human genome where individuals differ in their DNA sequence, often by a single base. Scientists believe such maps will help them identify the multiple genes associated with such complex diseases as cancer, diabetes, vascular disease, and some forms of mental illness. SNP maps provide valuable targets for biomedical and pharmaceutical research. (ORNL)

Genetic Staining and Labeling: the marking of biological material with a dye or other reagent for the purpose of identifying... components of tissues, cells or their extracts. (MeSH) Combination of stains and DNA probes applied to chromosomes used to identify chromosome rearrangements and extra or missing chromosomes. (Lewis, 238)

Chromosome Banding: staining of bands, or chromosome segments, allowing the precise identification of individual chromosomes or parts of chromosomes. Applications include the determination of chromosome rearrangements in ("chromosomal abnormalities") and “cancer,” the chemistry of chromosome segments, (and) chromosome changes during “evolution.” (Includes arrangements) in conjunction with cell hybridization studies and chromosome mapping. (MeSH)

DNA Probe: a labeled piece of DNA that binds to its complementary "base sequence" on a particular chromosome. Attached to molecules that "fluoresce" when illuminated, producing a flash of color precisely where the probe binds to a chromosome. (Lewis, 238) A single-stranded "sequence" of DNA or RNA used to search for its "complementary sequence" in a sample genome. The probe is placed into contact with the sample under conditions that allow the probe sequence to (form base pairs) with its complementary sequence. The probe is labeled with a “radioactive” or chemical tag that allows its binding to be visualized. In a similar way, labeled “antibodies” are used to probe a sample for the presence of a specific protein. (NHGRI) Also referred to as ‘probe.’

Fluorescence In Situ Hybridization (FISH): a laboratory technique used to look at genes or chromosomes in cells and tissues. Pieces of DNA that contain a fluorescent dye are made in the laboratory and added to cells or tissues on a glass slide. When these pieces of DNA bind to specific genes or areas of chromosomes on the slide, they light up when viewed under a microscope with a special light. (NCI1) Technique that localizes specific nucleic acid sequences within intact chromosomes through the use of specific DNA probes. (MeSH) Provides more specific chromosome bands than dyes. (Lewis, 242) Used to identify the presence of specific chromosomes or chromosomal regions. Examination under fluorescent lighting detects the presence of the hybridized fluorescent signal (and hence presence of the chromosome material) or absence of the hybridized fluorescent signal (and hence absence of the chromosome material). (GeneReviews)

Genome Assembly: process of taking a large number of short "DNA sequences" and putting them back together to create a representation of the original chromosomes from which the DNA originated. (HGPIA)

Genome Wide Association Study (GWAS): a study that compares the complete DNA of people with a disease or condition to the DNA of people without the disease or condition. These studies find the genes involved in a disease, and may help prevent, diagnose, and treat the disease. (NCIt) Examination of many common genetic variants in different organisms to see if any variant is statistically associated with a trait. (HGPIA) An approach used in genetics research to associate specific genetic variations with particular diseases. The method involves scanning the genomes from many different people and looking for genetic markers that can be used to predict the presence of a disease. Once such genetic markers are identified, they can be used to understand how genes contribute to the disease and develop better prevention and treatment strategies (NHGRI) A way for scientists to identify inherited genetic "variants" associated with risk of disease or a particular "trait." This method surveys the entire genome for genetic “polymorphisms,” typically “SNPs” that occur more frequently in people with the disease or trait being assessed than in controls (people without the disease or trait). (NCI13)

Affected Sibling Pair: (GWAS design in which) researchers scan genomes for SNPs that most siblings who have the same condition share, but that siblings who do not both have the condition do not often share. Logic is that because sibling share 50% of their genes, a trait or condition that many siblings share is likely to be inherited. (Lewis, 142)

Case Control Study: (GWAS design in which) each individual in one group is matched to an individual in another group who shares as many characteristics as possible, such as age, sex, activity level, and environmental exposures. SNP disorders are then associated with the presence or absence of the disorder. (Lewis, 142)

Cohort Study: (GWAS design in which) researchers follow a large group of individuals over time and measure many aspects of their health. Most famous is the ‘Framingham Heart Study’ which began tracking thousands of people and their descendants in Massachusetts in 1968. (Lewis, 143) A research study that compares a particular outcome (such as "lung cancer") in groups of individuals who are alike in many ways but differ by a certain characteristic. For example, female nurses who smoke compared with those who do not smoke. (NCIt)

