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Molecular diagnostics, genetic & genomic testing glossary & taxonomy
Evolving Terminologies for Emerging Technologies
Comments? Questions? Revisions? Mary Chitty 
mchitty@healthtech.com
Last revised August 13, 2014

 



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Related glossaries include  Biomarkers   Cancer diagnostics, prognostics, genomics & therapeutics  Clinical & Medical Informatics   Clinical trials   Drug safety & Pharmacovigilance   Molecular Medicine   Pharmacogenomics   Regulatory  Sequencing   SNPs & other genetic variations   Therapeutic areas including cardiovascular, CNS, immunology, infectious diseases & inflammation

For diagnostics, tests based on genes (mutations, SNPs), gene expression profiles and protein biomarkers are being added to the more standard diagnostics of clinical chemistry or immunoassays. Cambridge Healthtech Drug Discovery Map http://www.healthtech.com/drugdiscoverymap.asp  

$1,0000 genome: The cost of DNA sequencing might not matter in a few years,” says the Broad Institute’s Chad Nusbaum. “People are saying they’ll be able to sequence the human genome for $100 or less. That’s lovely, but it still could cost you $2,500 to store the data, so the cost of storage ultimately becomes the limiting factor, not the cost of sequencing. We can quibble about the dollars and cents, but you can’t argue about the trends at all.”  But these issues look relatively trivial compared to the challenge of mining a personal genome sequence for medically actionable benefit. Stanford’s chair of bioengineering, Russ Altman, points out that not only is the cost of sequencing “essentially free,” but the computational cost of dealing with the data is also trivial. “I mean, we might need a big computer, but big computers exist, they can be amortized, and it’s not a big deal. But the interpretation of the data will be keeping us busy for the next 50 years.” Or as Bruce Korf, the president of the American College of Medical Genetics, puts it: “We are close to having a $1,000 genome sequence, but this may be accompanied by a $1,000,000 interpretation.”  The road to the $1,000 Genome  Sept 2010 http://www.bio-itworld.com/2010/09/28/1Kgenome.html 
Kevin Davies $1,000 genome
, http://authors.simonandschuster.com/Kevin-Davies/1879979 

Analyte Specific Reagents (ASRs):  "antibodies, both polyclonal and monoclonal, specific receptor proteins, ligands, nucleic acid sequences, and similar reagents which, through specific binding or chemical reaction with substances in a specimen, are intended for use in a diagnostic application for identification and quantification of an individual chemical substance or ligand in biological specimens."  Classification information for ASRs can be found in 21 CFR 864. 4020(a)12.  Overview of IVD regulation, FDA, CDRH http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/IVDRegulatory

analytical selectivity: Note that IUPAC 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  "Selectivity in Analytical Chemistry. Recommendations for its use" Pure and Applied Chemistry Vol. 73, No. 8, pp. 1381–1386, 2001 http://pac.iupac.org/publications/pac/pdf/2001/pdf/7308x1381.pdf  Compare analytical specificity

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/reports/oversight_report.pdf   Related terms: clinical sensitivity and sensitivity. Labels, Signaling & Detection

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 200 http://www4.od.nih.gov/oba/sacgt/reports/oversight_report.pdf  Related terms: clinical specificity and specificity  Compare analytical selectivity.

camera pill: http://www.popsci.com/node/19963   Also known as "video pill", "capsule endoscope" WordSpy http://www.wordspy.com/ June 26, 2003

cancer diagnostics: Cancer 

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/reports/oversight_report.pdf 

It will be interesting to see how many people opt for carrier testing, given this recommendation.  Related terms: molecular genetic testing, preconception testing, prenatal diagnosis

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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/reports/oversight_report.pdf  Related term: analytical sensitivity.

clinical sequencing and diagnostics: Advances in Clinical Genome Sequencing and Diagnostics March 2013 Table of Contents | Tables and Figures  

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/reports/oversight_report.pdf   Related term: analytical specificity

combination therapies: Drug discovery & development   May refer to drug/diagnostic or drug/device as well as drug/drug combinations

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companion diagnostics:  Executive Summit: Global Strategies for Companion DiagnosticsExecutive Summit: Global Strategies for Companion Diagnostics  November 4-5, 2013 • Cambridge, MA Program | Register | Download Brochure

Assays (a test or measurement) intended to assist physicians in making treatment decisions for their patients.  They do so by elucidating the efficacy and/or safety of a specific drug or class or drugs for a targeted patient group or sub-groups. Targeted and tailored therapies and companion diagnostics are two pillars of personalized medicine. For diagnostics to be successfully integrated into clinical practice, several parties need to work collaboratively, including a diagnostic partner and a pharmaceutical partner, as well as regulators, clinicians and, not to be forgotten in haste, patients. 

