Glossar

A

Allele: Different, mutually exclusive forms of the same gene. Within a population there are usually many different "normal", i.e. multiple alleles. Differences between the alleles are caused by sequence variations which do not necessarily affect gene function. One individual inherits one allele from the mother and one from the father. Are these alleles identical, they are called homozygous for the respective gene, do they differ, they are heterozygous for the respective gene.
Anticipation: The tendency of certain diseases to appear at earlier age of onset and with increasing severity in successive generations is called anticipation. This usually applies to the so-called trinucleotide repeat diseases.

C

Carrier: An individual carrying a mutation in one of the two alleles of a gene but without clinical symptoms (heterozygous). In these cases the mutation is not sufficient for the clinical manifestation of a disease. In autosomal recessive conditions clinical symptoms only become manifest if also the second allele is altered by a mutation.
Compound heterozygosity: Different mutations are present on both chromosomes in autosomal recessive conditions.
Contiguous gene syndromes: Deletions characterized by a specific complex phenotype. The originally affected DNA segment involves several genes, which are located adjacently in one chromosomal region and which contribute to the phenotype independent from each other.

d

de novo deletion / mutation: A deletion / mutation which has not been inherited from one parent but which has arised newly in the affected individual.
de novo mutation: cf. mutation

D

Deletion: Missing of a chromosome or a chromosomal region.

Interstitial deletion: Missing of a fragment within a chromosome as opposed to

terminal deletion where terminal fragments of a chromosome are lost.
DHPLC: Denaturing high pressure liquid chromatography is a method to detect sequence variations in PCR products with high sensitivity as compared to wildtype sequences. The detection is based on the formation of heteroduplexes which always form when there is sequence variation on the second allele besides the wildtype allele. Heteroduplex DNA sequences are formed during PCR with high reproducibility and consist of one strand of the normal allele and one strand of the altered allele. These hybrids show an altered retention pattern in the DHPLC column which can be detected with a probability of more than 95%. The time for analysis for one fragment is around 4-5 minutes, making DHPLC a very cost-effective and efficient prescreening method prior to targeted sequencing.
Direkt diagnostics: If the localization and the nucleotide sequence of a gene are known in a hereditary disease, the molecular defect (mutation) of the respective gene can be directly identified in patients and carriers.
Disomy, uniparental (UPD): Presence of two homologous chromosomes or chromosomal regions (partial disomy) which have both been inherited by one parent.
DNA-Methylation: Covalent binding of a methyl residue to defined bases of DNA. In human cells exclusively cytosine residues are methylated to 5-methyl-cytosine in CpG-dinucleotides. DNA methylation has important functions in eucaryotic cells in that it is involved in the organization of DNA structure and in gene regulation.
DNA-replication: Prior to every cell division the chromosomal set has to be duplicated in order to transfer the complete genetic material to each daughter cell. The identical duplication of the DNA molecules in the cells is performed by specific enzymes during replication.
Duplication: Duplication of the same chromosomal segment or gene or gene region.

E

Exon: DNA segment of a gene which encodes the genetic information for the respective protein. Between the exons of a gene the non-coding regions, i.e. introns are interspersed.
Expression: cf. gene expression.
Expressivity: Type and extent of the phenotype of a defined gene (cf. also penetrance).

F

Fluoreszence-in-situ-Hybridisation (FISH): The method for colorful detection of chromosomes and chromosomal regions. Microdeletions, minimal chromosomal rearrangements and marker chromosomes can be identified by selected DNA probes. The number and localization of the fluorescent signals correspond to the number of chromosomal segments (normally 2) and their localization.
Fragment length analysis: Precise determination of the length of labeled PCR products via sequence electrophoresis.

G

Gel electrophoresis: DNA is negatively charged and therefore migrates in the electric field. In a suitable matrix (agarose or polyacrylamide) DNA molecules migrate according to their molecular weight and can be separated according to size.
Gene dose: All autosomal genes are present in double copy in the genome. Many genes need to be expressed in both alleles in order to maintain normal cellular function. The loss of one allele resulting in half of the gene dosis may therefore cause cellular dysfunction.
Gene expression: All processes which involve protein synthesis from a defined gene: first, RNA (messenger-RNA, mRNA) is produced from the nucleotide sequence of a gene (transcription); subsequently, the protein (gene product) is synthesized during translation.
Germline mutation: A mutation, which has arised in the germline (oocyte or sperm) of one of the parents. If a germline mutation is inherited to a child, it is found in all somatic cells of the child and also in its germ cells.

H

Haplotype analysis: Haplotype analysis by polymorphic markers enables us to follow inheritance of certain chromosomal regions within a family. Even if the precise localization and the sequence of the disease-causing gene within this region is unknown, indirect conclusions can be drawn from this analysis to the mode of inheritance of the mutation. Likewise, unknown mutations in known genes can be detected. This procedure is chosen in cases when direct mutation detection is too costly. Haplotype analysis is a family analysis. Therefore, as many family members as possible should participate in the examination.

