DNA: An organism’s DNA is the software that stores precise instructions determining the structure and function of an organism. At the same time it contains information for its self-replication, thus ensuring the transfer of genetic instructions from a cell to its progeny and from an organism to its offspring.
The first step in expressing the information contained in DNA is to transfer it to RNA through the process of transcription. RNA, in turn, transmits, through the process of translation, the information onto the proteins responsible for the structure and function of the cells and, by extension, of the organisms. This process of transferring genetic information is the central dogma of Molecular Biology. Genetic information is the set of bases, similar to the fact that the information of a written phrase is contained the order of the letters that make it up. The information is organized into segments of DNA with a particular sequence, the genes. These, through transcription (in mRNA) and translation, determine the order of amino acids in the final protein.
DNA library: Collection of cloned DNA fragments that either represent the entire genome (genomic library) or represent DNA copies of the total mRNA produced by a cell or tissue (cDNA library).
DNA polymerases: Enzymes that synthesize DNA. An initial RNA segment is required and also a single stranded DNA are required to begin synthesis. One type of polymerase fixes DNA replication errors.
FISH: This technique uses cloned fluorescent DNA fragments (termed probes), which under specific conditions are hybridized to the corresponding (homologous) regions of the chromosomes under investigation. Specific probes are used for the detection of specific abnormalities, such as:
- Probes containing highly repeatable DNA, for the rapid diagnosis of numeric abnormalities and for the identification of marker chromosomes of unknown origin
- Site-specific probes for detecting cryptic structural chromosomal abnormalities, such as micro-deletions, micro-duplications, rearrangements etc.
- Whole chromosome staining probes, which are mainly used to identify derivative chromosomes and translocations in a karyotype.
Next Generation Sequencing (NGS): DNA sequence analysis through Next Generation Sequencing (NGS) is the most up-to-date DNA sequencing technology, with its applications becoming more and more prevalent in both research and health services. The Next Generation Sequencing technique requires capture and/or amplification of genes or DNA segments in general and then massive parallel sequencing tens to thousands of times of each segment through a ‘library’ in which all the segments should be adequately represented.
PCR: The Polymerase Chain Reaction (PCR) is a basic technique for many different molecular genetics tests. The purpose of this technique is to selectively amplify DNA from a SPECIFIC AREA (e.g. of a single gene) so that we can then study it further. For example, if we want to detect possible damage to the hemoglobin gene, we use this technique to amplify (more than 1 billion times) the region of DNA that contains this gene, which represents a very small fraction of our total DNA.
An important prerequisite for applying the PCR technique is to know the order of the nucleotides located to the right and left of the portion of DNA that we want to amplify. The PCR reaction is catalyzed by a specific enzyme, Taq polymerase. In conjunction with the appropriate reagents, Taq polymerase synthesizes in the test tube copies of the desired region in successive cycles. The cycles are repeated 20-30 times until the target sequence is amplified/copied multiple times.
Messenger RNA (mRNA): The type of RNA that carries the information/message from the corresponding DNA, in order to produce a polypeptide chain (protein). In eukaryotic cells, the mRNA contains only the exons of each gene and is derived from the maturation of the precursor RNA.
Sister chromatids: Prior to the onset of cell division, DNA replication has already been completed and therefore genetic information has been duplicated. After this copying, each chromosome now consists of two copies of DNA, called sister chromatids. These are symmetrical and similar because they are identical DNA molecules, and are joined in one region, called the centromere.
Acrocentric chromosome: When the centromere is very close to one end of a chromosome, the chromosome is termed acrocentric (e.g. chromosome 13).
Alleles: Genes that control the same function and are in the same position on homologous chromosomes. An allele is an alternative form of a gene.
Amniocentesis: A few weeks after the onset of pregnancy a structure called the amniotic sac is formed. The amniotic sac contains the so-called amniotic fluid and the embryo develops within it. During amniocentesis, usually performed from the 16th to the 23rd week of gestation, with the help of a thin needle and under ultrasound guidance, a small amount of amniotic fluid is drawn containing fetal cells. These cells can then be used for DNA analysis or biochemical analysis of certain proteins and enzymes. These embryonic cells are used to diagnose chromosomal and/or gene abnormalities (see prenatal diagnosis from amniotic fluid cells), and the procedure is now generally regarded as a safe method and with a relatively lower risk for pregnancy complications compared to chorionic villi sampling.
