Last revised December 06, 2001 
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Links to websites recommended for information on diseases and for patients are under cancer genomics, clinical genomics, diagnostics, genetic testing, public health. 

Science's review of "The sequence of the human genome" (J. Craig Venter et al 291: 1304-1352 Feb. 16, 2001) concludes that a "paramount challenge awaits: public discussion of this information and its potential for improvement of personal health ... There are two fallacies to be avoided: determinism, the idea that all characteristics of the person are 'hard-wired" by the genome; and reductionism, the view that with complete knowledge of the human genome sequence, it is only a matter of time before our understanding of gene functions and interactions will provide a complete causal description of human variability."

Nature's "Initial sequencing and analysis of the human genome" (International Human Genome Sequencing Consortium, 409 (no. 6822:860-914, 15 Feb. 2001) concludes "Finally it has not escaped our notice [a graceful allusion to Crick and Watson] that the more we learn about the human genome, the more there is to explore." and ends by quoting T.S. Eliot's Four Quartets [Little Gidding] "We shall not cease from exploration. And the end of all our exploring will be to arrive where we started, and know the place for the first time."

We would be wise to keep these words in mind.

biologics: Include blood, vaccines, tissue, allergenics and biological therapeutics. [CBER, FDA, US website http://www.fda.gov/cber/about.htm  Compare drug. Related terms Drug approvals glossary CBER, FDA  In the US biologics and drugs are regulated by different Centers at the FDA.

camera pill: http://www.fda.gov/bbs/topics/ANSWERS/2001/ANS01094.html

cancer: Narrower terms include cancer genomics, familial cancer, family history, hereditary cancer, sporadic cancer.

cancer genomics: Cancer genomics is in its infancy. Most efforts continue to focus on discovery of cancer- associated genes and proteins, and a precise knowledge of how these genes and proteins contribute to the pathophysiology of cancer at various stages … In 1998 the US FDA approved the first drug that targets a genetic defect of cancer trastuzumab (Genentech's Herceptin) . .. most major pharmaceutical/biotechnology companies are conducting some level of genomics - or genetics- based oncology research ... Cancer affects the fundamental mechanisms governing genes and the cell cycle. [CHI, Impact of Genomics on Cancer Diagnosis, Therapeutics, and Pharmacogenomics, 2000] http://http://www.chireports.com/content/reports/impact_gen.asp   

Herceptin is an example of a drug for which specific suitable patients can now be identified.

Related terms familial cancer, family history, germline mutations, somatic cells, sporadic cancer.

Oncogenomics appears to be a synonym, but less frequently used than cancer genomics. (Glossary FAQ question # 2 outlines methodology.)

Cancer resources
Cancer and statistics Stephen Jay Gould's essay "The Median isn't the Message" is a wonderful essay on interpreting statistics and the medical literature, and particularly useful for those of us who quickly head to a library and/ or the web with very specific and personal interest in a medical topic. http://www.cancerguide.org/median_not_msg.html

OncoLink, University of Pennsylvania Cancer Center  http://www.oncolink.upenn.edu/ Comprehensive information about specific types of cancer, updates on cancer treatments and news about research advances. Updated every day,  information at various levels, from introductory  to in-depth.

PDQ, Physicians Data Query, National Cancer Institute, US  http://cancernet.nci.nih.gov/pdq.html  Cancer information for health professionals and patients.

Robert Weinberg's Racing to the Beginning of the Road : The Search for the Origin of Cancer 1998 is a very readable account of top rate biomedical research, a good reminder that these "races" are marathons and not 100 yard dashes. The title is one of my favorite metaphors for the complexity of biology. This explanation of how nonlinear progress from lab to clinic can be is highly recommended. To order: http://www.powells.com/biblio/78400-78600/0716732831.html or try your public library.

Other patient and disease related websites are under clinical genomics, diagnostics, genetic testing, public health.

clinical endpoint: Clinical trials & drug approvals glossary

clinical genomics: The linkage of clinical medical information to molecular information represents one of the primary challenges for bioinformatics in the next century. As the genome sequencing projects mature and complete, we will have the genetic DNA sequences of both humans and a host of human pathogens, and informatics tools will be necessary to deliver this information in appropriate ways to medical decision makers.  This information will impact decisions about diagnosis, prognosis, treatment and epidemiology. ... [these] data sources are extremely valuable independently, but may contain valuable information when properly combined. This becomes the challenge of what some have termed "clinical genomics" or the marriage of clinical investigation with genomic science. [Russ Altman "Bioinformatics in support of molecular medicine" American Medical Informatics Association Symposium 1998] www.amia.org/pubs/symposia/D005238.PDF

Genomics related diagnostics are apt to precede therapeutics for some time to come, but there is beginning to be a trickle of approved drugs (mostly for fairly rare conditions).  Look for progress to be difficult to predict and nonlinear for some time -- but physicians and patients are apt to be surprised by the speed with which medical decisions are affected.  That doesn't mean the decisions will necessarily be easy. They will almost certainly involve balancing various tradeoffs.

