Adenine (A). One of the four bases, or nucleotides, that make up the DNA molecule. Adenine only binds to thymine. See Nucleotide.
Affinal Method. A method for computing the single locus profile probabilities for a theoretical subpopulation by adjusting the single locus profile probability, calculated with the product rule from the mixed population database, by the amount of heterogeneity across subpopulations. The model is appropriate even if there is no database available for a particular subpopulation, and the formula always gives more conservative probabilities than the product rule applied to the same database.
Allele. In classical genetics, an allele is one of several alternative forms of a gene. A biallelic gene has two variants; others have more. Alleles are inherited separately from each parent, and for a given gene, an individual may have two different alleles (heterozygosity) or the same allele (homozygosity). In DNA analysis, the term is applied to any DNA region (whether or not it constitutes a gene) used for analysis.
Alu Sequences. A family of short interspersed elements (SINEs) distributed throughout the genomes of primates.
Amplification. Increasing the number of copies of a DNA region, usually by PCR.
Amplified Fragment Length Polymorphism (AMP-FLP). A DNA identification technique that uses PCR-amplified DNA fragments of varying lengths. The DS180 locus is a VNTR whose alleles can be detected with this technique.
Antibody. A protein (immunoglobulin) molecule, produced by the immune system, that recognizes a particular foreign antigen and binds to it; if the antigen is on the surface of a cell, this binding leads to cell aggregation and subsequent destruction.
Antigen. A molecule (typically found in the surface of a cell) whose shape triggers the production of antibodies that will bind to the antigen.
Autoradiograph (Autoradiogram, Autorad). In RFLP analysis, the x-ray film (or print) showing the positions of radioactively marked fragments (bands) of DNA, indicating how far these fragments have migrated, and hence their molecular weights.
Autosome. A chromosome other than the X and Y sex chromosomes.
Band. See Autoradiograph.
Band Shift. Movement of DNA fragments in one lane of a gel at a different rate than fragments of an identical length in another lane, resulting in the same pattern "shifted" up or down relative to the comparison lane. Band-shift does not necessarily occur at the same rate in all portions of the gel.
Base Pair (bp). Two complementary nucleotides bonded together at the matching bases (A and T or C and G) along the double helix "backbone" of the DNA molecule. The length of a DNA fragment often is measured in numbers of base pairs (1 kilobase (kb) = 1000 bp); base pair numbers also are used to describe the location of an allele on the DNA strand.
Bayes' Theorem. An elementary formula that relates certain conditional probabilities. It can be used to describe the impact of new data on the probability that a hypothesis is true.
Bin, Fixed. In VNTR profiling, a bin is a range of base pairs (DNA fragment lengths). When a database is divided into fixed bins, the proportion of bands within each bin is determined and the relevant proportions are used in estimating the profile frequency.
Bins, Floating. In VNTR profiling, a bin is a range of base pairs (DNA fragment lengths). In a floating bin method of estimating a profile frequency, the bin is centered on the base pair length of the allele in question, and the width of the bin can be dened by the laboratory's matching rule (e.g., ± 5% of band size).
Binning. Grouping VNTR alleles into sets of similar sizes because the alleles' lengths are too similar to differentiate.
Blind Proficiency Test. See Proficiency Test.
Capillary Electrophoresis. A method for separating DNA fragments (including STRs) according to their length. A long, narrow tube is filled with an entangled polymer or comparable sieving medium, and an electric field is applied to pull DNA fragments placed at one end of the tube through the medium. The procedure is faster and uses smaller samples than gel electrophoresis, and it can be automated.
Ceiling Principle. A procedure for setting a minimum DNA profile frequency proposed in 1992 by a committee of the National Academy of Science. One hundred persons from each of 15-20 genetically homogeneous populations spanning the range of racial groups in the United States are sampled. For each allele, the higher frequency among the groups sampled (or 5%, whichever is larger) is used in calculating the profile frequency. Cf. Interim Ceiling Principle.