Inversion: An inversion is generally caused by fractures at two different points of a chromosome and reunification of the segment after the inversion. Inversions results in a change in the order of the genes on the chromosome.
Haploid: Cells containing only one copy of each chromosome (e.g., oocytes, sperm).
Autosomal dominant inheritance: A trait or genetic disorder expressed in the autosomal dominant manner is observed in heterozygotes, that is, in individuals who have only one of the two homologous genes mutated. In other words, heterozygotes (with only one copy of a specific gene mutated) are usually expected to manifest the disease. A person affected by an autosomal dominant genetic disease has a 1/2 (50%) chance of transmitting it to his children.
Autosomal recessive inheritance: Autosomal recessive diseases occur in individuals who have inherited two abnormal copies of the same gene from both parents. Unaffected parents, who carry only one copy of the mutant gene, are called carriers or heterozygotes and are typically healthy or may exhibit very mild symptoms (such as in beta-thalassemia carriers). Parents who are both carriers of autosomal recessive genetic disease have a 1/4 (25%) risk of having affected children in every pregnancy.
Spontaneous abortion: It is the loss of pregnancy-fetus before the 24th week of pregnancy. The majority of spontaneous abortions (also known as miscarriages) take place before the 16th week and occur in ~12% of pregnancies. Studies have shown that at least 50% of miscarriages are due to fetal chromosomal abnormalities, usually trisomies.
Family tree: Pedigree analysis, through the formation of a family tree, is a systematic recording, usually with symbols, of an individual’s ancestors. If this recording concerns a large number of generations, then we are talking about a pedigree/family tree.
Genetics: Genetics is the science that generally studies the organization and mechanisms of the flow/regulation of information contained on the genetic material (DNA or RNA) of a cell-organism, e.g. from a simple virus or bacterium to more complex organisms, such as humans.
Genomics: Genomics constitutes rather recent branch of Genetics, combining and integrating into ‘classical’ Genetics recent developments, especially after 2009, concerning the results and knowledge gained from massive analysis of an organism’s genome. For example, with the introduction in the last ~10 years of Next Generation Sequencing (NGS), there has been a great deal of knowledge gained about the function of human genes, with the discovery of hundreds of new genes related to genetic diseases of previously unknown cause. Due to the large volume and complexity of genomic analysis data, the science of Bioinformatics has rapidly developed, which is now an integral part of any Genomic analysis, such as NGS analysis of the human genome (Whole Genome Sequencing), NGS analysis of all human genes (Whole Exome Sequencing), etc. Finally, the highly beneficial results of human genomic analyses concerning all types of genetic disorders have led to the development of Genomic Medicine and Precision Medicine, developments that allow us today to have a totally personalized approach to the prognosis, management and treatment of patients with genetic diseases.
Gene locus: The position of a gene on a chromosome.
Genetic code: The sequence of bases on the mRNA, as transcribed from DNA, determines the amino acid sequence of the proteins, based on a triplet nucleotide code corresponding to a specific amino acid, called the genetic code. The basic features of the genetic code are:
- the genetic code is a triplet-based code, that is, a trio of nucleotides, called codons, correspond to a particular amino acid, e.g. in humans, the triplet ATG corresponds to the amino acid methionine.
- the genetic code is continuous, that is, the mRNA is read, through the translation process, continuously in every three nucleotides, without missing a single nucleotide.
Genetic polymorhisms: It is defined as the presence of multiple alleles in a genetic locus, in which at least two alleles occur with a frequency greater than 1% in the population. In Medical Genetics polymorphisms are commonly used to:
- map genes on chromosomes through genetic linkage analysis
- in preimplantation genetic diagnosis of genetic diseases
- genetic studies for multi-factorial diseases, such as coronary heart disease, cancers, diabetes
- genetic profiling-human identification, paternity testing and testing for other relationships
Genetic counseling: Genetic counseling is the process of communication between a specialized geneticist and a person, which usually involves obtaining and analyzing a person’s family history and/or explaining the results of a genetic test. Indicatively, the procedure may include assessing family history and medical records, recommending appropriate genetic testing, interpreting the results for those concerned and providing useful instructions for themselves and their reproduction.
