Ø forensic ChrX research

GLOSSARY

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Ø Introduction to forensic
ChrX-research

Ø Go to the ChrX STR via
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Ø Go to the ChrX STR via
the linkage table

Ø Go to STR clusters via ChrX-
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Ø Diallelic ChrX-markers
(a project of the future)

Ø Ethical considerations

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Ø Calculate ChrX STR
parameteres

Ø Glossary

Ø useful links

Ø ChrX users

Ø ChrX bibliography

      References:
      Some terms included here are copied from sources available online in the
      world wide web:

      1.      The Online Biology Dictionary http://www.biology-online.org/dictionary.asp
2.      See-Kiong Ng: Automating Computational Molecular Genetics: Solving the Microsatellite Genotyping Problem,
      CMU-CS-98-105, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213
      http://reports-archive.adm.cs.cmu.edu/anon/1998/CMU-CS-98-105.pdf

In some cases term explanation from different sources were included in
parallel

· Adenine (A): A nitrogenous base that is a member of the base pair A-T (adenine and thymine).

· Allele: Any one of a series of two or more different genes that occupy the same position (locus) on a chromosome. Since autosomal chromosomes are paired, each autosomal locus is represented twice. If both chromosomes have the same allele, occupying the same locus, the condition is referred to as homozygous for this allele. If the alleles at the two loci are different, the individual or cell is referred to as heterozygous for both alleles.

· Alleles: Alternative forms of a gene or marker. Alleles are inherited separately from each parent, as the chromosomes from the sperm and the egg pair up in reproduction.

· Autosomes: Chromosomes that are not involved in sex determination. In human beings, each individual has two copies of each autosome (chromosomes 1 to 22), one inherited from each parent. See also sex chromosomes.

· AVACH: German term for MEC (Allgemeine Vaterschafts Ausschluss Chance), see MEC.

· Base pair (bp): Two complementary nitrogenous bases held together by weak bonds. The two strands of the DNA double helix are held together by the bonds between base pairs adenine and thymine or guanine and cytosine. The length of a DNA sequence is often given in bp.

· CA-repeats: A microsatellite marker that contains tandem repeats of the simple DNA sequence C-A (cytosine and adenine).

· Centimorgan (cM): A unit of measure of recombination distance. A recombination distance of 1 cM is equal to a 1% chance that a marker at one genetic location will be separated from a marker at another location due to meiotic recombination. In humans, 1 cM is roughly equal to 1 Mb (one million base pairs).

· Centimorgans: A unit of measure of recombination frequency. One centimorgan is equal to a 1% chance that a marker at one genetic locus will be separated from a marker at a second locus due to crossing over in a single generation. In human beings, 1 centimorgan is equivalent, on average, to 1million base pairs.

· Chromosomes: The threadlike structures found in a cell containing the cellular DNA that encode the information of heredity. Genes are arranged in linear order along the chromosomes. The human genome consists of twenty-three pairs of matching chromosomes; each chromosome in every pair is inherited separately from each parent.

· cM: See centimorgan.

· Crossing over: The process during meiosis in which an exchange occur between two corresponding chromosomes before one member of the chromosome pair is incorporated into a sperm or an egg. This process results in a reshuffling of genes; the further apart two genes are, the more likely it is for them to be reshuffled. This likelihood is used as a measure of how far apart two genes are, and is termed recombination distance with centimorgans as units.

· Crossing over: A process that occurs in meiosis where homologous chromatids exchange genetic information between one another, increasing genetic diversity in the process of it.

· Crossing over: The breaking during meiosis of one maternal and one paternal chromosome, the reciprocal exchange of corresponding sections of DNA along pairs of homologous chromosomes by symmetrical breakage and crosswise rejoining of the chromosomes. This results in the transfer of a block of genes from each chromosome to its homologue. In contrast to genetic recombination, which is a phenotypic phenomenon, crossing-over is genotypic. Any even number of crossing-overs between two loci will cancel out phenotypically and no recombination will occur. Recombination can result from DNA exchange of alleles between homologous chromatids in meiosis, giving rise to chiasmata. Compare: recombination.

· Cytosine (C): A nitrogenous base that is a member of the base pair G-C (guanne and cytosine).

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· DNA (deoxyribonucleic acid): The molecule that encodes hereditary information. It is a double-stranded molecule held together by weak bonds between base pairs of nucleotides.

· DNA sequence: The linear order of base pairs along a DNA molecule.

· Duo cases: Cases of disputed paternity consisting of child/ putative father. (Motherless cases). In ChrX testing this cases are only resolvable in father/daughter constellations, which equals a mother/son constellations in skeletal identification cases.

