GLOSSARY

A. See adenine.

AABB. The American Association of Blood Banks Parentage Testing Committee, the voluntary inspection and certification organization for parentage testing laboratories located in Arlington, Virginia.

AAFS. The American Academy of Forensic Sciences, the primary national forensic scientific organization headquartered in Colorado Springs, Colorado. They hold an annual scientific meeting and publish the Journal of Forensic Science.

adenine. An organic base, one of the four monomers or building blocks from which DNA is made.

AFLP. Amplified fragment length polymorphism. A VNTR containing alleles generally less than one thousand base pairs in length that have been amplified using the PCR process. The length of the resulting DNA fragments, which are separated by electrophoresis, is determined by the PCR primers rather than the restriction enzyme site as is the case in RFLP. STRs are a class of AFLPs in which the repeat units are even smaller.

agarose. A jello like substance derived from seaweed that is used as a medium for the size separation of DNA and proteins by the process of electrophoresis.

allele frequency. The representation of a specific allele out of the total alleles observed at that locus.

allele. Alternative forms or versions of a gene. Each person has two alleles of every gene which may be the same or different. There may be a few or many alleles of a gene found in a population; some may be common others rare.

AMPFLP. See AFLP.

analytical gel. The final gel in an RFLP test and the one that will be used to make the Southern blot.

ASCLD-LAB. The American Society of Crime Laboratory Directors Laboratory Accreditation Board. The voluntary inspection and certification organization for crime laboratories. It is a separate organization from ASCLD itself.

ASHG. The American Society of Human Genetics.

ASHI. The American Society of Histocompatibility and Immunogenetics.

autorad. A film exposed by a radioactive tracer. In the case of forensic RFLP analysis the tracer is attached to a DNA probe which is in turn attached to a VNTR allele immobilized on a Southern blot.

autoradiogram. See autorad

autoradiograph. See autorad

autoradiography. See autorad

band. The exposed area on an autorad film that detects the presence of a particular DNA fragment.

bandshift. The phenomena in which identical DNA fragments will move through an electrophoresis gel at different rates because of contamination or alterations to

the DNA itself. This phenomena is usually observed in forensic samples that are partially degraded.

base. The chemical units adenine (A), guanine (G), cytosine (C), and thymine (T) contained in DNA and that by virtue of their sequence determine the information content of the DNA.

base pair(ing). The complementary partnership of A with T and G with C that brings the two opposite strands of a DNA molecule together to form the double helix.

blot. See Southern blot.

C. See cytosine.

CAC. California Association of Criminalists.

CACLD. California Association of Crime Laboratory Directors.

CAP. College of American Pathologists. Supplies proficiency tests to forensic and parentage testing and medical laboratories.

ceiling principle. An extremely conservative method of calculating the estimated occurrence of DNA profiles in forensic samples. It's purpose is to compensate for any undetected substructure that may exist in the populations that have been sampled.

cell. The smallest unit of life that is capable of independent reproduction by the process of cell division. There are approximately 100 trillion cells in the human body almost all of which contain an identical complement of DNA known as the human genome.

chromosome. The units made up of proteins and DNA into which the DNA in cells is packaged. There are 23 pairs of chromosomes in each human cell.

cloning. The procedure for purifying and reproducing in the laboratory specific small identical DNA sequences.

CODIS. Combined DNA Identification System, the FBI's database of DNA profiles of convicted offenders supplied to them by the states.

complementarity. The characteristic of DNA resulting from the base pairing rules. If it is known that one strand has the sequence, GATC, then the sequence of the other complementary strand, CTAG, will also be known.

controls. Test samples for which the results are know. They are of two general types positive and negative. A positive control is used to confirm that the test worked correctly and a negative control to detect contamination. If a control test result does not meet specifications then the entire test can be rendered invalid.

CTS. Collaborative Testing Services, a commercial laboratory headquartered in Arlington, Virginia that supplies proficiency testing samples to forensic laboratories.

cytosine. An organic base, one of the four monomers or building blocks from which DNA is made.

degradation. The breaking down of DNA by biological or chemical processes. In the context of forensic science these processes are usually the result of cell death or exposure to the elements.

DNA. Deoxyribonucleic acid, the biological polymer that stores the genetic information in all free living organisms. Two linear molecules entwine to form the double helix.

DNA polymerase. An enzyme that produces or synthesizes DNA. These enzymes always use an existing DNA molecule as a template for producing a new strand of DNA.

DNA probe. A short piece of DNA made in the laboratory by chemical or biological means that can be labeled with a tracer and used to identify a specific gene. A specific gene is identified by a specific DNA probe.