I

Imprinting mutation: In some diseases, reduced or increased DNA methylation can be detected, which is most likely disease-causing. Those mutations leading to disturbances in methylation are called imprinting mutations.
Imprinting, genomic: Modification of certain genes in early embryonic development, depending on whether they are of maternal or paternal origin. Accordingly, imprinting results in differential gene activity, i.e., few genes are only active on the chromosomes inherited from the mother, others only on paternal chromosomes. Biochemically, imprinting is most likely related to methylation of DNA.
Index patient: Molecular genetic analyses with, e.g., autosomal dominant inheritance are first performed only in one affected family member (index patient), since the disease is most likely caused by the same mutation in all other affected family members. Following the identification of the disease-causing mutation in the index patient, the mutation is analyzed in all further patients in the family.
Indirect diagnostics: If the chromosomal position of a mutated gene is known and if the gene itself has not yet been isolated or is very large, the gene defect (mutation) can be detected in an indirect manner (cf. haplotype analysis).
Inheritance: Autosomal dominant inheritance: A single copy of the causative alteration (heterozygosity) is sufficient to cause disease. The respective gene is located on an autosome, not on a gonosome and is inherited independent of gender. For progeny of an affected person the risk is 50% to inherit the mutated allele and be symptomatic carrier as well.

Fig. 1: autosomal dominant Inheritance. Rhombic forms were selected in order to demonstrate that inheritance is independent of gender.

Autosomal recessive inheritance: Two copies of the causative alteration are necessary to cause disease. The mutations can be identical (homozygosity) or may also be two different genetic alterations (compound heterozygosity). Gene carriers cannot be identified by clinical signs. The respective gene is located on an autosome and is inherited independent of gender. The risk for an affected child of heterozygous, clinically healthy parents is 25 %.

Fig. 2: autosomal rezessive inheritance. Rhombic forms were selected in order to demonstrate that inheritance is independent of gender. In III/1 there is consanguinity.

X-linked recessive inheritance: The disease-causing gene is located on the X chromosome and leads to clinical symptoms in men (hemizygosity). Females are affected only seldom, i.e. in cases when both X chromosomes have mutations in the respective gene. Heterozygous women are generally without symptoms, but they can still transfer the mutation. The risk for affected sons is 50%. Likewise, the probability for daughters to be carriers is 50%.

Fig. 3: X-linked recessive Inheritance.

X-linked dominant inheritance: Rare pattern of inheritance. The disease-causing gene is located on the X chromosome and is sufficient to cause clinical symptoms. In contrast to X-linked recessive inheritance also heterozygous women are affected. Hemizygous males are affected, with the disease possibly being lethal.

Fig. 4: X-linked dominant Inheritance.
Intron: Non-coding DNA segment of a eucaryotic gene, located between the exons.
Inversion: Rearrangement of a chromosomal section following two chromosomal breaks and inversion of the chromosomal segment in between. In pericentric inversions, the break points are located on different chromosomal arms, in paracentric inversions on the same chromosomal arm.

K

Karyogram: Pair-wise arrangement of homologous chromosomes for systematic analysis of the chromosomes.
Karyotype: Complete chromosomal set of an individual, defined by the number and the morphology of the chromosomes in the mitotic metaphase.

M

Microdeletion

Very small deletions (<2Mb) which are generally not detectable cytogenetically. Microdeletions can be detected via FISH or using other molecular genetic methods.

Mismatch repair

Mistakes which arise during DNA replication such as wrong base pairs (mismatch) are repaired in the cell nucleus by an enzyme complex.

Missense mutation

The base substitution in a position of the DNA sequence may lead to an amino acid exchange in the corresponding protein.

Monogenic

Diseases which are caused by one single gene are called monogenic hereditary diseases. Up until now, approximately 6000 of such diseases have been described.

Monosomy

Missing of a single chromosome in an otherwise diploid (containing two homologous chromosomes each) chromosomal set. In partial monosomy only a fragment of one chromosome is missing.