Patient and disease related resources
Bandolier, National Health Service R & D Directorate, Oxford, UK http://www.jr2.ox.ac.uk/Bandolier/   Evidence based medicine

Healthfinder^R  http://www.healthfinder.gov/  A free guide to reliable consumer health and human services information, developed by the U.S. Department of Health and Human Service [to] lead you to selected online publications, clearinghouses, databases, Web sites, and support and self- help groups, as well as government agencies and not- for- profit organizations that produce reliable information for the public

HealthWeb, collaborating libraries of the Greater Midwest Region (GMR) of the National Network of Libraries of Medicine http://www.healthweb.org

Intelihealth, Inc., US http://www.intelihealth.com/IH/ihtIH/WSIHW000/408/408.html  Includes drug resource center, Merriam- Webster's Medical Dictionary, physician locator, tests and procedures directory, hospital locator and Health A- Z.  InteliHealth's expert editors "consumerize" health information to make it accessible to the widest possible audience. To ensure the highest quality, information provided by InteliHealth is reviewed and approved by the nation's leading medical experts. More than 150 top health care organizations contribute to InteliHealth's online and offline ventures, including the National Institutes of Health, other government agencies, major non- profits, other publishers and news media.

Mayo Clinic Health Oasis, US  http://www.mayohealth.org/  Searchable by drug name, as well as diseases and other topics.

MedlinePlus Health Information, National Library of Medicine, US, 2001 http://www.nlm.nih.gov/medlineplus/encyclopedia.html 

Merck Manual of Diagnosis & Therapy   http://www.merck.com/pubs/mmanual/   Full text of the 17th edition.

National Institutes of Health website  http://www.nih.gov/   Use the site search engine.

PubMed  (Medline)    http://www4.ncbi.nlm.nih.gov/PubMed/   

Other patient resources are under cancer genomics, genetic testing, public health.

clinical informatics: Drug approvals & clinical trials glossary

clinical trials: Drug approvals & clinical trials glossary

determinism (genetic): Philosophical doctrine that human action is not free but determined by external forces. [OED]

There has already been much debate about nature vs. nurture, and we clearly still have much to learn about the interplay among various influences.  The relevance of chaos theory and complexity seem likely to become increasingly clear. Note the reference to determinism in the second paragraph of this glossary.

One of  the more useful metaphors I've found is weather prediction. We are better now at predicting and reporting on hurricanes than we were 100 years ago, but are far from being able to control storms, or insure a sunny day when planning events.  We now have building codes for earthquake and hurricane prone areas (but can't predict earthquakes) and continue to build on flood plains and fragile barrier islands.

diagnosis: Allen Roses, worldwide director of genetics for Glaxo Wellcome [now Glaxo SmithKline] notes that “precise diagnoses leading to universal specific treatments are, for many illnesses, myths... for many diseases there is no accurate, single diagnostic test” . [A.D. Roses “Pharmacogenetics and future drug development and delivery” Lancet 355 (9212):1358-61 Apr 15, 2000] Related terms clinical genomics, diagnostics, disease intervention, diseases, prognosis

diagnostics: The growing momentum of genomics and molecular analysis has enormous promise for earlier and non (or less) invasive diagnostics, novel therapeutics and more precise prognoses in cancer, cardiovascular and infectious diseases. Improved patient stratification holds the allure of faster, smaller clinical trials and fewer adverse effects for patients. Advances in gene sequencing and analysis have made these processes higher throughput, more scaleable and reproducible. Microarrays are revolutionizing basic research. Proteomics and protein chips further broaden the range of possibilities.

But the diagnostics industry sector is an intensely competitive, cost-sensitive one. DNA/RNA diagnostics are perceived are slow, expensive and labor intensive. Biological and regulatory challenges are formidable. Thorny ethical and social issues are unresolved, and clinicians, patients and society have little background to prepare them to understand or utilize truly new paradigms.  Molecular Analysis for Research and Diagnostics Feb. 13-14, 2002. Narrower term molecular diagnostics; DNA diagnostics - miniaturization Miniaturization glossary

Intelihealth, Guide to diagnostics tests and procedures, Harvard Medical School, 1999. http://www.intelihealth.com/IH/ihtIH?t=25405&p=~br,IHW|~st,23436|~r,WSIHW000|~b,*|&k=navx408x25405 

disease expression: When a disease genotype is manifested in the phenotype.

disease intervention: Within the next decade, researchers will find most human genes. Explorations into the function of  each one - a major challenge extending far into the 21st century - will shed light on how faulty genes play a role in disease causation. With this knowledge, commercial efforts will shift away from diagnostics and toward developing a new generation of therapeutics based on genes. Drug design will be revolutionized as researchers create new classes of medicines based on a reasoned approach using gene sequence and protein structure function information rather than the traditional trial- and- error method. The drugs, targeted to specific sites in the body, promise to have fewer side effects than many of today's medicines. [Oak Ridge National Lab, US "Medicine and the new genetics, Feb. 2001] http://www.ornl.gov/hgmis/medicine/medicine.html  Related terms "good genes", "bad genes"; environmental factors In-depth. Narrower terms gene therapy

disease markers: See biomarkers Pharmacogenomics glossary

diseases: Collections of symptoms and signs (phenotypes) that appear to be similar … Similar clinical phenotypes may have very different underlying mechanisms. As genetic capabilities increase, we will have additional tools to subdivide disease designations that are clinically identical. [Allen D. Roses “Pharmacogenetics and future drug development and delivery” Lancet 355 (9212):1358-61 Apr 15, 2000] 