One trend in genetic diagnostics and therapeutics is to become increasingly intertwined.  Companion diagnostics identify subsets of patients who would benefit from a specific drug. 
Amgen, Biomarker Toolkit: Companion Diagnostics, 2008 http://www.amgen.com/pdfs/misc/vpk_biomarker_diagnostics.pdf    Related terms:  genetic diagnostics, molecular diagnostics;  /synonym? Pharmacogenomics  pharmacogenomics  

Companion Diagnostics and Other Aspects of Personalized Medicine May 2013 Table of Contents | Tables and Figures

computer aided diagnosis CAD: A real-time quantitative analysis workstation with functionality to evaluate multi-modality breast images could facilitate earlier and more accurate diagnosis and improve evaluation of the effectiveness of treatment plans, according to a presentation in the quantitative imaging reading room showcase at RSNA 2010. Health Imaging & IT 2010 http://www.healthimaging.com/index.php?option=com_articles&article=25490&publication=8&view=portals 

Wikipedia http://en.wikipedia.org/wiki/Computer-aided_diagnosis   

"designer babies":  Steven Pinker, Human Nature and Its Future, 2003 http://bioethics.georgetown.edu/pcbe/transcripts/march03/session3.html  Not as inevitable as many people seem to think. 

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: For diagnostics, tests based on genes (mutations, SNPs), gene expression profiles and protein biomarkers are being added to the more standard diagnostics of clinical chemistry or immunoassays. CHI’s Drug Discovery and Development Map  http://www.healthtech.com/drugdiscoverymap.asp

Diagnostics almost always precede therapeutics, and there are many unmet medical needs, for which no good therapeutics are yet available.   Related terms: biomarkers  Narrower terms: molecular diagnostics, molecular pathology, point of care diagnostics, research diagnostics;  Nanoscience & Miniaturization  DNA diagnostics - miniaturization 

digital pathology: A dynamic, image-based environment that enables the acquisition, management and interpretation of pathology information generated from a digitized glass slide.  Often used interchangeably with “Virtual Microscopy.” Glossary of Terms, Digital Pathology Association https://digitalpathologyassociation.org/glossary-of-terms_1 

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direct to consumer DTC genetic testing: The current marketplace for direct-to-consumer (DTC) genetic testing is very dynamic and fluid. At least 42 DTC genetic testing companies have been identified to date, and additional market entrants are likely. Firms marketing and selling genetic tests DTC have numerous factors to consider. This report focuses on health-related decision-making applications of DTC genetic tests and examines various components of this emerging business environment: Insight Pharma Reports, Direct to Consumer Genetic Testing, 2009 

familial cancer: Cancer genomics

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

General Purpose Reagent (GPR): "a chemical reagent that has general laboratory application, is used to collect, prepare, and examine specimens from the human body for diagnostic purposes, and is not labeled or otherwise intended for a specific diagnostic application …[General purpose reagents] do not include laboratory machinery, automated or powered systems."  Classification information for GPRs can be found in 21 CFR 864.4010(a)11.  Overview of IVD regulation, FDA, CDRH http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/IVDRegulatory

genetic counseling: The Genetic Counseling Definition Task Force of the National Society of Genetic Counselors (NSGC) developed the following definition of genetic counseling that was approved by the NSGC Board of Directors: Genetic counseling is the process of helping people understand and adapt to the medical, psychological and familial implications of genetic contributions to disease. This process integrates the following: Interpretation of family and medical histories to assess the chance of disease occurrence or recurrence. Education about inheritance, testing, management, prevention, resources and research. Counseling to promote informed choices and adaptation to the risk or condition.  A new definition of Genetic Counseling: National Society of Genetic Counselors' Task Force report. National Society of Genetic Counselors' Definition Task ForceResta RBiesecker BBBennett RLBlum SHahn SEStrecker MNWilliams JL.  J Genet Couns. 2006 Apr;15(2):77-83. http://www.ncbi.nlm.nih.gov/pubmed/16761103