Chip. A miniaturized system for genetic analysis. One such chip mimics capillary electrophoresis and related manipulations. DNA fragments, pulled by small voltages, move through tiny channels etched into a small block of glass, silicon, quartz, or plastic. This system should be useful in analyzing STRs. Another technique mimics reverse dot blots by placing a large array of oligonucleotide probes on a solid surface. Such hybridization arrays should be useful in identifying SNPs and in sequencing mitochondrial DNA.
Chromosome. A rod-like structure composed of DNA, RNA, and proteins. Most normal human cells contain 46 chromosomes, 22 autosomes and a sex chromosome (X) inherited from the mother, and another 22 autosomes and one sex chromosome (either X or Y) inherited from the father. The genes are located along the chromosomes. See also Homologous Chromosomes.
Coding DNA. A small fraction of the human genome contains the "instructions" for assembling physiologically important proteins. The remainder of the DNA is "non-coding."
CODIS (Combined DNA Index System). A collection of databases on STR and other loci of convicted felons maintained by the FBI.
Complementary Sequence. The sequence of nucleotides on one strand of DNA that corresponds to the sequence on the other strand. For example, if one sequence is CTGAA, the complementary bases are GACTT.
Cytosine (C). One of the four bases, or nucleotides, that make up the DNA double helix. Cytosine only binds to guanine. See Nucleotide.
Database. A collection of DNA profiles.
Degradation. The breaking down of DNA by chemical or physical means.
Denature, Denaturation. The process of splitting, as by heating, two complementary strands of the DNA double helix into single strands in preparation for hybridization with biological probes.
Deoxyribonucleic Acid (DNA). The molecule that contains genetic information. DNA is composed of nucleotide building blocks, each containing a base (A, C, G, or T), a phosphate, and a sugar. These nucleotides are linked together in a double helix--two strands of DNA molecules paired up at complementary bases (A with T, C with G). See Adenine, Cytosine, Guanine, Thymine.
Diploid Number. See Haploid Number.
D-loop. A portion of the mitochrondrial genome known as the "control region" or "displacement loop" instrumental in the regulation and initiation of mtDNA gene products.
DNA Polymerase. The enzyme that catalyzes the synthesis of double-stranded DNA.
DNA Probe. See Probe.
DNA Profile. The alleles at each locus. For example, a VNTR profile is the pattern of band lengths on an autorad. A multilocus profile represents the combined results of multiple probes. See Genotype.
DNA Sequence. The ordered list of base pairs in a duplex DNA molecule or of bases in a single strand.
DQA. The gene that codes for a particular class of Human Leukocyte Antigen (HLA). This gene has been sequenced completely and can be used for forensic typing. See Human Leukocyte Antigen.
DQ. The antigen that is the product of the DQA gene. See DQA, Human Leukocyte Antigen.
EDTA. A preservative added to blood samples.
Electrophoresis. See Capillary Electrophoresis, Gel Electrophoresis.
Endonuclease. An enzyme that cleaves the phosphodiester bond within a nucleotide chain.
Environmental Insult. Exposure of DNA to external agents such as heat, moisture, and ultraviolet radiation, or chemical or bacterial agents. Such exposure can interfere with the enzymes used in the testing process, or otherwise make DNA difficult to analyze.
Enzyme. A protein that catalyzes (speeds up or slows down) a reaction.
Ethidium Bromide. A molecule that can intercalate into DNA double helices when the helix is under torsional stress. Used to identify the presence of DNA in a sample by its fluorescence under ultraviolet light.
Fallacy of the Transposed Conditional. See Transposition Fallacy.
False Match. Two samples of DNA that have different profiles could be declared to match if, instead of measuring the distinct DNA in each sample, there is an error in handling or preparing samples such that the DNA from a single sample is analyzed twice. The resulting match, which does not reflect the true profiles of the DNA from each sample, is a false match. Some people use "false match" more broadly, to include cases in which the true profiles of each sample are the same, but the samples come from different individuals. Compare True Match. See also Match, Random Match.
Gel, Agarose. A semisolid medium used to separate molecules by electrophoresis.
Gel Electrophoresis. In RFLP analysis, the process of sorting DNA fragments by size by applying an electric current to a gel. The different-sized fragments move at different rates through the gel.