· DXS markers: D segs are chromosome-specific IDs that are useful for queries such as “d7s*” to find all markers on chromosome 7. D segs are commonly used to describe forensic markers with names such as dxs101. (X chromosome)

· Electrophoresis: A technique for separating large molecules (e.g. DNA) in a mixture. A medium (e.g. a gel) containing the mixture is exposed to an electric field. Different molecules travel at different rates, depending on their electrical charges and sizes. See also gel electrophoresis.

· EST: See expressed sequence tag.

· Expressed sequence tag (EST): A content-addressable label that is a subsequence of an expressed gene (cDNA).

· Exon: The protein-coding DNA sequence of a gene. See also introns.

· Exon : The sequences of the primary RNA transcript (or the DNA that encodes them) that exit the nucleus as part of a messenger RNA molecule. In the primary transcript neighbouring exons are separated by introns.

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· Gametes: Specialised haploid cells produced by meiosis and involved in sexual reproduction. Male gametes are usually small and motile (spermatozoa), whereas female gametes (oocytes) are larger and nonmotile.

· Gel electrophoresis: Electrophoresis of DNA molecules using agarose and acrylamide gels as the media containing the mixtures of molecules.

· Gene: Cell biology, molecular biology> Originally defined as the physical unit of heredity, it is probably best defined as the unit of inheritance that occupies a specific locus on a chromosome, the existence of which can be confirmed by the occurrence of different allelic forms. Genes are formed from DNA, carried on the chromosomes and are responsible for the inherited characteristics that distinguish one individual from another. Each human individual has an estimated 100,000 separate genes. Given the occurrence of split genes, it might be redefined as the set of DNA sequences (exons) that are required to produce a single polypeptide.

· Gene: The fundamental unit of heredity. A gene is a stretch of DNA that encodes a specific biological function or functional product (e.g. a protein).

· Gene localisation: Determination of the physical position of a gene on a chromosome.

· Genetic linkage map: See linkage map

· Genetic markers: See markers.

· Genome: The ordering of genes in a haploid set of chromosomes of a particular organism; the full DNA sequence of an organism; "the human genome contains approximately three billion chemical base pairs".

· Genome: All the genetic material contained in the chromosomes of a particular organism.

· Genotype: The genetic makeup of an individual; the genotype of an individual for a marker or a gene is comprises two alleles; genes on the sex chromosomes are a special case.

· Genotyping: Determination of which pair of alleles is present in an individual.

· Guanine (G): A nitrogenous base that is a member of the base pair G-C (guanine and cytosine).

· Haploid: Describes a nucleus, cell or organism possessing a single set of unpaired chromosomes. Gametes are haploid.

· Haploid: Pertaining to one set of each chromosome, for instance a human gamete is haploid, possessing one of each of the 23 chromosomes of the human genome.

· Haplotype: See phase.

· Haplotype: The set, made up of one allele of each gene, comprising the genotype. Also used to refer to the set of alleles on one chromosome or a part of a chromosome, i.e. One set of alleles of linked genes. Its main current usage is in connection with the linked genes of the major histocompatibility complex.

· Haplotypes: The genetic constitution of individuals with respect to one member of a pair of allelic genes; sets of single alleles or closely linked genes that tend to be inherited together, such as those of the major histocompatibility complex; portions of phenotypes determined by genes located on one of a pair of chromosomes.

· Hemizygous: A situation within a cell where only one copy of a gene or group of genes is present instead of the usual two copies per gene in a diploid genome. The word is used as in the following example: the cell is hemizygous for gene X.

· Hemizygous: Pertaining to diplpoid organisms that possess only one allele for a particular gene, an example is the single copy of genes in the sex chromosomes of male mammals, where the X and Y chromosomes are not homologous and therefore do not present matching genes against one another.

· Hemizygous gene: Any gene which is present as only one copy in a diploid genome, when most other genes in the genome are present as two copies. The genes on the sex chromosomes of members of the heterogametic sex of a species are all hemizygous genes (for example: in humans, males have hemizygous genes on their X and Y chromosomes because they do not have two copies of either of those chromosomes).

· Hemizygosity: The state of being hemizygous.

· Haplotyping: Setting the phase for a given individual.

· Heterozygosity : The presence of different alleles at one or more loci on homologous chromosomes.

· Heterozygosity: Probability that an individual is heterozygous for any two alleles at a gene locus. Mathematically,

where pi is the population frequency of the ith allele. See also polymorphic information content.