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 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.genome.gov/10002345 

I'd be very interested to hear of references in the scientific literature to back up the quantitative estimates of individual genetic flaws. The only one I've found is DL Halligan, PD Keightley, How many lethal alleles? Trends in Genetics 19(2): 57- 59, Feb. 2003  Related terms:  "good genes", "bad genes"

Genetic Discrimination: Position Paper, Council for Responsible Genetics 2001 http://www.councilforresponsiblegenetics.org/pageDocuments/2RSW5M2HJ2.pdf 
Genetic discrimination    
http://www.genome.gov/10002077  genetic discrimination in health insurance, NHGRI http://www.genome.gov/10002328

genetic enhancement: The use of genetic methodologies to improve functional capacities of an organism rather than to treat disease.  MeSH, 2002

The subject of much discussion and concern over the ethics of, though new disease diagnoses, treatments (and concepts of "disease") are much closer than true genetic enhancements. The popular conception of selective breeding focuses on optimization of one or a very few traits (which produces tomatoes which ship well but have no taste, and purebred dogs with congenital hip dysplasia. Little attention has been paid to the tradeoffs (predictable and not) inevitable among polygenic traits. 

"Regression to the mean" also factors in. While two tall or two bright people tend to have children who are taller or brighter than average, they are NOT usually taller or brighter than the parents are. Only microbes with their greatly enhanced opportunities for evolving (with such short reproductive spans) seem to quickly get reliably bigger, better (in a sense) and stronger. Biological homeostasis is incredibly powerful. We may never be able to "enhance" complex traits such as intelligence or strength.  But we need to learn how to talk about these issues -- preferably before actually being able to actually implement genetic enhancement.  Related term: designer babies

Beyond therapy: (enhancement), US President's Council on Bioethics http://bioethics.georgetown.edu/pcbe/topics/beyond_index.html 
Potential for Genetic Enhancements in Sports
, Dr. Ted Friedmann, Univ. of California- San Diego, Chairman, Recombinant DNA Advisory Committee, President’s Council on Bioethics, July 11, 2002 Session 4 http://bioethics.georgetown.edu/pcbe/transcripts/jul02/session4.html 

genetic privacy: http://epic.org/privacy/genetic/  

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 susceptibility:  Genetic susceptibility is a very broad term because not only does it describe genetic mutations that convey high levels of predisposition affecting a small proportion of the population, like BRCA1/2 mutations for breast cancer, but it also includes the huge number of unidentified genetic variations that are much more common in the population but convey lower levels of risk and often involve interaction with specific exposures in the environment. New tumors in cancer survivors, National Cancer Institute, Benchmarks 7 (1) : 2, 2007 http://benchmarks.cancer.gov/2007/01/new-tumors-in-cancer-survivors/  Broader term: susceptibility

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/reports/oversight_report.pdf 

Currently there is no uniform or comprehensive system to assess the analytic and clinical validity of tests before they are offered to patients, and there are no laboratory standards that specifically address molecular genetic testing or require uniform proficiency testing procedures for them. ... The Department of Health and Human Services (HHS) agencies involved in current genetic testing oversight include: The Centers for Medicare and Medicaid Services (CMS), the Food and Drug Administration (FDA), the Centers for Disease Control (CDC), and the Office for Human Research Protections. Currently, three statutory and regulatory mechanisms, which all fall under the purview of agencies within HHS, govern genetic tests: The Clinical Laboratory Improvement Amendments of 1988 (CLIA), the Federal Food, Drug and Cosmetic Act and other regulations for protecting human subjects of research.  Who regulates genetic tests? Audrey Huang, Shawna Williams, Genetics & Public Policy Center, 2007 http://www.dnapolicy.org/policy.issue.php?action=detail&issuebrief_id=10 