Disease phenotypes which now seem very similar (even to pathologists) may be quite distinguishable at the molecular level. Gene expression analysis and interpretation studies, particularly at the whole genome level are just beginning to produce intriguing results, and the National Cancer Institute (US) and other places are working on comparisons of gene expression in "normal" and diseased tissues.  Improvements in technology are needed.  Higher throughput, greater reliability and reproducibility and more automation are among the challenges. Greater knowledge of population genetics should also be useful. Related term diagnosis.

drug: Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. Synonymous with medicine, pharmaceutical.  [IUPAC Compendium]  Compare biologic. Related terms Drug approvals glossary CDER, FDA. In the US biologics and drugs are regulated by different Centers at the FDA.

environmental factors: May include chemical, dietary factors, infectious agents, physical and social factors. Related term public health

epidemiology: Related term public health In-depth environmental factors Narrower terms In-depth genomic epidemiology, human genome epidemiology, molecular epidemiology 

ethics: Basic genetics & genomics

gene-based therapy: Describes all treatment regimens that employ or target genetic material. Therapies which directly correct a defect associated with a particular disease would be included under this definition, of course. Also included would be therapies which introduce genes that can combat disease in a less direct (but not necessarily less effective) manner. These approaches would include efforts to cure diseases by i) introducing cells whose genetic make- up is modified (e.g.by transfection) so they may produce products of therapeutic benefit, ii) antisense therapy, and iii) naked DNA vaccination. [Haverford College Biology Dept. HHMI Seminar Series Gene-Based Therapy 1997-1998]  http://www.haverford.edu/biology/HHMI/Definition.html

gene therapy: An evolving technique used to treat inherited diseases. The medical procedure involves either replacing, manipulating, or supplementing nonfunctional genes with healthy genes. [NHGRI]

Gene therapy is in its infancy, and current gene therapy is primarily experimental, with most human clinical trials only in the research stages. ... Gene therapy can be targeted to somatic (body) or germ (egg and sperm) cells. In somatic gene therapy the recipient's genome is changed, but the change is not passed along to the next generation. In germline gene therapy, the parents egg and sperm cells are changed with the goal of passing on the changes to their offspring. Germline gene therapy is not being actively investigated, at least in larger animals and humans, although a lot of discussion is being conducted about its value and desirability.

Many people falsely assume that germline gene therapy already is being done with regularity.  News reports of parents selecting a genetically tested egg for implantation or choosing the sex of  their unborn child may lead the public to think that gene therapy is occurring. Actually, in these cases, genetic information is being used for selection. No cells are altered or changed. [Oak Ridge National Lab, US "Gene Therapy" Oct. 2000] Related term preimplantation diagnosis. http://www.ornl.gov/hgmis/medicine/genetherapy.html

genetic discrimination: Cindy Pelligrini, legislative director for Rep. Louise Slaughter (New York) as part of a roundtable discussion on genetic discrimination said "It's Rep. Slaughter's view that all of us are ultimately uninsurable. The more that we learn about our genes, everyone has enough genetic flaws that we're anywhere from 5-30 or 5-50 depending who you are listening to, genetic flaws that predispose you to major, severe illnesses at some point in your lifetime.

And so really what we are doing right now by allowing discrimination to happen is punishing the people with the bad luck to have the genes we have discovered first." [Dept. of Health and Human Services, National Committee on Vital and Health Statistics, Subcommittee on Privacy and Confidentiality, transcript, November 29, 2000]  http://ncvhs.hhs.gov/001129tr2.htm

Francis Collins, director of the National Institute for Human Genome Research, speaking at an American Association for the Advancement of Science event on the day Bill Clinton signed an executive order prohibiting federal government agencies from obtaining genetic information from employees or job applicants or from using genetic information in hiring and promotion decisions noted "But genetic information and genetic technology can be used in ways that are fundamentally unjust. Genetic information can be used as the basis for insidious discrimination. Already, with but a handful of genetic tests in common use, people have lost their jobs, lost their health insurance, and lost their economic well being because of the misuse of genetic information. It is estimated that all of us carry dozens of glitches in our DNA - so establishing principles of fair use of this information is important for all of us." [NHGRI in the news, "Dr. Francis Collins, Director of NHGRI, Applauds President Clinton's Action to Protect Federal Workers From Genetic Discrimination" Feb. 8, 2000] http://www.nhgri.nih.gov/NEWS/Executive_order/collins.html

I'd be very interested to hear of references in the scientific literature to back up the quantitative estimates of individual genetic flaws.  Or are these basically guesses? I don't doubt that some estimate will prove to be true. I just haven't found specific references to support even ballpark numbers yet.  But I haven't tried terribly hard. 

