DNA Consulting

D1S80 Gel Image

Adenine- A purine base; one of the four molecules containing nitrogen present in the nucleic acids DNA and RNA; designated by letter A

Allele- one of a series of alternative forms of a gene (or VNTR) at a specific locus in a genome.

Allelic Ladder- a mixture of the most common STR alleles that are used to compare with the amplified samples.

Amelogenin- a PCR amplified locus that varies between males (212 and 218 bp) and females (212 bp only)

Amplification- An increase in the number of copies of a specific DNA fragment; see PCR

AMP-FLP- polymerase chain reaction amplified restriction fragment lengths polymorphism consisting of variable number tandem repeats.

Autosome- A chromosome not involved in sex determination. The diploid human genome consists of 46 chromosomes, 22 pairs of autosomes, and one pair of sex chromosomes (the X and Y chromosomes).

Base pairs (bp)- in DNA the bases adenosine (A) always pairs with Thymine (T) and  Cytosine (C) always pairs with Guanine (G).  Because DNA is a double stranded helix, the size of DNA molecules is often expressed in base pairs.

Buccal Cells- cells derived from the inner cheek lining.  These cells can be gently scraped from the inner cheek surface and are present in the saliva.

Buffer- a solution that resists changes in pH (acidity/alkalinity)

Chromosome- structures, composed of DNA and protein, found in the nucleus of the cell.  Most human cells contain 46 chromosomes; 23 derived from the mother and 23 derived from the father.  Gametes (sperm or egg cells) contain 23 chromosomes until conception.

Complementary sequences- DNA sequences that form a double-stranded structure by matching base pairs; the complementary sequence to G-T-A-C is C-A-T-G

Crime specimen- a biological specimen (blood, semen, hair, etc.) left at the crime scene by a perpetrator or, often the blood of a victim, recovered from a suspect.

Cytosine- A pyrimidine base; one of the four molecules containing nitrogen present in the nucleic acids DNA and RNA; designated by letter C.

Denaturation- use of heat or alkali to disrupt hydrogen bonds that hold the two strands of the DNA double helix together.

Diploid- two complete genomes in every cell, one derived from mom and the other from dad.

DNA sequence-order of bases in a DNA molecule.

DNA- deoxyribonucleic acid. DNA is the double helix molecule of hereditary.  It is composed of 4 bases or building  adenine (A), thymine (T), cytosine (C) and guanine (G).  These bases are strung along two opposing strands, like pearls on a string.  The A is always bound to T and G is always bound to C by week hydrogen bonds.  The specific order of bases is the DNA sequence.

Electropherogram- the pattern of fluorescent peaks produced by alleles during electrophoresis.  Collectively, this pattern is the DNA profile.

Electrophoresis- the process of separating charged molecules, such as fragments of DNA, in an electric field.  The electric current is passed through an agarose gel, which allows the DNA fragments to separate, by size.

Enzyme- A protein that can speed up a specific chemical reaction without being changed or consumed in the process

Exclusion- when the DNA from a crimes scene fails to match that of a suspect.  Inclusions are probability statements, exclusions are absolute.

Fluorescence- molecules that are fluorescent emit light upon excitation with light.  In practice, DNA molecules are tagged with fluorescent molecules. Upon excitation with laser light, fluorescent scanners (such as the FMBIO II or ABI 377) or capillary electrophoresis instruments (ABI 310) can detect and size the tagged DNA.  Since it is possible to tag DNA with different fluorescent molecules that emit light in different regions of the spectrum, it is possible for instruments to detect and distinguish between DNA fragments of similar size.

Formamide- amplified DNA is mixed with formamide to retain DNA in single stranded state.  Poor quality formamide have been associated with DNA degradation and artifacts on the ABI 310. These effects are not generally seen on polyacrylamide gel based systems.

Gel- polyacrylamide or agarose used in DNA electrophoresis; provides a sieving action on DNA fragments as they migrate in an electric field.

Gene- unit of heredity, region of DNA that encodes or regulates the expression of a protein.

Genome- all of the genetic material or DNA in a cell.

Genotype- the genetic makeup of an organism

Guanine- a purine base; one of the four molecules containing nitrogen present in the nucleic acids DNA and RNA; designated by letter G

Heterozygous- an individual that containing two different allele (genetic traits), one from mom and the other from dad, for a given trait.  In RFLP this means that an individual produces two different bands on a gel.

Homozygous- an individual that contains two of the same alleles (genetic traits), one from mom and the other from dad, for a given trait.  In RFLP this means that an individual produces a single band on a gel.

Hybridization- denatured or single stranded DNA will bind to its complimentary sequence according to base pairing rules (i.e. A=T and G=C).  Hybridization is the step, during RFLP, a specific DNA probe, binds to its target genomic DNA on a nylon membrane.