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:  genetic counseling, genetic discrimination, risk communication  Narrower terms: carrier testing, genetic screening, genetic test, molecular genetic testing, newborn screening, predictive testing, predictive testing, predisposition test, pre-implantation diagnosis, prenatal diagnosis, presymptomatic test 

genomic testing: Extensive media coverage of genomic discoveries has fueled the public appetite for personalized medicine and a rush to develop and market new genomic tests, often without the necessary intervening research. Public health sciences have an important role in evaluating the validity and utility of genomic tests, which include not only DNA-based tests for single gene variants, but complex genotypes, tests for acquired mutations, and measures of gene expression, from RNA microarrays to biochemical assays. Before a genomic test can be used for epidemiologic research or clinical practice, laboratory comparison with a gold standard must demonstrate analytic validity. Epidemiologic studies are needed to establish clinical validity (sensitivity, specificity, and predictive value).  Research Priorities for Public Health Sciences in the Post- Genomic Era, Marta Gwinn and Muin J. Khoury, Centers for Disease Control, US Genetics in Medicine 4(6): 410- 411, 2002 http://journals.lww.com/geneticsinmedicine/Fulltext/2002/11000/Research_priorities_for_public_health_sciences_in.2.aspx 

germ cells: Reproductive cells in multicellular organisms. Unified Medical Language System, National Library of Medicine, US http://ghr.nlm.nih.gov/ghr/glossary/germcells 

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  http://cancernet.nci.nih.gov/dictionary/dictionarya-g.html#g     

Current genetic tests focus on germline mutations.  Related term: somatic cell 

GINA Genetic Information Nondiscrimination Act: http://en.wikipedia.org/wiki/Genetic_Information_Nondiscrimination_Act 

"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." Science Hosts Press Event to Announce Sequencing of Human Genome, Science News Archives, 2001  http://www.aaas.org/news/releases/2001/human.shtml 

We now have glimpses of the concept that genes that confer advantages at one time in a person's life may have adverse effects as well. One of the best known examples is heterozygotes for sickle cell anemia being less susceptible to malaria (while homozygotes express the disease).  Another possible example is 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.

in vitro diagnostic multivariate index assays IVDMIAs: emerging diagnostic vehicles growing in popularity for a wide variety of illnesses; in fact, many experts estimate that over 200 of these tests are in the development pipeline. IVDMIAs harness multiple molecular and non-molecular markers to produce a diagnostic, prognostic and/or predictive index (value) for a patient.  IVDMIA, College of American Pathologists 2010 http://www.cap.org/apps/cap.portal?_nfpb=true&cntvwrPtlt_actionOverride=%2Fportlets%2FcontentView...mmittees%2Ftechnology%2Fivdmia.html&_state=maximized&_pageLabel=cntvwr 

Draft Guidance for Industry, Clinical Laboratories and FDA Staff, In Vitro Diagnostic Multivariate Index Assays, CDRH, FDA, 2007 http://www.fda.gov/downloads/MedicalDevices/DeviceRegulationandGuidance/GuidanceDocuments/ucm071455.pdf 

in vitro diagnostics: Tests that can detect diseases, conditions, or infections. Some tests are used in laboratory or other health professional settings and other tests are for consumers to use at home.  CDRH-Office of In Vitro Diagnostic Device Evaluation and Safety, FDA  http://www.fda.gov/medicaldevices/productsandmedicalprocedures/invitrodiagnostics/default.htm 

In vitro diagnostic products are those reagents, instruments, and systems intended for use in diagnosis of disease or other conditions, including a determination of the state of health, in order to cure, mitigate, treat, or prevent disease or its sequelae. Such products are intended for use in the collection, preparation, and examination of specimens taken from the human body. [21 CFR 809.33]  Overview of IVD regulation, FDA, CDRH http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/IVDRegulatoryAssistance/ucm123682.htm   