DNA profiling or typing. A variety of DNA tests used by forensic scientists to aid in the identification of the individual source of evidence or to resolve a parentage question.

electrophoresis. The process of moving DNA or proteins through a sieving matrix that will separate them by size. This process is possible because most biological molecules have an electric charge and so will move in response to the electrical field that is applied to the separation matrix.

enzymes. Proteins that serve as catalysts for specific biological reactions. A catalyst is a substance that helps a chemical reaction occur. It remains unchanged itself and so is required in trace amounts. The two most commonly used in DNA testing are the restriction endonuclease Hae III and Taq DNA polymerase.

ethidium bromide (EtBr). A dye that stains DNA and is illuminated by ultraviolet or black light on a device called a transilluminator. It is used to visualize DNA in gels following electrophoresis and can be added to the DNA before or after

electrophoresis. Its presence slightly alters the speed at which the DNA migrates through the gel. This fact has been the source of controversy in the past, but ample studies demonstrate that whether EtBr is added before or after electro-phoresis does not significantly affect the results.

exclusion. In forensic and paternity testing the situation that exists when testing has demonstrated that a particular sample could not have come from an individual who was also tested or that the alleged father in a paternity case cannot be the father of the child.

forensic. Pertaining to, connected with, or used in courts of law.

forensic science. The application of scientific knowledge to questions of civil and criminal law, especially in court proceedings.

G. See guanine.

gel. A semi-solid matrix used in the electrophoretic separation of DNA and proteins. The two most commonly used in DNA testing are agarose and polyacrylamide.

gene. The fundamental unit of heredity, most commonly thought of as a stretch of DNA sequence that codes for a specific protein. The individually variable stretches of DNA that are examined by forensic scientists are not considered genes by strict definitions of the gene. For simplicity the term gene is used throughout this text when referring to these DNA fragments.

gene frequency. see allele frequency.

genome. The total genetic complement of an organism as defined by one copy of the total DNA found in each of its cells.

genotype. The genetic makeup of an individual consisting of both copies of the genetic information. The genotype is distinguished from the phenotype or physical characteristics of the individual. The pair of alleles at a locus or set of loci.

guanine. An organic base, one of the four monomers or building blocks from which DNA is made.

Hardy-Weinberg Principle. The concept that the presence of a particular allele at a locus has no predictive value as to what the other allele at that locus will be. It is a simple mathematical expression (p2+2pq+q2=1 where p and q are the allele frequencies of a pair of genes) based on the assumptions of a large population in which there is random mating. Population databases in use by forensic scientists must be tested to ensure that they obey this principle.

heredity. The phenomena whereby biological traits are passed from one generation to the next. Heredity results from parents passing genes to their offspring and is why related family members tend to have similar physical characteristics.

heterozygosity. In forensic science often used to describe the percentage of individ-uals in a population database who are heterozygotes.

heterozygote. An individual who has inherited and so carries different alleles of a gene.

HLA. Human leukocyte antigen, a substance found on the surface of most cells that differs from person to person. One of these, the DQA1 gene, is examined by the most widely used PCR based forensic DNA test.

homozygote. An individual who has identical alleles of a gene. An excess of homozygosity in a population database, according to the Hardy-Weinberg Principle, would indicate that there are problems with the data and that it should not be used.

hybridization. The joining together of complementary strands of DNA by the process of base pairing when the two strands are from different sources. For example, a DNA strand immobilized on a blot and its complementary radioactively labeled DNA probe.

hypervariable. A DNA locus that shows extremely high variation in people. Many alleles exist in the population.

inclusion. In forensic and paternity testing the situation that exists when testing has demonstrated that a particular individual belongs to the group of individuals who could be the source of the sample or in a paternity case the father of the child. They have not been excluded.

isotope. The radioactive form of an atom known as a radioisotope.

Kb. The abbreviation for kilobase or 1000 base pairs of DNA.

locus (pl. loci). A specific physical position on a chromosome at which a gene or gene pair resides. As scientists map genes to specific chromosomal locations they are registered with the Human Gene Mapping Workshop, assigned a name, and entered onto the genetic map of that chromosome.

linkage disequilibrium. A specific allele of one locus being found with a specific allele of another locus more often than would be expected by chance. Occurs when the two loci are close together on the same chromosome. They are then said to be linked because they will tend to be inherited together.

Marker. 1. A genetic marker is a gene that has been mapped and can be identified. 2. A molecular weight marker is a DNA fragment of known size used as a comparison standard in estimating the size of a DNA fragment of unknown size.

membrane. The solid support, usually nylon membrane, to which the DNA is transferred and affixed during the Southern blotting process.

microgram. One millionth of a gram.

milliliter. One thousandth of a liter, the same as a cc or cubic centimeter.

mitochondria. Organelles that exist inside cells and that contain a small amount of DNA (16,000 bp). A small region of the mitochondrial DNA varies from person to person. Because a cell may contain many thousands of mitochondria there are correspondingly many more copies of the mitochondrial DNA available for testing. molecular weight or size marker. See marker.

molecular biology. A modern branch of biology that attempts to explain biological phenomena in molecular terms. Most work in molecular biology is concerned with or uses genetic techniques.

molecule. The smallest physical unit of a chemical compound, the defined collection of atoms bound together in a specific fashion.

monomorphic probe. A DNA probe that will detect a DNA fragment that is the same size in everyone. Monomorphic probes are used to detect band shifting.

multilocus probe. The original Jefferys process of simultaneously detecting up to ten or fifteen genetic loci simultaneously. Because of technical problems with this method it has been supplanted in forensic science by the single locus probe method.

mutation. Any inheritable changes in the DNA sequence that occurs during reproduction or cell division.

nanogram. One billionth of a gram.

nucleotide. The monomer units that are used to make up the DNA molecule. Each has one of the four bases, A, G, T, or C attached to a sugar phosphate that forms the backbone of the DNA polymer.

obligate gene. In parentage testing the gene that must have been passed by the father to the child.

paternity index (PI). In parentage testing, the genetic odds in favor of paternity. When the alleged father has all the markers required to be the father, he cannot be excluded from paternity. The paternity index is the ratio between the chance that the alleged father may pass the obligatory gene compared to the chance that a random man of the same race may pass the obligatory gene.