Gene. A set of nucleotide base pairs on a chromosome that contains the "instructions" for controlling some cellular function such as making an enzyme. The gene is the fundamental unit of heredity; each simple gene "codes" for a specific biological characteristic.
Gene Frequency. The relative frequency (proportion) of an allele in a population.
Genetic Drift. Random fluctuation allele frequencies from generation to generation.
Genetics. The study of the patterns, processes, and mechanisms of inheritance of biological characteristics.
Genome. The complete genetic makeup of an organism, comprising 40,000-100,000 genes in humans.
Genotype. The particular forms (alleles) of a set of genes possessed by an organism (as distinguished from phenotype, which refers to how the genotype expresses itself, as in physical appearance). In DNA analysis, the term is applied to the variations within all DNA regions (whether or not they constitute genes) that are analyzed.
Genotype, Single Locus. The alleles that an organism possesses at a particular site in its genome.
Genotype, Multilocus. The alleles that an organism possesses at several sites in its genome.
Guanine (G). One of the four bases, or nucleotides, that make up the DNA double helix. Guanine only binds to cytosine. See Nucleotide.
Hae III. A particular restriction enzyme.
Haploid Number. Human sex cells (egg and sperm) contain 23 chromosomes each. This is the haploid number. When a sperm cell fertilizes an egg cell, the number of chromosomes doubles to 46. This is the diploid number.
Haplotype. A specific combination of linked alleles at several loci.
Hardy-Weinberg Equilibrium. A condition in which the allele frequencies within a large, random, intrabreeding population are unrelated to patterns of mating. In this condition, the occurrence of alleles from each parent will be independent and have a joint frequency estimated by the product rule. See Independence, Linkage disequilibrium.
Heteroplasty. The condition in which some copies of mitochondrial DNA in the same individual have different base pairs at certain points.
Heterozygous. Having a different allele at a given locus on each of a pair of homologous chromosomes. See Allele. Compare Homozygous.
Homologous Chromosomes. The 44 autosomes (non-sex chromosomes) in the normal human genome are in homologous pairs (one from each parent) that share an identical set of genes, but may have different alleles at the same loci.
Human Leukocyte Antigen (HLA). Antigen (foreign body that stimulates an immune system response) located on the surface of most cells (excluding red blood cells and sperm cells). HLAs differ among individuals and are associated closely with transplant rejection. See DQA.
Homozygous. Having the same allele at a given locus on each of a pair of homologous chromosomes. See Allele. Compare Heterozygous.
Hybridization. Pairing up of complementary strands of DNA from different sources at the matching base pair sites. For example, a primer with the sequence AGGTCT would bond with the complementary sequence TCCAGA on a DNA fragment.
Independence. Two events are said to be independent if one is neither more nor less likely to occur when the other does.
Interim Ceiling Principle. A procedure proposed in 1992 by a committee of the National Academy of Sciences for setting a minimum DNA profile frequency. For each allele, the highest frequency (adjusted upward for sampling error) found in any major racial group (or 10%, whichever is higher), is used in product-rule calculations. Cf. Ceiling Principle.
Kilobase (kb). One thousand bases.
Linkage. The inheritance together of two or more genes on the same chromosome.
Linkage Equilibrium. A condition in which the occurrence of alleles at different loci are independent.
Locus. A location in the genome, i.e., a position on a chromosome where a gene or other structure begins.
Mass Spectroscopy. The separation of elements or molecules according to their molecular weight. In the version being developed for DNA analysis, small quantities of PCR-amplified fragments are irradiated with a laser to form gaseous ions that traverse a fixed distance. Heavier ions have longer times of flight, and the process is known as "matrix-assisted laser desorption-ionization time-of-flight mass spectroscopy." MALDI-TOF-MS, as it is abbreviated, may be useful in analyzing STRs.
Match. The presence of the same allele or alleles in two samples. Two DNA profiles are declared to match when they are indistinguishable in genetic type. For loci with discrete alleles, two samples match when they display the same set of alleles. For RFLP testing of VNTRs, two samples match when the pattern of the bands is similar and the positions of the corresponding bands at each locus fall within a preset distance. See Match Window, False Match, True Match.