liquid biopsy: an upcoming medical diagnostics tool, which describes the detection of pathologic events, such as cancer progress or organ transplantation rejection through blood testing. Digital PCR is particularly suited to fulfill the needs of precision and reliability, enabling an unprecedented diagnostic sensitivity. This new level of sensitivity allows more detailed monitoring of patients at reasonable costs, which lowers the burden of disease, with health economic implications by earlier intervention options. Ekkehard Schütz, Chronix Biomedical, Inc.  Digital PCR conference Oct 2014http://www.healthtech.com/ Conferences_Overview.aspx?id= 138531&libID=138502

medical genetics : The ACMG provides education, resources and a voice for the medical genetics profession. To make genetic services available to and improve the health of the public, the ACMG promotes the development and implementation of methods to diagnose, treat and prevent genetic diseases. American College of Medical Genetics, Mission Statement, 2001-2007 

medical genomics:  Term that is sometimes used interchangeably with clinical genomics. For the purposes of this report, medical genomics refers to any application of genomics to medicine, which includes preclinical as well as clinical applications.  Those areas of medical genomics that occur in laboratory or clinical settings would therefore be considered a type of clinical genomics. CHA Cambridge Healthtech Advisors, Clinical Genomics: The Impact of Genomics on Clinical Trials and Medical Practice report, 2004  

molecular diagnostics: Industry-leading growth rates, expanding applications and innovation characterize the molecular diagnostics sector. This report presents a synthesis of these developments including the increased diversity of assay targets, emergence of new and proposed point of care (POC) products, the appearance of sequencing-based assays that could fundamentally alter the field and automated low-density microarray-based assays. Insight Pharma Reports: Molecular Diagnostics: Double Digit Growth Anticipated  2011

Molecular diagnostic tools are driving innovation and investment, shaping a core business area in biotech, pharma and device companies. The shift toward developing diagnostic platforms comes from the advances in sequencing, microarrays, and microfluidics. The availability of new sequencing platforms and point-of-care assays will stimulate the growth in the field by providing greater speed, convenience and sensitivity, leading to improved outcomes and greater cost savings. Molecular Diagnostics Summit Europe  October 11-13, 2011 • Hannover Germany Program | Register | Download Brochure

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The Journal of Molecular Diagnostics, the official publication of the Association for Molecular Pathology, co-published by the American Society for Investigative Pathology, seeks to publish high quality original papers on scientific advances in the 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 or clinicopathologic correlations including studies in oncology, infectious diseases, inherited diseases, predispositiion 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 or disease predisposition. http://www.journals.elsevierhealth.com/periodicals/jmdi/aims

"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.  Is this changing?

Broader term: diagnostics  Related terms: companion diagnostics, molecular pathology; microarrays  Narrower terms: next generation diagnostics, Point of Care Diagnostics  

molecular diagnostics - cancer: Cancer genomics  & diagnostics

molecular diagnostics non-invasive: 

molecular diagnostics techniques: MOLECULAR BIOLOGY techniques used in the diagnosis of disease. Included are such techniques as IN SITU HYBRIDIZATION of chromosomes for CYTOGENTIC ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS of gene expression patterns in disease states; identification of pathogenic organisms by analysis of species specific DNA sequences; and detection of mutations with PCR (POLYMERASE CHAIN REACTION).  MeSH, 2002

molecular pathology: A subspecialty of pathology concerned with the molecular basis (e.g., mutations) of various diseases. MeSH 2010

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.     Related terms: digital pathology, molecular diagnostics

multiplex assays: Multiplex assays for simultaneously detecting several biomarkers in a single sample, traditionally used in discovery proteomics, are becoming popular in clinical diagnostics research. The range of clinical applications for these assays is broad and includes autoimmune disease, infectious disease, oncology, cardiology, and endocrinology testing, as well as metabolomics and toxicology screening. The anticipated advantage of multiplex assays in clinical diagnostics is the fact that a panel of several biomarkers has better diagnostic value than a single analyte. However, some substantial obstacles are in the way of clinical utility of identified sets of biomarkers. 

