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| ACGT is an acronym for the four types of bases found in a DNA molecule: adenine (A), cytosine (C), guanine (G), and thymine (T). A DNA molecule consists of two strands wound around each other, with each strand held together by bonds between the bases. Adenine pairs with thymine, and cytosine pairs with guanine. The sequence of bases in a portion of a DNA molecule, called a gene, carries the instructions needed to assemble a protein. |
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| Bioinformatics is a field of computational science that has to do with the analysis of sequences of biological molecules. [It] usually refers to genes, DNA, RNA, or protein, and is particularly useful in comparing genes and other sequences in proteins and other sequences within an organism or between organisms, looking at evolutionary relationships between organisms, and using the patterns that exist across DNA and protein sequences to figure out what their function is. You can think about bioinformatics as essentially the linguistics part of genetics. That is, the linguistics people are looking at patterns in language, and that's what bioinformatics people do--looking for patterns within sequences of DNA or protein. |
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| Copy Number Variation (CNV) |
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Definition
| A copy number variation (CNV) is when the number of copies of a particular gene varies from one individual to the next. Following the completion of the Human Genome Project, it became apparent that the genome experiences gains and losses of genetic material. The extent to which copy number variation contributes to human disease is not yet known. It has long been recognized that some cancers are associated with elevated copy numbers of particular genes. |
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| DNA sequencing is a laboratory technique used to determine the exact sequence of bases (A, C, G, and T) in a DNA molecule. The DNA base sequence carries the information a cell needs to assemble protein and RNA molecules. DNA sequence information is important to scientists investigating the functions of genes. The technology of DNA sequencing was made faster and less expensive as a part of the Human Genome Project. |
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| The epigenome is the collection of all of the epigenetic marks on the DNA in a single cell. The epigenomic marks different between different cell types. So, a blood cell will have different marks or modifications than a liver cell. The epigenomic modifications, the whole collection of all of the epigenetic marks on my blood cell DNA should be more similar to all of the marks on your blood cell DNA than to the collection of all the marks on my liver cell DNA. So this is a way of defining a particular type of cell. Now due to individual differences my epigenome will differ from your epigenome even in the same tissue. It's those differences that make us all individuals, and we'll see even greater changes in a state of disease. So a comparison of a normal cell and all of its epigenetic marks, or the epigenome of that cell, will differ from the diseased state of that same cell type. And we can use these differences to figure out mechanisms of disease. |
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| Gene expression is the process by which the information encoded in a gene is used to direct the assembly of a protein molecule. The cell reads the sequence of the gene in groups of three bases. Each group of three bases (codon) corresponds to one of 20 different amino acids used to build the protein. |
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| The Human Genome Project was announced in 1990. It was an international effort, but the United States was in a very strong leadership position. And it had this audacious goal of reading out all letters of the human DNA code by 2005. To the great relief of those of us involved in it, and I think the joy of the general public, we finished that project in 2003, more than two years ahead of schedule, and under budget, and produced all of this data in the public domain where, for all time, people can be working on understanding how it works and applying it for medical benefit. |
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| In situ hybridization. "In situ" is a Latin term for "in place", and then it's used in this context for detecting either RNA or DNA in the situation of the actual animal or the cells. It's a laboratory technique where it uses a probe, and this probe is usually made with DNA or RNA. It's single-stranded and it has some sort of moiety that you can detect either chemically or radioactively, and then that single-stranded is hybridized, and that's where the hybridization part comes in. You mix this probe in with your tissue sample, and you look for the single-stranded to bind in situ to the expressed mRNA or the DNA that you're looking for. You wash away the unbound probe, and then you look for where that gene is being expressed or where that piece of DNA is in the cell. This is a way of detecting things in sort of three-dimensional space, which is often very important for scientists to know where things are expressed both in terms of time and space. |