Hybridization: formation of a "hybrid." Cross-fertilization. (Lawrence) The process of combining two complementary single-stranded DNA or RNA molecules and allowing them to form a single double-stranded molecule through base pairing. In a reversal of this process, a double-stranded DNA molecule can be heated to break the base pairing and separate the two strands. Hybridization is a part of many important laboratory techniques such as “polymerase chain reaction” and “southern blotting.” (NHGRI) Laboratory procedure in which single stranded nucleic acids are allowed to interact so that hybrids are formed by molecules with sufficiently similar, complementary sequences. By this means the degree of sequence identity can be assessed and specific sequences detected. (NCIt)

Knockouts: applies to living organisms extensively used in medical and biological research such as mice or fruit flies. The knockout mouse or fly contains an artificially induced mutation of a specific gene so that the gene(s) will not function correctly. The effects of this malfunction can be investigated and this can be used to mimic human disease and in the testing of potential drugs to understand how they work. (Bynum, 292) (Process) where one or more genes have been selectively turned off. Remove or disable a gene and, if the organism continues to live, you can assume that particular gene did not have a critical role; if the organism dies, the gene was clearly essential. Capecchi, Smithies, and Evans shared the 2007 Nobel Prize for their work on the technology used to create knockouts in mice. (Venter, 58)

Pedigree: a family tree diagram that shows how a particular genetic trait or disease has been inherited. (HGPIA) A diagram that shows relationships among family members. In medicine, a pedigree may also show the pattern of certain genes or diseases within a family. (NCIt) The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition. (MeSH) Describes interrelationships of parents and children over many generations. (Norman, 7/21/09) A family tree that diagrams the inheritance of a trait or disease though several generations. The pedigree shows the relationships between family members and indicates which individuals express or silently carry the trait in question. (NHGRI) 

Polymerase Chain Reaction (PCR): a laboratory technique used to amplify DNA sequences. The method involves using short DNA sequences called “primers” to select the portion of the genome to be amplified. The temperature of the sample is repeatedly raised and lowered to help a "DNA replication enzyme" copy the target DNA sequence. The technique can produce a billion copies of the target sequence in just a few hours. (NHGRI) Method for speeding up the (normally) slow process of “DNA replication.” Invented in 1984 by Kary Mullis, a Nobel Prize winner. (Norman Labs, 81) The essence of the PCR method is the use of an enzyme known as ‘TAQ Polymerase.’ This enzyme, purified from a bacterium isolated from hot springs, is stable at very high temperatures. Three steps (of PCR) constitute one cycle. The process is typically repeated for 25 to 50 cycles, amplifying the target exponentially. PCR is performed in an instrument known as a ‘thermal cycler,’ which is programmed to heat the sample at the designated temperature of each step and then rapidly change temperature for the following step. (Edvotek, 8) Editor's note - the steps in the PCR process follow in order of occurrence.

Denaturation: when a protein unravels (looses shape) at high temperatures. The DNA complementary strands are separated at 94 degrees celsius, while the (enzyme) remains stable. (Norman, 6/17/09) Verb - 'denature.'

Annealing: a sample is cooled to a temperature in the range of 42 degrees celsius to 65 degrees celsius to allow hybridization of small synthetic nucleotides, to the target to be amplified. (Edvotek, 8)

Extension: the temperature is raised to 72 degrees celsius and the DNA polymerase then adds nucleotides to the primers to complete each new complementary strand of the target. (Edvotek, 8)

Punnett Square: method used to express genotype and phenotype of genetic crosses. (Norman, 7/21/09) A conventional representation used to calculate the proportions of different "genotypes" in the (descendants) of a genetic cross. (Lawrence)

Southern Blotting: “electrophoresis” based technique used in genetic testing to detect large deletions in DNA that can be missed by PCR-based genetic testing methods. (NCI3) Laboratory technique used to detect a specific DNA sequence in a blood or tissue sample. A “restriction enzyme” is used to cut a sample of DNA into fragments that are separated using “gel electrophoresis.” The DNA fragments are transferred out of the gel to the surface of a membrane. The membrane is exposed to a DNA probe labeled with a radioactive or chemical tag. If the probe binds to the membrane, then the probe sequence is present in the sample. (NGHRI)