See also ethics Basic genetics & genomics, and "good genes", "bad genes".

genetic testing: Until now, government sponsored committees convened to address ‘genetic testing’ have generally limited their definition and their reports to concerns regarding diseases caused by single gene mutations… Another class of  ‘genetic tests’ is related to pharmacogenetics,  including ... variants or other inherited polymorphic traits that are not diagnostic of disease ... Clear language and differentiation of respective ethical, legal and societal issues are required to prevent inaccurate vernacular usage creating a confused public perception.  [Allen Roses “Pharmacogenetics and the practice of medicine” Nature 405: 857-865 June 15 2000] Related terms In-depth genetic counseling, genetic discrimination, risk communication. Narrower terms In-depth carrier testing, genetic screening, genetic test, newborn screening, predictive testing, predictive testing, predisposition test, pre-implantation diagnosis, prenatal diagnosis, presymptomatic test. 

Genetic testing resources
Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, US June 2000 http://www4.od.nih.gov/oba/sacgt/gtdocuments.html

GeneClinics, Univ. of Washington, Seattle, US  http://www.geneclinics.org/  A clinical information resource for health professionals, relating genetic testing to the diagnosis, management, and genetic counseling of individuals and families with specific inherited disorders. Disease-specific information on molecular genetic testing and its role in diagnosis, genetic counseling, and when appropriate, surveillance of at-risk relatives

GeneTests, Children's Hospital, Seattle, US  http://www.genetests.org/  Online genetics resource, which provides reliable, easy- to- use and current genetic counseling and testing information for the benefit of families and their healthcare providers.  Contains a directory of laboratories worldwide (with a North American emphasis) providing testing for heritable disorders, directory of genetics and prenatal diagnosis clinics in the United States;  introduction to genetic counseling and testing concepts; summary reports for healthcare payors, health policymakers, and authors on availability of genetic testing. 

Gene Tests, Q & A, Human Genome Project, Oak Ridge National Lab, US   http://www.ornl.gov/hgmis/medicine/genetest.html

Genetic Alliance http://www.geneticalliance.org/  Includes Online Directory of genetic resources. Coalition of 300+ consumer and health professional organizations.

Promoting Safe and Effective Genetic Testing in the United States:  Final Report of the Task Force on Genetic Testing  Editors: Neil A. Holtzman, Michael S. Watson, Sept. 1997 Appendix 3. State of the art of genetic testing in the US: Survey of biotechnology companies and nonprofit clinical laboratories (1994-1995) has some interesting observations. http://www.nhgri.nih.gov/ELSI/TFGT_final/

Understanding Gene Testing, National Cancer Institute, US
http://rex.nci.nih.gov/PATIENTS/INFO_TEACHER/bookshelf/NIH_gene_testing/gene00.html

Other patient and disease related resources are under cancer genomics, clinical genomics, public health.

genetics: Clearly defined terminology should form the basis for informative discussions so that the word ‘genetics’ is not demonized.  For example, tests that are specific to disease genes can help diagnose disease, determine the carrier status of an individual or predict the occurrence of disease. These are quite distinct from profiles ... which provide information on how a medicine will be metabolized in an individual. … Language needs to be more precise so that there can be clarity, especially for public policy debates.  [Allen D. Roses “Pharmacogenetics and the practice of medicine” Nature 405: 857-865 June 15 2000] Related terms genetic testing, ""good genes" "bad genes"", predisposition, susceptibility, public health In-depth  heterozygous, homozygous  Narrower term cytogenetics.

germline mutation: A gene change in the body's reproductive cells (egg or sperm) that becomes incorporated into the DNA of  every cell in the body of offspring; germline mutations are passed on from parents to offspring. Also called hereditary mutation. [Cancernet (NCI) Dictionary of Cancer Terms, 2000] Current genetic tests focus on germline mutations. http://cancernet.nci.nih.gov/dictionary/dictionarya-g.html#g     Related term somatic cell. 

"good genes", "bad genes": "There are no 'good' genes or 'bad' genes, there are merely networks that exist at various levels and at various connectivities, and at different states of sensitivity to perturbation," concluded Venter, Celera's president and chief scientific officer. "The notion that one gene equals one disease, or that one gene produces one key protein, is flying out the window."  http://www.aaas.org/news/human.html

Increasingly we get glimpses of the concept that genes that confer advantages at one time in a person's life may have adverse effects as well with the example of APOE-4, associated with Alzheimer's disease, which may be correlated with a decreased risk of kidney damage following heart bypass surgery.   