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| LOD score is actually an acronym for "log of the odds," LOD. LOD score actually refers to a numerical result when estimating whether two genes, or a gene and a disease, are linked to one another. LOD scores are most often used to describe the data one gets out of family studies where you are looking at large families and an inheritance of traits or diseases within the families. So you can have the gene of interest unlinked to your disease and have a very low LOD score. In a family where the gene and a particular disease are segregating or being inherited together the odds of those being linked can actually be quite great and that would be a large LOD score. For example, in a pedigree to prove that a gene is linked to a condition we usually say that the LOD score has to be above 3. 3 is translated roughly into about 1,000-to-one odds that this gene really is linked to this disease as opposed to the alternative hypothesis which is unlinked. So therefore the higher the LOD score the more likely the two things you are following, usually a disease and a gene or a marker, actually are truly linked in the family. |
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| Microarray technology is a developing technology used to study the expression of many genes at once. It involves placing thousands of gene sequences in known locations on a glass slide called a gene chip. A sample containing DNA or RNA is placed in contact with the gene chip. Complementary base pairing between the sample and the gene sequences on the chip produces light that is measured. Areas on the chip producing light identify genes that are expressed in the sample. |
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| Nanotechnology is an area of research and application of that research to make devices and products. It studies the properties of materials that are between one and 100 nanometers in size. So what's a nanometer? It's 10 to the minus-nine meters or .000000001 meters. That's one ten-thousandths the diameter of the human hair. Or another way to look at it is the DNA molecule is about two and a half nanometers in diameter. Nanotechnology's interesting because scientists observe unusual properties of materials at that size scale. The materials don't behave either like the atoms from which they're made or like the bulk material with which we are familiar. Examples of nanometer particles are gold, that instead of appearing the familiar color we call gold, appear red or blue or other colors depending on their exact size. And they also have different electrical properties from bulk gold that we use in jewelry or electronic devices. Or carbon nanotubes that are made of the same material as the graphite in your pencil lead that are incredibly strong, not brittle, and also have different electrical properties depending on how exactly the atoms come together. As biomedical scientists, we're interested in nanotechnology because we think we can use these new materials to make better devices to diagnose disease or to improve imaging agents that are used for MRI tests and even to deliver drugs more effectively. |
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| Population genomics really refers to a new concept in terms of ancestry, in terms of sequencing the human genome, which really has lead to the development of spectacular technology that is helping us to now search the genome in a way that we were unable to do before. So population genomics is really applying biotechnology to the genome in a way that we can characterize, you know, things like genetic variation, you know, understand how they relate to different diseases, and how they contribute generally to the health and well-being of people. And it will also help us to understand human evolutionary history. For example, population genomics is applied to development of the HapMap project, which really tells us and gives us good information about genetic variation across continents. |
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| Single Nucleotide Polymorphism (SNP) |
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Definition
| Single nucleotide polymorphisms (SNPs) are a type of polymorphism involving variation of a single base pair. Scientists are studying how single nucleotide polymorphisms, or SNPs (pronounced "snips"), in the human genome correlate with disease, drug response, and other phenotypes. |
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| Transgenic means that one or more DNA sequences from another species have been introduced by artificial means. Animals usually are made transgenic by having a small sequence of foreign DNA injected into a fertilized egg or developing embryo. Transgenic plants can be made by introducing foreign DNA into a variety of different tissues. |
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| A YAC is not a large, furry animal who lives in cold climates. It's actually a Y-A-C, a yeast artificial chromosome... Actually, not used too much anymore, but important for historical reasons. One of the very early ways that scientists--geneticists--manipulated large pieces of DNA...very important to be able to isolate and reproduce large pieces of DNA for the purposes of isolating disease genes. So what scientists did was they co-opted the parts of a yeast chromosome, which are important for packing that DNA, and replicating the DNA, and they took out all the yeast sequences in the middle and they put in human sequences or some other sequence, and then stuck it back in the yeast cell, and the yeast cell didn't know the difference and replicated the human DNA instead, and so served as a Trojan horse for the genetics researchers to be able to replicate, and therefore study, the human and other organism DNA that they were interested in. |
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