Appendix A
Glossary


Acetaminophen:

A crystalline compound, C8H9NO2, used in medicine to relieve pain and reduce fever.3

ACMG:

American College of Medical Genetics.

Allele:

Any alternative form of a gene. Allelic variation in a gene arises through mutation of the DNA sequence defining the gene and may or may not be associated with trait variation (e.g., height, eye color). For example, if a particular DNA sequence is mutated from an A (adenine) to a G (guanine), then there are two alleles—an A allele and a G allele.

Allelic Heterogeneity:

Different mutations of the same gene that produce similar phenotypes.

ASTHO:

Association of State and Territorial Health Officers.


Biobank:

A collection of biological samples and sample information organized in a systematic way for research purposes. Biobanks containing DNA samples have been set up in multiple countries to help identify genetic risk factors for disease and to understand the prevalence of these genetic mutations.

Bioinformatics:

The collection, annotation, classification, storage, and analysis of high-dimensional biological information (e.g., genomic, transcriptomic, proteomic, metabolomic) using computers.



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Implications of Genomics for Public Health: Workshop Summary Appendix A Glossary Acetaminophen: A crystalline compound, C8H9NO2, used in medicine to relieve pain and reduce fever.3 ACMG: American College of Medical Genetics. Allele: Any alternative form of a gene. Allelic variation in a gene arises through mutation of the DNA sequence defining the gene and may or may not be associated with trait variation (e.g., height, eye color). For example, if a particular DNA sequence is mutated from an A (adenine) to a G (guanine), then there are two alleles—an A allele and a G allele. Allelic Heterogeneity: Different mutations of the same gene that produce similar phenotypes. ASTHO: Association of State and Territorial Health Officers. Biobank: A collection of biological samples and sample information organized in a systematic way for research purposes. Biobanks containing DNA samples have been set up in multiple countries to help identify genetic risk factors for disease and to understand the prevalence of these genetic mutations. Bioinformatics: The collection, annotation, classification, storage, and analysis of high-dimensional biological information (e.g., genomic, transcriptomic, proteomic, metabolomic) using computers.

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Implications of Genomics for Public Health: Workshop Summary Biomarker: A biochemical indicator (e.g., cholesterol level) of an underlying disease risk factor or process. Biometrician: One who specializes in the statistical analysis of biological observations and phenomena.3 Candidate Gene: A gene whose protein product is involved in the metabolic or physiological pathways associated with a particular disease. Chemopreventive Agents: Chemical agents, drugs, or food supplements used to prevent disease.3 Clinical Utility: The degree to which a test alters medical management in a way that results in a net health benefit to the patients and is a function of the efficacy of an available treatment and the acceptance of the test by patients and clinicians. Comparative Genomics: A field of research in which the genome sequences of different species such as humans, mice, and the fruit fly are compared to identify regions of similarity and difference.4 Competencies in Genomics: Professional standards of knowledge and ability to use genomics terms and concepts appropriately in practice. The CDC competencies in genomics are divided into three levels: those for all public health workers; those for all public health professional workers; and those in specialty or concentration-specific positions such as leaders/administrators, clinicians, epidemiologists, etc. Continental Ancestry: Individuals whose ancestral origins are from a particular continent. Because the history of a mutation is dependent upon the geographic and demographic history of the people in which the mutation occurred, continental ancestry often provides a surrogate measure of the many mutations that occurred during the early part of human history and that now differ among the major ethnic groups. DNA (Deoxyribonucleic Acid): DNA is the chemical substance associated with the biological heredity material passed down from parent to child. It contains adenine (A), guanine (G), cytosine (C), and thymine (T). It is present in the nucleus of almost all cells in an organism. The DNA molecule contains the coded information that cells need to produce proteins that govern all life processes.

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Implications of Genomics for Public Health: Workshop Summary Ecogenetics: The study of the interaction between the environments in our human ecology and the genetic variations within humans that influence the continuum between health and disease. Epitasis: The masking of the phenotypic effect of alleles at one gene by alleles of another gene.1 It is a term used to describe gene–gene interactions. Ethnogenetics: The field focused on genetic variation in different populations. Ethnogenetics specifically looks at different populations with different genetic and/or environmental causes of the same phenotype. Etiologic Heterogeneity: Differing causes of disease. FDA: Food and Drug Administration. Gene: DNA sequences that contain a code that can be translated into a particular protein. Genetic Heterogeneity: A single phenotype that can be the result of mutations in several different genes Genetic Knock-Out: Refers to experimental organisms where a particular gene has been deleted or manipulated so it no longer functions. Genogram: A diagram outlining the history of the behavior patterns (such as divorce, abortion, or suicide) of a family’s members over several generations in order to recognize and understand past influences on current behavior patterns; also a similar diagram detailing the medical history of the members of a family as a means of assessing a family member’s risk of developing disease.3 Genome: The DNA sequence of all an organism’s chromosomes. Genomics: The study of the entire human genome. Genomics explores not only the actions of single genes, but also the interactions of multiple genes with each other and with the environment. Genotype: People inherit one allele for a gene from each parent such that they have two copies of each gene. The pair of alleles defines a person’s genotype. For a gene that has two alleles in the population (e.g., an A allele and a G allele), there are three possible genotypes—AA, AG, and GG.