Gene knockouts in Model organisms have demonstrated that the absence of many genes may have no apparent effect upon phenotypes (though stress situations may reveal specific susceptibilities).  Other single knockouts may have a catastrophic effect upon the organism or be lethal so that the organism cannot develop at all.

immunotherapy: The concept of using the immune system to treat disease, for example, developing a vaccine against cancer. Immunotherapy may also refer to the therapy of diseases caused by the immune system, allergies for example. [NHGRI]

molecular diagnostics: The scope note of the Journal of Molecular Diagnostics mentions "translation and validation of molecular discoveries in medicine into the clinical diagnostic setting, and the description and application of technological advances in the field of molecular diagnostic medicine.  The editors welcome for review articles that contain: novel discoveries with direct application to clinical diagnostics or clinicopathologic correlations including studies in oncology, infectious diseases, inherited diseases, predisposition to disease, or the description of polymorphisms linked to disease states or normal variations; the application of diagnostic methodologies in clinical trials; or the development of new or improved molecular methods for diagnosis or monitoring of disease predisposition."  http://jmd.amjpathol.org/misc/ifora.shtml  Broader term: diagnostics

"The term molecular diagnostics has a relatively narrow clinical definition, namely, the use of nucleic acids as analytes in assays designed to investigate given disease states." Review by Charles P. Cartwright of Molecular Diagnosis of Infectious Diseases by U. Reischl, Humana Press, 1998, American Journal of Clinical Pathology Archive http://www.ajcp.com/Archives/Reviews/0599_1/0299_2/0299_2.html  Is this changing?

molecular piracy: An increasing number of viral proteins, particularly from large DNA viruses, such as herpesviruses and poxviruses, have been described that present homology with those of the host cell (Lalani et al. 2000). Viruses use this molecular mimicry, also known as molecular piracy, as part of their survival strategy, since it involves important factors of antiviral defense, such as complement factors, cytokines, chemokines and their receptors, presently known as virokines and viroceptors (Kotwal 2000, McFadden & Murphy 2000). Molecular mimicry has been interpreted as due do the capture of host genes by the virus (Murphy 1994, Cohen 1999). However, the possibility that homologous proteins coded by host genome result from the capture of viral genes cannot be ruled out. [Carlos Eduardo Tosta "Coevolutionary Networks: Transconnections: Adaptations and Evolution through diversity" Memorias de Instituto Oswald Cruz Online 96 (3): April 2001] http://www.dbbm.fiocruz.br/www-mem/963/4211hmsub3.html

molecular pathology: The collection and analysis of tissue samples is a long-established technique in pathology. What is new in "molecular pathology" is the emphasis on assessing gene expression in addition to morphology, and the use of gene expression analysis to validate large numbers of targets. (However, histochemistry and immunohistochemistry have been used, for specific proteins, since before the advent of genomics.) Corporate genomic researchers are increasingly seeking access to human tissue samples via collaborations with pathology departments at clinical research institutions [CHI Target Validation]

nonlinear: Informatics overview

nutraceuticals: Foods with specific health or medical benefits. Differentiate from supplements, which supplies missing nutrients. Examples include folic acid (to prevent birth defects) or pectin (to lower cholesterol) and fiber (to reduce the risk of color cancer). Sometimes spelled nutriceutical.

oncogenomics: See under cancer genomics.

penetrance:  Genomics glossary

point of care diagnostics: Relative simplification and miniaturization have moved a number of diagnostic tests from laboratories into doctor's offices , hospital bedsides and homes.  The Dept. of Defense has spent a good deal of money on developing robust, miniaturized and disposable pathogen diagnostic instrumentation.  Some of these technologies will be as applicable to the home or clinic as to the detection of bioterrorism.  Related terms Assays, labels, signaling & detection glossary

predictive data mining: Algorithms & data management glossary

predisposition, genetic: Susceptibility of an organism to develop a specific disease due to genetic alterations (mutations). Because environmental factors play a large part in the expression of certain traits, the organism may or may not actually develop the predicted disease. [SNP Consortium] Related term susceptibility.

prognosis: The probable outcome or course of a disease; the chance of  recovery. [ORD]

Not a major emphasis in clinical medicine today. Nicholas Christakis' Death Foretold is an eloquent book about the delicate balance between medical reality and optimism, and how seldom this is discussed in either classrooms or hospital rooms today.

psychoneuroimmunology: A new field emerging in medicine. It brings together knowledge from multiple fields of study in endocrinology, immunology, psychology, neurology and other fields. The emerging field of psychoneuroimmunology holds great promise in many ways. I t has the potential to integrate the systems of the body into a unified view of how the body works and interacts with itself and its environment. PNI is the study of how all these mechanisms and bodily functions interact to produce states of health and disease. There is, however, no formal consensus on the actual definition of what constitutes PNI or its research (Petellier 199). http://raptor.slc.edu/~synapse/papers/pni.html

public health, genetics and genomics: There is much talk of  the world as a global village these days. Nowhere is that more true than in public health.  It is not just third world countries that need to be concerned about vaccines, herd immunity and drug resistance. Early intervention and epidemiological investigation of environmental factors hold promise for better understanding the complex interplay of variables in individual and public health. Related terms In-depth morbidity (compressing), mortality (reducing), phenotypic prevention.  