Match Window. If two RFLP bands lie with a preset distance, called the match window, that reflects normal measurement error, they can be declared to match.
Microsatellite. Another term for an STR.
Minisatellite. Another term for a VNTR.
Mitochondria. A structure (organelle) within nucleated (eukaryotic) cells that is the site of the energy producing reactions within the cell. Mitochondria contain their own DNA (often abbreviated as mtDNA), which is inherited only from mother to child.
Molecular weight. The weight in grams of one mole of a pure, molecular substance.
Monomorphic. A gene or DNA characteristic that is almost always found in only one form in a population.
Multilocus Probe. A probe that marks multiple sites (loci). RFLP analysis using a multilocus probe will yield an autorad showing a striped pattern of thirty or more bands. Such probes rarely are used now in forensic applications in the United States.
Multilocus Profile. See Profile.
Multiplexing. Typing several loci simultaneously.
Mutation. The process that produces a gene or chromosome set differing from the type already in the population; the gene or chromosome set that results from such a process.
Nanogram (ng). A billionth of a gram.
Nucleic Acid. RNA or DNA.
Nucleotide. A unit of DNA consisting of a base (A, C, G, or T) and attached to a phosphate and a sugar group; the basic building block of nucleic acids. See Deoxyribonucleic Acid.
Nucleus. The membrane-covered portion of a eukaryotic cell containing most of the DNA and found within the cytoplasm.
Oligonucleotide. A synthetic polymer made up of fewer than 100 nucleotides; used as a primer or a probe in PCR. See Primer.
Paternity index. A number (technically, a likelihood ratio) that indicates the support that the paternity test results lend to the hypothesis that the alleged father is the biological father as opposed to the hypothesis that another man selected at random is the biological father. Assuming that the observed phenotypes correctly represent the phenotypes of the mother, child, and alleged father tested, the number can be computed as the ratio of the probability of the phenotypes under the first hypothesis to the probability under the second hypothesis. Large values indicate substantial support for the hypothesis of paternity; values near zero indicate substantial support for the hypothesis that someone other than the alleged father is the biological father; and values near unity indicate that the results do not help in determining which hypothesis is correct.
pH. A measure of the acidity of a solution.
Phenotype. A trait, such as eye color or blood group, resulting from a genotype.
Polymarker. A commercially marketed set of PCR-based tests for protein polymorphisms.
Polymerase Chain Reaction (PCR). A process that mimics DNA's own replication processes to make up to millions of copies of short strands of genetic material in a few hours.
Polymorphism. The presence of several forms of a gene or DNA characteristic in a population.
Point mutation. See SNP.
Population Genetics. The study of the genetic composition of groups of individuals.
Population Structure. When a population is divided into subgroups that do not mix freely, that population is said to have structure. Significant structure can lead to allele frequencies being different in the subpopulations.
Primer. An oligonucleotide that attaches to one end of a DNA fragment and provides a point for more complementary nucleotides to attach and replicate the DNA strand. See Oligonucleotide.
Probe. In forensics, a short segment of DNA used to detect certain alleles. The probe hybridizes, or matches up, to a specific complementary sequence. Probes allow visualization of the hybridized DNA, either by radioactive tag (usually used for RFLP analysis) or biochemical tag (usually used for PCR-based analyses).
Product rule. When alleles occur independently at each locus (Hardy-Weinberg equilibrium) and across loci (linkage equilibrium), the proportion of the population with a given genotype is the product of the proportion of each allele at each locus, time factors of two for heterozygous loci.
Proficiency Test. A test administered at a laboratory to evaluate its performance. In a blind proficiency study, the laboratory personnel do not know that they are being tested.
Prosecutor's Fallacy. See Transposition Fallacy.
Protein. A class of biologically important compounds made up of smaller units (amino acids). The order of the certain base pairs in DNA determines which amino acids, and hence, which proteins are made within a cell.
Quality Assurance. A program conducted by a laboratory to ensure accuracy and reliability.
Quality Audit. A systematic and independent examination and evaluation of a laboratory's operations.