Mutation

Missense mutation: The base substitution in a position of the DNA sequence may lead to an amino acid exchange in the corresponding protein.
De novo mutation: Mutation which arises newly after fertilization of the oocyte. According to the timepoint during development, two different cases are distinguished: if the mutation arises very early during development, nearly all somatic cells of the individual are affected, even the germ cells. This usually results in complete clinical manifestation of disease. If the mutation arises later during development, only cells of defined tissue are affected. This phenomenon is called a somatic mutation with a tissue-specific mosaicism. Clinically, all variations from severely to not affected are possible.
Nonsense mutation: During protein biosynthesis termination is accomplished by so-called stop codons, which are recognized during translation. If a stop codon is generated as mutation in the coding region of a gene, protein synthesis is terminated earlier and a shortened, maybe dysfunctional protein is produced.
Point mutation: Mutation only mildly affecting the sequence of a gene with the exchange of only one nucleotide.
Splice-site mutation: The coding exon sequences of a gene have to be put together on the RNA level which involves the removal of intronic sequences. This process is called splicing. Due to specific recognition sequences, the splicing machinery recognizes the beginning and the end of an exon, the so-called intron-exon boundary. When an essential nucleotide in the recognition sequence is exchanged, the corresponding exon is not considered during splicing. This leads to the synthesis of an altered protein.
Triplet repeat expansion, dynamic mutation: Sequential identical nucleotide triplet repeats occur in the human genome in many sites. The number of such triplet repeats is variable in the population, but confined to a normal range and exhibits only few changes over many generations within a family. Based on a yet unknown mechanism, the number of triplet repeats can be increased over a critical threshold level. If this large number of repeats is present in the coding region of genes it may cause disease. The effects of increased repeat length are variable. Generally, protein synthesis or function is impaired. One peculiarity of this mutation type lies in its dynamic nature: once the repeat length has surpassed the critical threshold level, repeat length may increase from one generation to the next (dynamic mutation). The severity of disease and the age at onset correlates to the number of repeats which also explains the phenomenon of anticipation.

N

Nonsense mutaton: cf. mutation
Nukleotide triplett: Sequence of three nucleotides e.g. ACG.

O

OLA: Oigonucleotide ligation assay

P

PCR, Polymerase chain reaction: PCR, Polymerase chain reaction: Method for in-vitro amplification of defined DNA sequences by the means of DNA polymerases. Amplification is accomplished by the cyclic annealing of single-stranded synthetic DNA fragments (primer) to denatured single-stranded genomic DNA and extension of these fragments by a DNA polymerase. The DNA sequences important for primer annealing have to be known.

Abb. 5: PCR-Reaktion
Penetrance: Percentage of cases in which a mutation becomes manifest in a particular phenotype.
Point mutation: cf. mutation
Polymorphism: Genetic polymorphism: Presence of two or more different genotypes in a population. The different genotypes are based on sequence variations which are found in the population in a certain percentage (> 1%).
Promotor: An approximately 100 bp long DNA segment in eucaryotic genes before the start of transcription of a gene. From this promotor sequence, transcription is regulated. In this region recognition sequences for the transcriptional enzyme complex and for regulatory proteins are embedded.

R

Replication: Prior to every cell division the chromosomal set has to be duplicated in order to transfer the complete genetic material to each daughter cell. The identical duplication of the DNA molecules in the cells is performed by specific enzymes during replication.
Restriction enzymes: DNA endonucleases cutting the DNA strand at specific nucleotide sequences.

S

Sequence analysis, Sequencing: Automated procedure to analyze the nucleotide sequence of DNA fragments.
Sequence gel electrophoresis: Particular type of gel electrophoresis to analyze the nucleotide sequence of DNA fragments. Very short, single stranded (denatured) DNA strands are separated in a polyacrylamide gel according to length and nucleotide sequence.
Somatic mutation: If a mutational event occurs after the fertilization of the oocyte, not all tissues are affected by this mutation. By definition, germ cells are not affected by the mutation.
Southern Blot Hybridisation: A technique to analyze specific DNA fragments. Genomic DNA is cut in fragments by restriction enzymes. These fragments are separated according to size and subsequently transferred to a membrane (Southern-Blot). This membrane is incubated with a specifically labeled DNA probe. In the presence of the complementary DNA sequence the probe "binds", i.e. hybridizes to this sequence and can finally be detected.
SSCP-Analyse, single-stranded conformation polymorphism-analysis: Single strand conformation polymorphismus analysis:

Screening for mutations, based on different elektrophoretic run of single strand-DNAs with minimal different nukleotide sequences.

Abb. 6: SSCP-Analyse

T

Transcription: First step during gene expression. An RNA-polymerase-enzyme complex produces a messenger-RNA copy from a coding DNA fragment in the cell nucleus. Subsequently, translation takes place in the cytosol of the cell.
Translation: Second step during gene expression. All genetic information encoded by messenger-RNA is read at the ribosomal protein synthesis apparatus and translated to the corresponding amino acid sequence by means of different transfer RNAs.
Translocation: Structural chromosomal extension by the transfer of one chromosomal fragment to a non-homologous chromosome.
Trinukleotide repeat, triplet repeat: Multiple sequences of repetitive DNA fragments, consisting of three nucleotides (e.g. CAG) each.

X

X-lnactivation: In early embryonic development one of the two X chromosomes is inactivated in somatic cells of the female organism (Lyon hypothesis). Originally paternal or maternal X chromosomes are inactivated at random (random X-inactivation).