Public health genetics & genomics resources
Genetics and Public Health in the 21st century, CDC Centers for Disease Control and Prevention, US http://www.cdc.gov/genetics/info/books/21stcentury.htm   The term "public health genetics" seems to be used primarily in the United States, while "community genetics" is more widely used in Europe

Genomic Competencies for the Public Health Workforce, CDC Centers for Disease Control and Prevention, US, 2001  http://www.cdc.gov/genetics/training/competencies/default.html  Information about the role of genes in health and disease is evolving rapidly because of the mapping of all human genes by the Human Genome Project. The number and types of genetic tests and services now available commercially are growing exponentially, and public health workers are increasingly aware of the potential role of genetic information in preventing common diseases. Everyone involved in public health should become aware of these advances and begin to incorporate genomic competencies into their public health specialties

Public Health Genetics, Cambridge UK http://www.medinfo.cam.ac.uk/phgu/   News and information about advances in genetics and their impact on public health and the prevention of disease.

Other patient and disease related resources are under cancer genomics, clinical genomics, genetic testing, public health.

reductionism: Research glossary

somatic cells:  All body cells, except the reproductive cells. Somatic gene mutations (such as those caused by sun damage or radiation) are not inherited. Related terms germline mutation, susceptibility.  

surrogate endpoints, surrogate markers: Pharmacogenomics glossary

susceptibility: This large diversity in responsiveness among individuals to environmental toxicants makes it difficult to determine actual risks, particularly at the low doses to which most people are exposed. Opportunities now exist for studies of genetic susceptibility for cancer and other diseases in which an environmental component can be presumed. Knowledge from such studies could, in the future, allow markers of genetic susceptibility to be incorporated into epidemiologic studies. This, in turn, would permit adjustment of  interpretation of results to account for genetic susceptibility, thus greatly enhancing the sensitivity and power of these studies to detect environmental components of important diseases. Other projects being considered are a nutrition initiative to determine how nutritional status alters disease susceptibility, and development of transgenic mice that carry important environmental response gene. [NIEHS Strategic Plan 2000 "Individual susceptibility", National Institute of Environmental Health Sciences, US, March 2000]  http://www.niehs.nih.gov/external/plan2000/suscptblty.htm

Susceptibility seems essentially synonymous with predisposition. Are there differences? Related terms genetic screening, predisposition test, predictive test, risk communication; toxicogenomics. Pharmacogenomics glossary.

therapeutics: See disease interventions; drug In-depth.

time delay data mining: Algorithms & data management glossary

trends based data mining: Algorithms & data management glossary

Bibliography

[CHI Cancer] Impact of Genomics on Cancer Diagnosis, Therapeutics, and Pharmacogenomics, Cambridge Healthtech Institute report, Aya Yamamura, Feb. 2000. 

Alpha glossary list

In-depth Clinical genomics glossary

analytical sensitivity: The proportion of persons with a disease genotype who test positive.  [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000 http://www4.od.nih.gov/oba/sacgt/gtdocuments.html

The probability that a test will detect an abnormality when it is present in a specimen. [Myriad Genetics "Genetics Glossary"] http://www.myriad.com/gtpatg.html    See also clinical sensitivity and sensitivity. Assays, Labels, Signaling & Detection glossary.

analytical specificity: The proportion of persons without a disease genotype who test negative.  [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000 http://www4.od.nih.gov/oba/sacgt/gtdocuments.html

The probability that a test will be negative when an analyte is absent from a specimen.  [Myriad Genetics "Genetics Glossary"] http://www.myriad.com/gtpatg.html   Related terms clinical specificity and specificity Assays, Labels, Signaling & Detection glossary

But note that IUPAC (in a provisional recommendation) prefers the term "selectivity" instead of specificity, citing the many papers in which the two are used interchangeably. "This is very unfortunate as specificity is considered as an absolute term, and cannot be graded. [IUPAC Analytical Chemistry Division, Commission on General Aspects of Analytical Chemistry Provisional Recommendations "Selectivity in Analytical Chemistry. Recommendations for its use" Feb. 27, 2001] http://www.iupac.org/reports/provisional/abstract01/vessman_300901.html

carrier testing: Performed to determine whether an individual carries one copy of an altered gene for a particular recessive disease. [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000] http://www4.od.nih.gov/oba/sacgt/gtdocuments.html

clinical sensitivity: The proportion of persons with a disease phenotype who test positive. [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000 http://www4.od.nih.gov/oba/sacgt/gtdocuments.html

The probability that a person with a disease, or who will develop a disease, will have a positive test result. [Myriad Genetics "Genetics Glossary"]  http://www.myriad.com/gtpatg.html    See also analytical sensitivity.

clinical specificity: The proportion of persons without a disease phenotype who test negative. [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000] http://www4.od.nih.gov/oba/sacgt/gtdocuments.html

The probability that test will be negative in a person free of a disease, and who will not develop the disease. [Myriad Genetics "Genetics Glossary"] http://www.myriad.com/gtpatg.html  Related term analytical specificity.

developmental site agreements: Companies work with hospitals to develop instrumentation and clinical research applications.