· Heterozygous: An individual is heterozygous at a gene locus if the two alleles in the genotype are different. See also homozygous.

· Homozygous: An individual is homozygous at a gene locus if the two alleles in the genotype are the same. See also heterozygous.

· Hybridization: The binding of single strands of DNA or RNA to form double-stranded molecules.

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· Introns: Portions of the DNA sequence of a gene that are not part of the protein-coding sequence of the gene. See also exons.

· Introns: Non-coding, intervening sequences of DNA that are transcribed, but are removed from within the primary gene transcript and rapidly degraded during maturation of messenger RNA. most genes in the nuclei of eukaryotes contain introns, as do mitochondrial and chloroplast genes.

· In vitro: Outside a living organism.

· Linkage: The proximity between genes or markers along a chromosome. The closer the markers are, the less likely they are to be separated due to crossing over, hence the more likely that they will be inherited together.

· Linkages: Tendency for two or more non-allelic genes to be inherited together, because they are located more or less closely on the same chromosome. Thus parental combinations of characters are found more frequently in offspring than nonparental. Linkage is measured by the percentage recombination between loci.

· Linkage: Tendency for two or more non-allelic genes to be inherited together, because they are located more or less closely on the same chromosome. Thus parental combinations of characters are found more frequently in offspring than nonparental. Linkage is measured by the percentage recombination between loci.

· Linkage analysis: Study aimed at establishing linkage between genes. Today linkage analysis serves as a way of gene-hunting and genetic testing.

· Linkage disequilibrium: The occurrence of some genes together, more often than would be expected. Thus, in the HLA system of histocompatibility antigens, HLA A1 is commonly associated with B8 and DR3 and A2 with B7 and DR2, presumably because the combination confers some selective advantage.

· Linkage equilibrium: Situation that should exist in a population undisturbed by selection, migration, etc., in which all possible combinations of linked genes should be present at equal frequency. The situation is no more common than are such undisturbed populations.

· Linkage group: A set of two or more loci that have been shown by linkage analysis to be physically close in the genome but that have not yet been assigned to specific chromosomes. It is rapidly becoming an outmoded term.

· Linkage marker: A locus at which there is a high probability of heterozygotes (indispensible state for linkage analysis), but in itself perhaps of no clinical interest.

· Linkage map: A map of the relative positions of genetic loci on a chromosome, determined onthe basis of how often the loci are inherited together. Distance is measured in centimorgans (cM).

· Linkage map: A map of the relative position of the markers and genes on a chromosome, determined by measuring how often the loci are inherited together. The unit of such a map is centimorgan (cM). See also physical map.

· Locus: A location on a chromosome that can be identified in a distinctive manner.

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· Marker: An identifiable location on a chromosome that expresses some measurable form of polymorphism so that its inheritance can be traced in a pedigree. It can be a gene itself or some segment of DNA with no known function but whose inheritance can be traced in a pedigree.

· MEC: Mean exclusion chance. MEC describes the power of markers for the exclusion of non biological father's.

· MEC for autosomal markers in trio cases (mother/ child/ putative father) after Krüger:

· MEC for ChrX markers in trio cases (mother/ daughter/ putative father) after Kishida:

· MEC for ChrX markers in trio cases (mother/ daughter/ putative father) after Desmaresis:
(synonym: PE = Power of exclusion)

· MEC for ChrX markers in duo cases (daughter/ putative father) after Desmaresis:(synonym: PE = Power of exclusion)

· Megabase (Mb): Unit of length for DNA fragments equal to one million nucleotides or base pairs. It is also approximately equal to 1 cM.

· Meiosis: The cell division process that results in the creation of the sex cells.

· Meiosis: A type of nuclear division where four haploid cells are created from one diploid cell, and is the process used to create gametes in humans.

· Meiotic recombinations: Recombination events caused by crossing over during meiosis.

· Mendelian disease: A disease that is caused by a defective genotype at a single gene locus. Usually, only one disease mechanism is operating in a given family, and possession of the high-risk genotype is necessary for disease expression. See also non-Mendelian disease.

· Mutation: A change in form, quality or some other characteristic. A permanent transmissible change in the genetic material, usually in a single gene. Also, an individual exhibiting such a change. Also called (in classical genetics) a sport. Origin: L. Mutatio from mutare = to change

· Mutation rate: The frequency with which a particular mutation appears in a population or the frequency with which any mutation appears in the whole genome of a population. Normally the context makes the precise use clear.