Gene mutations: Self-replication of genetic material and mitotic division ensure the unchanged transfer of genetic information from cell to cell and from generation to generation, thus maintaining genetic stability. However, during the transfer of genetic information and / or adaptation of an organism to the constantly changing environment, there may be several changes in its genetic material, namely changes in the bases/nucleotides of genetic material (DNA or RNA). These changes, or mutations, are usually inherited from the ancestors or may occur for the first time in an organism/individual (new – de novo mutations). Generally, gene mutations are divided into: (a) germline mutations, that typically exist in all cells of an organism, or (b) somatic mutations, which exist only in cells of a particular type/tissue of an organism (such as in most cancers) and are typically not inherited. Mutations in a gene may be innocent (such as most polymorphisms), i.e. without any consequence on its proper function, or may be pathological, resulting in disruption of the proper function of the gene with its corresponding consequences.
Gene: A gene is a part of the genetic material (e.g. DNA) that through its expression controls and influences certain functions of a cell/organism. This information is usually about the production of a particular protein (or sometimes only RNA). The gene contains biological information in such a way that it can be replicated and transferred from one cell to its offspring. In humans, most genes are organized on different chromosomes, which we inherit from our parents. However, there are some genes that are found in the DNA of mitochondria, organelles that are found only in the cytoplasm, for example in the cytoplasm of the mother’s oocytes and follow a different mode of inheritance in humans, being transmitted only by the mother (the sperm has no mitochondria).
Gene therapy: The process by which a genetic disease can be treated by appropriate modification/replacement/correction of the gene(s), usually in the patient’s somatic cells.
Genome: The genetic material of a cell/organism. It usually refers to the genetic material contained in the nucleus, but not necessarily.
Genotype: The genetic make-up of an organism/person at a particular location on his genetic material (e.g. chromosome or gene). The term is also used to describe different alleles for one or more genes.
Transgenic organisms: They are plant or animal species that are created by genetic engineering techniques and contain genes from another organism, usually of a different species.
Duplication: Duplication is the existence of two copies (instead of one) of a piece of genetic material, typically on the same chromosome.
Diploid: Cells/organisms in which their genetic material exists in two copies.
Structural chromosomal abnormalities: Structural chromosomal abnormalities are changes in the proper structure of one or more chromosomes. Structural changes in the chromosome may refer to small or large portions of the chromosome. The creation of structural chromosomal abnormalities is the result of various mechanisms during the cell cycle. Structural chromosomal abnormalities result in a change in the amount and/or proper arrangement of genetic information on the chromosomes.
Deletion: A loss of one copy of genetic material (e.g. gene or chromosome).
Enzymes: Enzymes are protein molecules that catalyze chemical reactions at high speed, typically in cells.
Exons: Exons are the DNA sequences of the genes contained in the mRNA and which are largely eventually translated into the amino acids of the respective protein.
Introns Introns are the intermediate DNA sequences located between the exons of the genes and linking them. They are eventually cleaved/removed to form the final mRNA and they are not translated into amino acids.
Repair enzymes: A group of enzymes involved in repairing mistakes on the nucleotide sequence-bases of the DNA
Heterozygote: A diploid organism that has two different alleles for one or more genes. For example, a person with two different mutations in each allele/gene is called a double heterozygote, whereas a single mutation in one allele/gene is called a heterozygote (see also homozygote).
Banding: Staining of the chromosomes in such a way as to create dark and light bands along their entire length. Every human chromosome is recognized by the specific pattern of its bands.