familial cancer:  The expression 'familial cancer' is used by some as a synonym of hereditary cancer, however, many (including the authors of  this program) use it simply to refer to the familial occurrence of  cancer (> 1 case in a family), not necessarily due to an inherited cancer predisposition. Some proven hereditary disorders include the word ‘familial’ in their name. [Familial Cancer Database On-line Manual. R.H. Simons & G.T.N. Burger, Groningen, The Netherlands, 2000] http://facd.uicc.org/manual.shtml    See also hereditary cancer, sporadic cancer.

family history: Interpreting family histories can be complicated by many factors, including small families, incomplete or erroneous family histories and particularly by variable penetrance and the current lack of real understanding of  the multiple genes involved in polygenic diseases. Family risk is often cited in terms of absolute number of affected relatives with a disease, when (particularly in larger families) the ratio of affected to non- affected relatives may be a more telling statistic.  Interpreting statistics and risk factors are no easy tasks under any circumstances, much less one as potentially significant as genetic testing. Related term sporadic cancer

genetic counseling: A short-term educational counseling process for individuals and families who have a genetic disease or who are at risk for such a disease. Genetic counseling provides patients with information about their condition and helps them make informed decisions. [NHGRI]  Related term risk communication

genetic screening: Testing a population group to identify a subset of individuals at high risk for having or transmitting a specific genetic disorder. [NHGRI]

genetic test: An analysis performed on human DNA, RNA, genes and/or chromosomes to detect heritable or acquired genotypes, mutations, phenotypes, or karyotypes that cause or are likely to cause a specific disease or condition. A genetic test also is the analysis of human proteins and certain metabolites, which are predominantly used to detect heritable for acquired genotypes, mutations or phenotypes.  The purposes of these genetic tests include predicting risks of disease, screening of newborns, directing clinical management, identifying carriers, and establishing prenatal or clinical diagnoses or prognoses in individuals, families or populations. Tests that are used primarily for other purposes, but that may contribute to diagnosing a genetic disease (e.g. blood smear, certain serum chemistries), would not be covered by this definition. Also excluded from the definition are tests conducted exclusively for forensic identify purposes. [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000] http://www4.od.nih.gov/oba/sacgt/gtdocuments.html

genomic epidemiology: An emerging discipline involving population studies and microarray/ expression studies. Related terms environmental factors, public health; In-depth molecular epidemiology, human genome epidemiology, phenotypic prevention.

hereditary cancer: The hallmark of hereditary cancer is that the associated germ- line mutation confers a high lifetime risk of cancer (often  >50 %, but no precise risk percentage has been defined in the literature). As a general rule, tumor development is a multi- step process in which in addition to the germline mutation in a gene, the normal ("wild type") copy of that gene and/ or other genes need to undergo somatic mutations before cancer develops. [Familial Cancer Database On- line Manual. R.H. Simons & G.T.N. Burger, Groningen, The Netherlands, 2000] http://facd.uicc.org/manual.shtml   Related terms familial cancer, sporadic cancer.

human genome epidemiology: An evolving field of inquiry that uses systematic applications of epidemiologic methods and approaches in population based studies of the impact of human genetic variation on health and disease. Human genome epidemiology represents the intersection between genetic epidemiology and molecular epidemiology. The spectrum of topics addressed in human genome epidemiology range from basic to applied population based research on discovered human genes. [HuGE Net, Centers for Disease Control and Prevention, US]  http://www.cdc.gov/genetics/hugenet/rationale.htm

molecular epidemiology: Looking at epidemiology from a genetic and biochemical viewpoint. Narrower term genomic epidemiology.

morbidity - compressing: Ultimately only premature mortality can be reduced (in various ways such as by stopping smoking, wearing seatbelts and helmets). With a number of (first world) countries having rapidly aging populations we are just beginning to see some of the tradeoffs involved in extending longevity for a number of people. Related term mortality - reducing

mortality - reducing: In the long run mortality is going to be 100%, and every family has a history of it.  Compressing morbidity may be a more realistic goal. Related term morbidity - compressing.

new-born screening: Performed in newborns in state public health programs to detect certain genetic diseases for which early diagnosis and treatment are available. [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000] http://www4.od.nih.gov/oba/sacgt/gtdocuments.html 

phenotypic prevention: Achieved by interrupting harmful interaction of environmental cofactors with human genetic variation or by using gene therapy to correct deficiencies in gene products. [Genetics and Public Health in the 21st century, CDC Centers for Disease Control and Prevention, US] http://www.cdc.gov/genetics/info/books/21stcentury.htm    Related terms environmental factors, molecular epidemiology, public health. 

predictive testing: Determines the probability that a healthy individual with or without a family history of a certain disease might develop that disease. [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000] http://www4.od.nih.gov/oba/sacgt/gtdocuments.html

predisposition test: A test for a genetic predisposition (incompletely penetrant conditions). Not all people with a positive test result will manifest the disease during their lifetimes. [Promoting Safe and Effective Genetic Testing in the United States:  Final Report of the Task Force on Genetic Testing  Editors: Neil A. Holtzman, Michael S. Watson, Sept. 1997]  http://www.nhgri.nih.gov/ELSI/TFGT_final/  Related terms predictive testing, predisposition, susceptibility

preimplantation diagnosis: Used following in vitro fertilization to diagnose a genetic disease or condition in a preimplantation embryo. [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000] http://www4.od.nih.gov/oba/sacgt/gtdocuments.html