Quality Control. Activities used to monitor the ability of DNA typing to meet specified criteria.
Random Match. A match in the DNA profiles of two samples of DNA, where one is drawn at random from the population. See also Random Match Probability.
Random Match Probability. The chance of a random match. As it is usually used in court, the random match probability refers to the probability of a true match when the DNA being compared to the evidence DNA comes from a person drawn at random from the population. This random true match probability reveals the probability of a true match when the samples of DNA come from different, unrelated people.
Random mating. The members of a population are said to mate randomly with respect to particular genes of DNA characteristics when the choice of mates is independent of the alleles.
Recombination. In general, any process in a diploid or partially diploid cell that generates new gene or chromosomal combinations not found in that cell or in its progenitors.
Reference Population. The population to which the perpetrator of a crime is thought to belong.
Replication. The synthesis of new DNA from existing DNA. See Polymerase Chain Reaction.
Restriction enzyme. Protein that cuts double-stranded DNA at specific base pair sequences (different enzymes recognize different sequences). See Restriction Site.
Restriction Fragment Length Polymorphism (RFLP). Variation among people in the length of a segment of DNA cut at two restriction sites.
Restriction Fragment Length Polymorphism (RFLP) Analysis. Analysis of individual variations in the lengths of DNA fragments produced by digesting sample DNA with a restriction enzyme.
Restriction site. A sequence marking the location at which a restriction enzyme cuts DNA into fragments. See Restriction Enzyme.
Reverse Dot Blot. A detection method used to identify SNPs in which DNA probes are affixed to a membrane, and amplified DNA is passed over the probes to see if it contains the complementary sequence.
Sequence-Specific Oligonucleotide (SSO) Probe. Also, Allele-Specific Oligonucleotide (ASO) Probe. Oligonucleotide probes used in a PCR-associated detection technique to identify the presence or absence of certain base pair sequences identifying different alleles. The probes are visualized by an array of dots rather than by the electrophoretograms associated with RFLP analysis.
Sequencing. Determining the order of base pairs in a segment of DNA.
Short Tandem Repeat (STR). See Variable Number Tandem Repeat.
Single-Locus Probe. A probe that only marks a specific site (locus). RFLP analysis using a single-locus probe will yield an autorad showing one band if the individual is homozygous, two bands if heterozygous.
SNP (Single Nucleotide Polymorphism). A substitution, insertion, or deletion of a single base pair at a given point in the genome.
Southern Blotting. Named for its inventor, a technique by which processed DNA fragments, separated by gel electrophoresis, are transferred onto a nylon membrane in preparation for the application of biological probes.
Thymine (T). One of the four bases, or nucleotides, that make up the DNA double helix. Thymine only binds to adenine. See Nucleotide.
Transposition Fallacy. Confusing the conditional probability of A given B [P(A|B)] with that of B given A [P(B|A)]. Few people think that the probability that a person speaks Spanish (A) given that he or she is a citizen of Chile (B) equals the probability that a person is a citizen of Chile (B) given that he or she speaks Spanish (A). Yet, many court opinions, newspaper articles, and even some expert witnesses speak of the probability of a matching DNA genotype (A) given that someone other than the defendant is the source of the crime scene DNA (B) as if it were the probability of someone else being the source (B) given the matching profile (A). Transposing conditional probabilities correctly requires Bayes' Theorem.
True Match. Two samples of DNA that have the same profile should match when tested. If there is no error in the labeling, handling, and analysis of the samples and in the reporting of the results, a match is a true match. A true match establishes that the two samples of DNA have the same profile. Unless the profile is unique, however, a true match does not conclusively prove that the two samples came from the same source. Some people use "true match" more narrowly, to mean only those matches among samples from the same source. Compare False Match. See also Match, Random Match.
Variable Number Tandem Repeat (VNTR). A class of RFLPs due to multiple copies of virtually identical base pair sequences, arranged in succession at a specific locus on a chromosome. The number of repeats varies from individual to individual, thus providing a basis for individual recognition. VNTRs are longer than STRs.
Window. See Match Window.
X chromosome. See Chromosome.
Y chromosome. See Chromosome.