Thalassemias: Thalassaemias, often described together with another group of similar genetic diseases, the hemoglobinopathies, is a class of hematologic genetic (inherited) diseases affecting the synthesis of hemoglobin in the red blood cells. The hemoglobin molecule is composed of 2 α-type chains/proteins and 2 β-chains/proteins. In thalassemia and generally in hemoglobinopathies, there is an abnormality involving the quantity or structure of one of the α- and/or β-chains, resulting in α-thalassemia or β-thalassaemia (and other hemoglobinopathies, such as sickle-cell disease). The disease is inherited in the autosomal recessive manner, which means that heterozygous carriers with a single copy of the mutated gene are not affected. In affected patients, hemoglobin production may be partially or completely suppressed, and this can lead to different types and severity of anemia. Carriers are sometimes referred to as having the thalassemia ‘trait’.
Karyotype: Karyotype is the microscopic depiction of the number and structure of an organism’s chromosomes, arranged and sorted from the largest chromosome to the smallest.
Centromere: Each normal chromosome consists of two sister chromatids, which are held together by the centromere. The centromere divides each chromatid into two arms, one large and one small. The metaphase chromosomes of a cell differ in terms of size and location of the centromere. The position of the centromere determines the shape of the chromosome.
Cell: The cell is a living system containing various organelles, each of which performing a specific function. One of the most basic concepts in Biology is that cells are created through the division of pre-existing cells. Cell division is a very basic process and it forms the basis of every living organism’s reproduction. Cell division begins with the division/separation of the nucleus, so that the genetic information is transmitted to the new cell. There are two forms of division of the nucleus: mitosis and meiosis. Cells are divided into two main categories: prokaryotes (e.g. bacteria and other micro-organisms without a nucleus) and eukaryotes (cells of complex organisms and animals, with a nucleus).
Cytogenetics: A scientific laboratory branch of genetics that studies the structure of chromosomes and their inheritance.
Metacentric chromosome: When the centromere is located about the middle of the chromosome, this chromosome is called metacentric (e.g. human chromosome 1).
Translocation: A translocation is the result of breakage of one part/segment of a chromosome and then joining this to another non-homologous chromosome (see structural chromosomal abnormalities). In reciprocal translocations we have “exchange” of chromosomal segments between non-homologous chromosomes. Reciprocal translocations usually do not result in loss of genetic material and the individuals carrying them usually exhibit a normal phenotype. However, translocation carriers are at risk of having affected offspring with chromosomal abnormalities, as a result of the creation of abnormal gametes during meiosis.
Meiosis: The germ cells, or gametes, of diploid organisms are formed through a different kind of cell division, called meiosis. The zygote resulting from gamete fusion (fertilization) must have the same number of chromosomes as its parent cells. For this to happen, every gamete must have all the genetic information at one copy. That is to say, it must have half the number of chromosomes (haploid number) relative to the somatic cells, which are diploid. Meiosis is therefore the process ensuring the haploid chromosome number of the gametes. It occurs in specific diploid cells, called immature germ cells. These will eventually result in gametes of the multi-cellular organism. Prior to the start of meiosis, DNA replication has already taken place, with each chromosome consisting of two sister chromatids united by the centromere. At the beginning of process, the two sister chromatids of each chromosome coalesce. The homologous chromosomes are arranged in pairs, opposite each other. Then the homologous chromosomes of each pair are separated (but not the sister chromatids) and two new cells are formed, each of which now has half the chromosomes relative to the original. This is the 1st meiotic division. Subsequently, in each of the two cells the sister chromatids of each chromosome are separated and two new cells emerge, each of which has a single sister chromatid of each homologous pair of chromosomes (2nd meiotic division). In total, therefore, from an initial diploid cell, four haploid germ cells are produced, each having half the number of chromosomes relative to the original cell.
Microarrays: Microarrays (otherwise known as genomic or gene chips) are a set of small or large size/length nucleotides (DNA or RNA) that correspond to specific regions of the genome and are immobilized on a solid surface (usually a glass). They are used either to investigate the amount of DNA along the chromosomes, i.e. chromosomal abnormalities, detecting for example deletions or duplications of DNA (aCGH), or to quantitate gene (expression arrays). Quantitative or qualitative measurements with microarrays exploit the selective nature of the principle of complementarity between DNA-DNA or DNA-RNA or recently also between the amino acids of proteins, under strictly controlled temperature conditions and the use of fluorescent labels. For example, one application of the method, often referred to as molecular karyotype, has the advantage of being able to analyze in one step and in depth the possible existence of sub-microscopic deletions or duplication of regions along all human chromosomes, which would not be visible through classical microscopic karyotype analysis.