PCR. See polymerase chain reaction.

phenotype. The physical characteristics of an organism resulting from the interaction of their genotype with the environment.

Polymerase chain reaction. An in vitro method for reproducing DNA in the laboratory. Many millions of copies of a defined short sequence can be made in a short time. Repeated cycling of the reaction allows the new DNA to increase in a geometric fashion.

polymorphic locus. A genetic locus for which there are many alleles in existence. The loci used in forensic science are the most polymorphic known.

population. A defined group of individuals for which databases of gene frequencies are collected by sampling members of the population. In forensic science population databases are collected and maintained by major racial or ethnic group.

population substructure. The hypothesis that within the major population groups there exist subgroups whose allele frequency patterns would differ from the parent population to such an extent that the database would not be suitable for forensic use. This phenomena is described by the Wahlund principle.

primer. A short piece of DNA, usually synthetic, that defines the specific site on a DNA molecule for a DNA polymerase to start making new DNA. An essential ingredient in the PCR reaction mix.

probability of paternity. A statistic, expressed as a percentage, incorporating the genetic evidence (paternity index) and the non-genetic evidence (prior chance), which compares the likelihood the tested man may pass the required genes to the likelihood that an untested random man of the same race may pass these genes. This value may approach, but never reach, 100%. Also know as the W value.

product rule. The concept from elementary probability theory that allows the frequency of occurrence of independent events to be multiplied together to estimate how often they would occur together.

proficiency tests. Testing of laboratory personnel performed as part of a quality assurance program. Samples of known composition are supplied to analysts by outside agencies or laboratory management as a way of evaluating and maintaining performance standards.

protein. A biological polymer made up of amino acids whose structure is coded for by the DNA. Proteins are the primary structural, functional and regulatory molecules of the body. Enzymes are a major class of proteins.

protocol. Laboratory procedures manual.

quality assurance. Externally administered programs that are design to assess and maintain a minimum level of laboratory performance. It includes laboratory inspection and accreditation, personnel training, examination and certification, regular proficiency testing and the maintenance of a quality control program.

quality control. Systematic regular activities for verifying and maintaining a specified level of quality in a product or process. It includes careful planning, regular documentation, continued inspection and measurement and the implementation of corrective action when necessary.

replication. The enzymatic process of making new DNA based on the use of use of an existing strand of DNA as a template. The enzymes that perform this process require a primer, a short piece of DNA complementary to the template that defines the base at which the replication will start and that will become part of the newly synthesized DNA.restriction enzymes (RE), restriction endonucleases. A class of enzymes obtained from microorganisms that cut the DNA strands at specific four to twelve base pair sequences. There are over one hundred restriction enzymes commercially available each having a different recognition site. In forensic science the most commonly used RE is called Hae III although there are some labs who still use Hinf I or Pst I.

RE test gel. A gel used to analyze DNA that has been cut by a restriction enzyme (RE) to ensure that the cutting of the DNA has been complete. Sometimes contaminants in forensic samples will inhibit the action of the enzyme and prevent it from cutting the DNA.

restriction fragment length polymorphism (RFLP). Variations in the length of a DNA restriction fragment caused by the presence of a polymorphic locus within the fragment. Analysis of RFLPs by the Southern blotting method is the most common and definitive forensic DNA test.

RNA ribonucleic acid. A nucleic acid polymer similar to DNA and used to translate the genetic code into a form useful by the cells.

scanner. Common term for the computer driven video devices used to electronically estimate the sizes of DNA restriction fragments detected in a forensic RFLP test.

serology. In forensic science the study of body fluids and body fluid stains. Forensic DNA analysis is generally performed by specially trained forensic serologists.

single locus probe. The currently used practice in forensic DNA analysis of detecting the restriction fragments in a DNA profile one locus at a time.

Southern blotting. The technique of transferring DNA fragments in a gel to a solid support such as a sheet of nylon. The resulting sheet of nylon with the DNA permanently affixed to it is referred to as the blot.

STR. Short tandem repeat see AFLP.

T. See thymine.

Taq DNA polymerase. The heat stable DNA polymerase used in the PCR reaction.

thymine. An organic base, one of the four monomers or building blocks from which DNA is made.variable number of tandem repeat (VNTR). The class of genetic loci most commonly used in forensic DNA analysis. They are composed of 9 to 75 base pair sequences that are repeated different numbers of times in different people. Hence, the physical length of the DNA molecule at these loci will vary from person to person.

yield gel. A gel run for the purpose of assessing the quantity and quality of the DNA extracted from a sample.