Not a routine procedure, most often used when parents have previously had a child with a serious genetic illness.  Genetic conditions can be diagnosed in embryos of only a few cells.

prenatal diagnosis: Used to diagnose a genetic disease or condition in a developing fetus. [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000]  http://www4.od.nih.gov/oba/sacgt/gtdocuments.html  

The [American College of Medical Genetics'] [Sub]Committee [on cystic fibrosis [CF] carrier screening] recommends that CF carrier screening be offered to non- Jewish Caucasians and Ashkenazi Jews, and made available to other ethnic and racial groups who will be informed of their detectability through educational brochures, the informed consent process, and/ or other efficient methods. For example, Asian- Americans and Native-  Americans without significant Caucasian admixture should be informed of the rarity of the disease and the very low yield of the test in their respective populations. Testing should be made available to African- Americans, recognizing that only about 50% of at- risk couples will be detected. An educational brochure and a consent form which recites this information as well as a sign- off for those choosing not to be tested after reading these materials is being prepared by the Working Group on Patient Education and Informed Consent. 

We recommend that preconception testing be encouraged whenever possible, although we recognize that for practical purposes, testing will often occur in the prenatal setting. [Wayne W. Grody et. al. "Laboratory Standards and Guidelines for Population- based Cystic Fibrosis Carrier Screening" Genetics in Medicine 3 (2): 149-154 March/ April  2001]  http://www.faseb.org/genetics/acmg/pol-32.htm   It will be interesting to see how many people opt for carrier testing, given this recent recommendation.

presymptomatic test: Predictive testing of individuals with a family history. Historically, the term has been used when testing for diseases or conditions such as Huntington's disease where the likelihood of developing the condition (known as penetrance) is very high is people with a positive test result. [Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, June 2000] http://www4.od.nih.gov/oba/sacgt/gtdocuments.html   

Current experience with genetic testing involves only a limited number of tests involving single genes.  Our thinking about genetics is shaped by the Mendelian model of monogenic disorders with high penetrance (which tend to be relatively rare).  How will we interpret -- and begin to make decisions about tests involving multiple genes (polygenic) disorders with varying penetrance.  Will we become more aware of various tradeoffs, or continue to look for silver bullets to "cure" conditions (both acute and chronic)?  Will the level of understanding of both biology and statistics be sufficient to allow informed public debate?  Related terms predisposition, susceptibility

risk communication: An educational process through which a genetic counselor attempts to interpret how a genetic condition is inherited and the chances that it might be passed on to children. [NHGRI]

SACGT: Secretary's Advisory Committee on Genetic Testing. See under genetic testing.

screening: Carrying out of a test or tests, examination(s) or procedure(s) in order to expose undetected abnormalities, unrecognized (incipient) diseases, or defects: examples are mass X-rays and cervical smears.  [IUPAC Tox] Not the same as screening Drug discovery & development glossary

selectivity: See analytical specificity

sensitivity (in analytical chemistry): Extent to which a small change in concentration of an analyte can cause a large change in the related measurement. (Gold, Loening, McNaught and Sehmi, 1987) [IUPAC Tox]

sensitivity (of a screening test): Extent (usually expressed as a percentage) to which a method gives results that are free from false negatives; the fewer the false negatives, the greater the sensitivity. Quantitatively, sensitivity is the proportion of truly diseased persons in the screened population who are identified as diseased by the screening test (Galen and Gambino, 1975)  Related Term specificity (of a screening test)  [IUPAC Tox] 

Related terms analytical sensitivity, clinical sensitivity.

specificity: See analytical specificity, clinical specificity.

sporadic cancer: A subset of cancer in which the disease-causing mutations occur in somatic cells. The term sporadic cancer is sometimes used to differentiate cancers occurring in people who have not inherited a mutation that confers increased susceptibility to cancer from cancers occurring in people who are known to carry a predisposing mutation (hereditary cancer). Sporadic is also sometimes used to describe cancer occurring in individuals without a family history of cancer (as opposed to familial cancer). ... genetic background may influence the likelihood of cancer even in the absence of a specific predisposing mutation, for instance: given alleles of modifying genes will determine the predisposition to sporadic cancer that any given individual has. Mutations which trigger tumorigenesis are not present in the germline cells, thus affecting only the individual,  not his offspring. The vast majority of cancer cases are sporadic ones. [European School of Genetic Medicine, Vth Course in Cancer Genetics, Genova Italy Sept. 27- )ct. 1, 2000]  http://www.cineca.it/networking/streaming/sestri/courses/cancgen/glossary/gl_Fodde1.htm

Related terms familial cancer, family history, hereditary cancer.