Mitosis: It is worth remembering that our life began from a single cell, the fertilized egg or the zygote. This cell will eventually result in a multi-cellular organism, of whose all cells contain the same genetic information as the initial zygote. The growth of organisms, the renewal of tissues, for example the skin, the healing of a wound, but also the proliferation of certain eukaryotic unicellular organisms, such as amoeba, require cellular proliferation. The resulting new cells should contain the same number of chromosomes and the same genetic information as the original. This is ensured by cell division through a process called mitosis.
Homozygote: A diploid organism that has two identical alleles for one or more genes is called a homozygote. The term typically refers to a person who has exactly two identical mutations in the two alleles/gene copies and is called homozygous (see also heterozygote).
Homologous chromosomes: A pair of chromosomes that have exactly the same shape and size and contain the same set of genes controlling the same function, in a possibly different way.
Prenatal diagnosis from amniotic fluid cells: Prenatal diagnosis from amniotic fluid cells follows amniocentesis and is used in order to identify a possible or known genetic disorder in the embryo. It can detect, for example, whether the fetus has no chromosomal or gene abnormalities. Typically, we apply chromosomal analysis of the fetal cells in the amniotic fluid, either through classical karyotype or, more recently, with molecular karyotype (aCGH) which are both able to reveal structural and/or numerical chromosomal abnormalities. Also, following extraction of DNA from the fetal cells, we can also perform gene testing for the detection of mutations in one or more genes.
Prenatal diagnosis from chorionic villi cells::
Prenatal diagnosis from chorionic villi cells is is used to detect a genetic, or non-genetic, disorder in the fetus. It can detect, for example, whether the fetus has no chromosomal or gene abnormalities. Typically, we apply chromosomal analysis of the fetal cells in the chorionic villi sample, either through classical karyotype or, more recently, with molecular karyotype (aCGH) which are both able to reveal structural and/or numerical chromosomal abnormalities Also, following extraction of DNA from the fetal cells, we can also perform gene testing for the detection of mutations in one or more genes. It is recommended and applied in high-risk cases, for example, when serious ultrasound abnormalities have been detected in the 1st trimester, or in cases where we know in advance that one or both parents carry pathogenic gene mutations.
Edwards syndrome (trisomy 18): Edwards syndrome is a chromosomal abnormality that is caused in the majority of cases by an extra copy of chromosome 18 (trisomy 18). Newborns with trisomy 18 have serious abnormalities and only a few survive until the first year of life, while a significant proportion is automatically aborted in the first trimester of pregnancy. It is the second most common chromosomal abnormality after trisomy 21 (Down syndrome), affecting all organs of the body and causing distinct phenotypic facial features. Neonates with trisomy 18 appear weak and with fragile health, have an unusually small head, have severe heart and kidney problems and overlapping fingers. In >99% of cases it is not hereditary, except in rare cases where a parent is a carrier of a structural chromosomal abnormality involving chromosome 18.
Down syndrome (trisomy 21): Down Syndrome is a chromosomal abnormality that in the majority of cases is caused by an extra copy of chromosome 21 (trisomy 21) and is the most common viable chromosomal abnormality. The risk of a couple having children with trisomy 21 increases exponentially with respect to the mother’s age, especially after the age of 35 years. People with the syndrome have typical phenotypic features such as: broad neck, flat nose, moon-shaped face often with an open mouth and a protruding tongue. In >99% of cases it is not hereditary, except in rare cases where a parent is a carrier of a structural chromosomal abnormality involving chromosome 21.
syndrome (trisomy 13): Patau Syndrome is a less common viable chromosomal trisomy compared to Edwards Syndrome (trisomy 18) and Down Syndrome (trisomy 21). The overwhelming majority of fetuses with trisomy 13 are automatically aborted in the 1st trimester. Those who are born and reach infancy have severe mental disability due to incomplete brain development, have serious heart problems and generally have several abnormalities in their physical appearance, such as polydactyly, cleft palate (a slit at the roof of the mouth between the nasal and oral cavities) etc.. In >99% of cases it is not hereditary, except in rare cases where a parent is a carrier of a structural chromosomal abnormality involving chromosome 13.