Inclusion- a probability statement that describes a DNA match between a crime specimen and suspect.

Kilobase (kb)- Unit of length for DNA fragments equal to 1000 nucleotides

Ladder- a mixture of the most common STR alleles that are used to compare with the amplified samples.

Linkage- a measure of association between two loci.  Loci on different chromosomes are non-linked.  Those that are close together on the same chromosome are closely linked and are likely to be inherited together.

Locus- (pl., loci) the location of a genetic trait on a chromosome.

Mitosis- The process of nuclear division in cells that produces daughter cells that are genetically identical to each other and to the parent.

Multiplexing- A sequencing approach that uses several pooled samples simultaneously, greatly increasing sequencing speed.

Mutation- Any inheritable change in DNA sequence.

Nanogram- (ng) one billionth of a gram

Nucleotide- a building block of DNA or RNA

Off-Ladder Alleles- an allele that is not included in the allelic ladder. These can be true, rare alleles or artifacts.

Oligonucleotide- a short length of synthetic DNA. Used as primers in PCR

PCR-polymerase chain reaction.  A method of amplifying a defined region or target of DNA by repeated cycles of denaturation (heat), annealing and extension.  After 30 cycles, a single target DNA can be amplified over a billion fold.

Polymerase (DNA)- Enzymes that catalyze the synthesis of DNA on preexisting nucleic acid templates

Polymorphic- a highly variable genetic trait in a population.  An RFLP locus that is polymorphic will have many possible size variants between individuals.

Population- A group of individuals residing in a given area at a given time.

Primer- a short length of synthetic DNA used to initiate PCR.  Also known as an oligonucleotide.

Profile- a discription of an individual or evidence resulting from the examination of one or more polymorphic loci

Protein-A large molecule composed of one or more chains of amino acids in a specific order; the order is determined by the base sequence of nuceotides in the gene coding for the protein. Proteins are required for the structure, function, and regulation of the body cells, tissues, organs, and each protein has unique functions.

Proteinase K- an enzyme that digests protein.  Used to isolate DNA from cells or tissue.

Pull-up- an artifact resulting from an intense peak in one color channel, which is detected as a minor peak in another color channel.

Race- (in genetics) a population or group that has a characteristic set of gene frequencies

RFLP- Restriction Fragment Length Polymorphism; a method in which the target DNA is cut, using a restriction enzyme, at specific sequences resulting in a range of fragment sizes. The DNA fragments are separated by agarose electrophoresis and transferred (blotted) to a nylon membrane.  The nylon bound DNA is hybridized with a labeled (radioactive or enzyme) DNA probe.  A DNA profile is produced by exposure to X-ray film.

rfu-      relative fluorescence units.  The scale, usually from 0-6,000, used to measure the relative intensity (amounts) of a signal.  Because the intensity of a signal can vary depending on the intensity of the excitation, the amount of light absorbed, re-absorption, quenching and other biophysical parameters, the measured intensity is relative.

rfu threshold- a minimum value, usually 150 rfu, programmed into Genotyper, as a minimum to call a peak an allele.

Semen- seminal fluid containing sperm.

Silver Stain- a method used to visualize STR fragments on polyacrylamide gels.

Spike- a peak on an electropherogram that can be caused by dust or an electrical disturbance, resulting in a peak that is seen across all color channels.

STR- Short Tandem Repeat; short, repetitive sequence elements of 2-5 bases.  STR's used in DNA profiling are polymorphic, which is to say that the number of repeat elements varies between individuals in a population.  STR alleles can be sized by polyacrylamide gel electrophoresis (PAGE) or capillary electrophoresis (CE).

Stutter- an artifact of STR amplification, in which the n-1 allele (n is the true allele; n-1 is the true allele minus one repeat unit) produces a signal that is 5-10% of the peak height of the true allele. For some loci, this can be as high as 20%. Stutter peaks can rarely occur at the n-2 and very rarely at the n-3 position.

Tandem repeat- the end-to-end duplication of short, identical DNA sequences in the genome.

Taq polymerase- an enzyme isolated from bacteria that live at high temperature, that catalyzes the polymerase chain reaction.

Template- genomic DNA, from crime scene samples or reference samples, that are the targets for PCR amplification.

Variant Allele- an STR allele with an incomplete allele. A common THO1 variant allele is 9.3.  This allele has 9 full repeats plus 3 nucleotides.

VNTR- variable number tandem repeats. regions of DNA, that are repeated end to end within the genome.  The exact number of repeats is highly variable within a population. The length of the repeat unit ranges from 9-80 bp.