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Implications of Genomics for Public Health: Workshop Summary GRAD: Genomic Research in African Diaspora. Haplotype: A haplotype is an extension of the concept of an allele that pertains to multiple mutations along a chromosome. Specifically, it is the combination of mutations inherited that defines a haplotype. Consider a segment of the genome with three sites that vary among people: For an individual with a GG genotype at the first site, TA at the second site, and CC at the third site, the haplotype for that individual is GTC and GAC. This is the combination of genetic variations inherited separately from the individual’s mother and father. Haplotype Blocks: A haplotype block is a set of closely linked genetic markers that show low haplotype diversity because of high linkage disequilibrium. Identifying haplotype blocks may enable scientists to measure only a single mutation, rather than an entire set of mutations, in a genomic region that could be very important for expensive disease association studies. Haplotype blocks along a chromosome may be separated by regions of high recombination. HapMap: A partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom, and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals. HapMap’s goal is to ultimately develop a haplotype map of the human genome and identify haplotype blocks. Heterogeneous Disorder: A disorder composed of subtypes with a spectrum of variable inheritance ranging from polygenic to monogenic inheritance.6 Heterozygote: An organism that has two different versions of an allele, for instance, one for blue eyes and the other for brown eyes.5 Heterozygous: A genotype in which the two copies of the gene are different. HGRD: Human Genetic Research Database. HIPAA: Health Insurance Portability and Accountability Act of 1996. Homozygous: A genotype in which the two copies of the gene that determine a particular trait are the same.4

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Implications of Genomics for Public Health: Workshop Summary Informatics: The sciences concerned with gathering, manipulating, storing, retrieving, and classifying recorded information.3 IRB: Internal Review Board. ISONG: The International Society of Nurses in Genetics. Junk DNA/Non-Coding Region: A region of the genome where the DNA has no known function (i.e., it does not code for a protein, regulatory sequence, or other functional elements). These regions usually consist of repeating DNA sequences. The majority of the human genome has no known function; only 2 percent to 5 percent of the DNA sequence codes for genes. Linkage Analysis: Traditionally, linkage analysis is the statistical analysis of the pattern of disease segregation and allele segregation in families to identify regions of the genome that may contain a gene causing the disease. There have been many extensions of this basic idea to try to identify genes for both common and rare diseases using genetic variations measured throughout the genome. Linkage Disequilibrium: Occurs when the alleles at two different sites along a chromosomal region are correlated in their frequencies. Linkage disequilibrium can occur because a new mutation happens on a particular allelic background. Linkage disequilibrium can be detected by investigating whether observed frequencies of haplotypes in a population are equal to the expected frequencies when the alleles are not correlated. Locus: The position of a gene on a chromosome. This term is a classical genetic concept used to understand gene order, gene distance, and gene function before gene and genomic DNA sequences were known. Locus Heterogeneity: Mutations in different genes that produce the same phenotype. This term is synonymous with genetic heterogeneity. Mendelian Disorders/Single-Gene Disorders: A disorder that is caused by mutations in a single gene (such as hemophilia), as opposed to polygenic disorders (such as hypertension) which involve the influence or interaction of several genes.4

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Implications of Genomics for Public Health: Workshop Summary Mendelian Inheritance: Named for Gregor Mendel, it is the pattern of inheritance of genes and chromosomes from parent to offspring. Mendel’s theory of inheritance was biologically confirmed when meiosis was discovered. Meiosis is the process by which individuals create egg or sperm to carry half of their genetic material (i.e., one of each type of chromosome) to the next generation. MeSH: The National Library of Medicine’s controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in hierarchical structure that permits searching at various levels of specificity. Metabolic Profile/Metabolome: The quantitative assessment of all the low molecular weight molecules present in cells in a particular physiological or developmental state. Microarray: In the most general sense, a microarray is an array of assays designed at the microscopic level that can be placed on a single solid base (e.g., a glass slide). Different microarray designs or platforms have been developed to type thousands of DNA mutations, gene expression transcripts, or proteins in a single individual. Microarray Experiments/Gene Expression Array: A new way of measuring the expression of large numbers of genes simultaneously in a single individual or organism. Gene expression patterns (also known as profiles or signatures) are being used for everything from molecularly classifying tumors, to understanding gene regulatory networks, to identifying potential side effects of new drugs being developed. Molecular Profile: A biomolecular (e.g., gene expression, protein, metabolite, chemical) pattern that is unique and associated with some specific biological context such as a tissue type, chemical exposure, or disease state. Synonym is Molecular Signature. Molecular Signature: A biomolecular (e.g., gene expression, protein, metabolite, chemical) pattern that is unique and associated with some specific biological context such as a tissue type, chemical exposure, or disease state. Synonym is Molecular Profile. mRNA: Messenger RNA, or a single-stranded molecule of ribonucleic acid that is transcribed from the DNA and then translated into protein. Multifactorial Disorder: A disorder resulting from the contributions and interactions among multiple genetic and environmental factors. Most