Phenotype: The set of apparent external characteristics of an individual, determined either by genes or by the environment or through their interaction.
Carrier: A person harboring a change/mutation in a single allele/gene that is associated with the expression of a genetic disease. The term usually refers to an individual who is heterozygous for an autosomal recessive genetic disease or to a female heterozygous for a X-linked recessive allele.
X-linked inheritance: Diseases due mutations in genes located on the X chromosome have particular characteristics, which are related to the biology of the X chromosome itself. In X-linked recessive inheritance, the genetic disease is expressed mainly or exclusively in males with a pathological mutation in the corresponding gene (since males have only one X chromosome), while all female offspring of an affected male are obligatory carriers and affected males cannot have affected male offspring (as they transmit to them the Y chromosome). Correspondingly, in X-linked recessive inheritance, females with a pathogenic mutation in one copy/allele of the gene (heterozygotes) are typically healthy carriers of the disease (having 2 X chromosomes) and have a 1/2 (50%) risk of having affected male offspring. In X-linked dominant inheritance, males are usually severely affected, but also females with a pathogenic mutation in one copy/allele of the gene (heterozygotes) are affected. The above rules are a rather complicated and not completely applicable, due to the biological phenomenon of non-random or skewed X-inactivation.
Sex chromosomes: A pair of chromosomes that determine sex in most organisms, including humans. In humans, the presence of the Y chromosome determines the male individual and its absence the female. In females we have 2 X chromosomes (XX), whereas males have one X chromosome and one Y chromosome.
Chorionic villi (sampling): Oxygenation and nutrition of the fetus are regulated by an organ called the placenta that mediates between the mother’s body and the fetus. The formation of the placenta involves a membrane composed of embryonic cells, called the chorion. The chorion forms certain characteristic projections called chorionic villi. When obtaining a chorionic villi sample, a procedure performed between the 10th-13th week of gestation, fetal cells are obtained by means of a special needle from these chorion projections-villi. Typically, chromosomal analysis of chorionic villi cells is then performed, either through classical karyotype or more recently through molecular karyotype, which are both able to reveal structural and /or numerical chromosomal abnormalities. Also, from the DNA of the chorionic villi cells we can also perform gene testing for the detection of mutations in one or more genes. The main advantage of the method over amniocentesis is that results of testing are obtained early in pregnancy (1st trimester), reducing the period of uncertainty and allowing early termination of pregnancy, if necessary.
Chromosome: During the short phase of a cells lifespan, genetic material together with specific proteins (histones) are concentrated in the form of a “rod”. These rods are called chromosomes and are located in the nucleus of each cell. In humans, all genes are found on different chromosomes, except for few genes located on the mitochondrial DNA. Humans have 23 pairs of chromosomes, forming the diploid number 46. This diploid number is also the number of chromosomes of a normal cell. The haploid number is the number of chromosomes (23 chromosomes) contained in the gametes (oocyte or sperm).
Chromosomal abnormalities: Chromosomal abnormalities are changes in either the structure of chromosomes (structural abnormalities) or their number (numerical). Numerical chromosomal abnormalities are basically the result of errors in meiotic division. If during meiosis there is abnormal chromosomal segregation, then gametes with chromosome numbers greater or less than normal are created. The resulting cells have an excess or lack of a chromosome(s) and are called aneuploid. The absence of a single chromosome is called monosomy, whereas the presence of an extra chromosome is called trisomy. Monosomies are usually lethal to the body because chromosomes and their genes (except for the sex chromosomes X and Y) must exist in duplicate to ensure proper development of the zygote. Numerical chromosomal abnormalities can occur for both autosomal and sex chromosomes. Finally, there are also sub-microscopic chromosomal abnormalities, that is, micro-deletions and micro-duplications involving specific regions of the chromosomes, which may be pathological and are associated with many known chromosomal syndromes (e.g. DiGeorge syndrome). It is well known that all humans have micro-deletions and micro-duplications, which in their majority are innocent polymorphisms.