· Mutation rate (in the context of this page:) number of mutations / number of meiosis observed

· Microsatellites: Genetic markers that contain tandem repeats of short simple DNA sequences.

· Nitrogenous bases: A nitrogen-containing molecule that behaves chemically as a base.

· Non-Mendelian disease: A disease caused by a complex interaction of multiple genetic and non-genetic factors. Non-Mendelian diseases are multifactorial: programmed by interacting genes and modified by mostly unknown environmental factors. Most common genetic diseases are non-Mendelian. See also Mendelian disease.

· Nucleotides: A DNA subunit, consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine) chemically linked to a phosphate molecule and a sugar molecule. A DNA molecule is made up of thousands of nucleotides linked to one another.

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· PCR: See polymerase chain reaction.

· PCR stutter: Additional trailing shadow bands that occur during gel electrophoresis of PCR-amplified microsatellites. These bands are caused by the extraneous PCR products generated by polymerase slippage during PCR amplification.

· Penetrance: Conditional probability of observing the corresponding phenotype given the specified genotype.

· Phase: The combined genotypes of two or more polymorphic loci on the same parental chromosome.

· Phenotype: The observable features of an organism that are the result of the genotype.

· Physical map: A map of the actual location of genes and markers on a chromosome measured in base pairs. See also linkage map.

· PIC: See polymorphic information content.

· Polymerase: Enzymes that catalyze the synthesis of DNA on preexisting DNA templates.

· Polymerase chain reaction (PCR): A technique for rapidly amplifying a DNA fragment by alternatively denaturing double-stranded DNA, annealing pairs of primers to both ends of the DNA segment, and synthesizing the DNA bracketed by the primers using a heat-stable polymerase .

· Polymorphic information content (PIC): Probability that the marker genotype of a given offspring can be haplotyped. Mathematically, where pi and pj are the population frequencies of the ith and jth alleles. See also heterozygosity.

· Polymorphism: Genetic variations in the DNA sequence of a gene or marker. A highly polymorphic gene or marker has a large number of possible alleles.

· Primer: Short polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase.

· Proband: The affected person through which a pedigree is discovered and explored.

· Probe: A labeled DNA or RNA sequence used to detect the presence of a complementary sequence by molecular hybridisation. For example, a probe can be used to recognise a particular clone in a complex mixture of DNA or RNA molecules.

· Purine: A single-ring nitrogenous basic compound that occurs in nucleic acids. Examples of purines are adenine and guanine.

· Pyrimidine: A double-ring nitrogenous basic compound that occurs in nucleic acids. Examples of pyrimidines are cytosine and thymine.

· Recombination: The process by which an offspring receives a combination of genes different from that of either parent. See also meiotic recombination.

· Recombination: Occurring during meiosis, recombination is the re-arrangement of genes that results in a new combination of chromosomes that is capable of creating a unique gamete.

· Reverse transcriptase: An RNA-dependent DNA polymerase or enzyme that synthesises DNA from an RNA template.

· RNA (ribonucleic acid): The ribonucleotide polymer into which DNA is transcribed.

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· Sequence tagged site (STS): A short DNA sequence (200 to 500 base pairs) with known location and base sequence that has a single occurrence in the genome. The STSs are used as unique landmarks in developing the physical map.

· Sequencing: Determination of the exact order of nucleotides in a DNA.

· Sex chromosomes: The X and Y chromosomes in human beings that determine the sex of an individual. Females have two X chromosomes; males have an X and a Y-chromosome. See also autosomes.

· Sex cells: The sperm or egg cells. In the sex cells, there are only twenty-three chromosomes and not twenty-three pairs.

· STS: See sequence tagged site.

· Tandem repeats: Multiple copies of the same nucleotide sequence on a chromosome, useful as markers in genetic analysis.

· Telomere: The rounded off tip found at the end of chromosomes.

· Tetra nucleotid repeats: A microsatellite marker that contains tandem repeats of the simple DNA sequence consisting of 4 nucleotides (i.e. GATA, CTCA, AAAG etc).

· Thymine (T): A nitrogenous base that is a member of the base pair A-T (adenine and thymine).

· Trio cases: Cases of disputed paternity consisting of mother/ child/ putative father)

· Vector: DNA molecule (e.g. from a virus) which can be inserted with another DNAfragment without losing its self-replicating capacity. Vectors are used to introduce foreign DNA into host cells where it can then be reproduced in large quantities.

· Yeast artificial chromosome (YAC): An artificial yeast chromosome constructed by cloning DNA fragments (up to 1.5 mb) into vectors that can replicate in yeast cells.

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