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Implications of Genomics for Public Health: Workshop Summary common chronic diseases such as heart disease, hypertension, and diabetes are multifactorial disorders. Multifactorial Inheritance: Multifactorial diseases aggregate in families but do not segregate in families as a single-gene disorder would segregate according to Mendelian inheritance patterns. Multigenic Disorder: A disorder resulting from the combined influence of multiple genes. Mutation: A mutation is a change in a DNA sequence. If the mutation occurs during the development of an egg or a sperm (i.e., gametes), then it becomes a heritable mutation. If the mutation occurs in any other body cell (i.e., part of the soma), then it is called a somatic mutation and it is not heritable. Somatic mutations are a cause of cancer. Mutations can be of many different types—substitutions, deletions, or insertions. NCHPEG: National Coalition for Health Professional Education in Genetics. NEDSS: National Electronic Data Surveillance System. NHANES: National Health and Nutrition Examination Survey. OHRP: Office of Human Research Protection. Penetrance: The probability of developing disease (or some other outcome of interest) given that an individual has a particular genotype. The penetrance of a genotype is often estimated by examining the proportion of people with a particular genotype who develop the disease or outcome of interest. Pharmacogenetics: The branch of genetics that studies the genetically determined variations in responses to drugs in humans or laboratory organisms.3 Phenome: The comprehensive representation of all phenotypes.2 Phenotype: A generic term used to describe attributes and characteristics of an organism—e.g., a biochemical phenotype, physiological phenotype, behavioral phenotype, or disease phenotype. PHIN: Public Health Information Network.

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Implications of Genomics for Public Health: Workshop Summary Polygenic Inheritance: The inheritance pattern of a trait, such as height, that is governed by a large number of genes with variations that have small effects. Since each parent contributes half of their child’s genotypic profile, polygenic inheritance predicts that the child will have a phenotype that is approximately the average value of the two parents. Polymorphism/Polymorphic Variants: A mutation that is found at a frequency of greater than 1 percent in a population. All polymorphisms are mutations, but not all mutations are considered polymorphisms because they are not prevalent enough in a population. Single nucleotide polymorphisms (SNPs) are a class of polymorphisms being studied for their association with disease. Population Based Cohort Study: A study where subjects are representative of the “at risk” population at large and are followed over time to determine the incidence of health outcomes. Often particular risk factors (e.g., genetic and environmental factors) are measured at the start of the study to determine if they predict who will and who will not develop disease. Population Screening: The examination of a population of usually asymptomatic individuals to detect those with a high probability of having or developing a given disease.3 Prevalence: The proportion of a population that has a particular disease or health outcome at a particular point in time. Proteome: The complete set of proteins found in a cell, tissue, or organism. Proteomics: A branch of biology concerned with applying the techniques of molecular biology, biochemistry, and genetics to analyzing the structure, function, and interactions of the proteins in a particular cell, tissue, or organism. PubMed: The U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature. RNA (Ribonucleic Acid): A chemical found in the nucleus and cytoplasm of cells; it transcribes the protein-coding instructions of DNA into a code that the protein-building ribosomes of a cell can understand. The chemical structure of RNA is similar to DNA—RNA also contains adenine (A), guanine (G), and cytosine (C), but instead of thymine (T), RNA contains uracil (U).5

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Implications of Genomics for Public Health: Workshop Summary SACGHS: Secretary’s Advisory Committee on Genetics, Health, and Society. SAGCT: Secretary’s Advisory Committee on Genetic Testing. SNPs (Single Nucleotide Polymorphisms): Currently, there is estimated to be about 6 million positions in the human genome where a mutation occurred at a single nucleotide (A, T, C, or G) and both its alleles are now greater than 1 percent prevalent in the population. These SNPs are important for studies of genetic or genomic associations with disease because the alleles are common in the population. Toxicogenomics: A new scientific subdiscipline that combines the emerging technologies of genomics and bioinformatics to identify and characterize mechanisms of action of known and suspected toxicants.2 Transcriptome: The population of mRNA transcripts in the cell and their expression levels.2 UMLS (Unified Medical Language System): The National Library of Medicine project that develops and distributes multi-purpose, electronic “knowledge sources” And associated lexical programs for systems developers. Researchers find the UMLS products useful in investigating knowledge representation and retrieval questions. Unaffected Carrier: An individual who carries a specific gene mutation allele but has not been diagnosed with the associated disease. REFERENCES 1. The Biology Teaching Organisation. A Genetics Glossary. http://helios.bto.ed.ac.uk/bto/glossary/. Accessed January 19, 2005. 2. Cambridge Healthtech Institute. Functional Genomics Glossary. http://www.genomicglossaries.com/. Accessed January 19, 2005. 3. Dictionary.com. http://dictionary.reference.com/. Accessed January 19, 2005. 4. Human Genome Project. Genome Glossary. http://www.ornl.gov/sci/techresources/Human_Genome/glossary/glossary.shtml. Accessed January 19, 2005. 5. Smith G. 2005. The Genomics Age. New York: American Management Association. 6. Velho G., Froguel P. 1997. The genetic determinants of NIDDM: Strategies and recent results. Diabetes Meta 23: 7–17.