nanotechnology in the clinical laboratory setting:  The technology that employs micro fabricated devices for biomedical applications i.e. using sample and reagents in minute amounts e.g. nanoliter range, has seen an almost exponential growth. The potential of this technology for analytical purposes in biomedicine has been demonstrated for immunoassays, the polymerase chain reaction (PCR), cell isolation, electrophoresis and mass spectrometry. This technology will also offer large scale screening possibilities for a wide range of analytes and be applicable outside the traditional laboratory through the introduction of robust and simplified instruments. The recommendations will address issues related to traceability of calibrators, transferability of results and other data performance specifications and quality assessment. IUPAC, Recommendations for the use of nanotechnology in clinical laboratories, project number: 2000-014-1-700, 2001 http://www.iupac.org/projects/2000/2000-014-1-700.html

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/reports/oversight_report.pdf  

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personalized medicine: Molecular medicine

pharmacogenetic tests: Pharmacogenomics  See also pharmacogenomic tests

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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.  

point of care diagnostic technologies: The Point-of-Care Technologies Research Network (POCTRN) was created to drive the development of appropriate point-of-care diagnostic technologies though collaborative efforts that simultaneously merge scientific and technological capabilities with clinical need.  ... Core functions include Conduct in-house clinical testing of prototype point-of-care devices, Collaborate with physical scientists, biochemical scientists, computational scientists, and engineers on exploratory technology development projects. Complete clinical needs assessments in areas anticipated to advance the field of point-of-care testing and disseminate this information to the technology development community.  Point of Care TEchnologies Research NEtwork, NIBIB, NIH http://www.nibib.nih.gov/Research/POCTRN 

population genetics, population genomics: SNPs and other genetic variations
post-genomic, post-Mendelian: Genomics
preconception testing: See carrier testing, prenatal diagnosis

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/reports/oversight_report.pdf 

predisposition, genetic: Increased susceptibility to a particular disease due to the presence of one or more gene mutations, and/or a combination of alleles (haplotype), not necessarily abnormal, that is associated with an increased risk for the disease, and/or a family history that indicates an increased risk for the disease. Definition from:  GeneTestsThis link leads to a site outside Genetics Home Reference. from the University of Washington and Children's Health System, Seattle via Genetics Home Reference http://ghr.nlm.nih.gov/ghr/glossary/geneticpredisposition  Related term: susceptibility.

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/reports/oversight_report.pdf 

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 eight or even fewer cells, with one or more healthy embryos reimplanted..

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/reports/oversight_report.pdf  Related terms: carrier testing, molecular genetic screening

prenatal molecular diagnostics: The transition in favor of array-based cytogenetic assays in place of traditional karyotyping is well underway.  For higher risk pregnancies the use of sequence-based testing of cell-free DNA in maternal blood is becoming more common, although evidence of genetic abnormalities must then still be confirmed with more invasive procedures.  Research aimed at isolation of nucleated fetal cells from maternal blood could provide better answers with lower risk in the future.  Advances in single cell sequencing are being applied to pre-implantation diagnostics and could be particularly powerful when combined with fetal cell isolation from maternal blood.  Progress is also being made in the development of biomarkers to assess the risk of both pre-term labor and preeclampsia, which offers the potential of much earlier steps to limit these dangers. Advances in Prenatal Molecular Diagnostics Conference September 2013 Order CD  http://www.healthtech.com/prenatal-diagnostics/   

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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/reports/oversight_report.pdf 

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; Genomics pre-Mendelian

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research diagnostics: Hard to predict the speed at which these will move into the clinic. 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.   

GeneTests http://www.genetests.org/  lists  March 17 2011 530 GeneReviews, 1,193 clinics, 594 Labs testing for  2,296 diseases  2,030 Clinical 266 Research Only 
Nov 10, 2006 365 GeneReviews, 1,150 Clinics, 608 Laboratories testing for 1,317 Diseases. 1,024 Clinical, 293 research only  
Oct. 15, 2003 had 993 diseases, with 645 clinical tests and 348 research only.  

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

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

sex selection:  President's Council on Bioethics, http://bioethics.georgetown.edu/pcbe/topics/sex_index.html 

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.  

specificity: See analytical specificity, clinical specificity
sporadic cancer: Cancer genomics

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? Narrower term: genetic susceptibility Related terms: genetic screening, predisposition test, predictive test, risk communication;  Pharmacogenomics  toxicogenomics  See also drug safety & pharmacovigilance

theranostics: "A tremendous amount of discovery and clinical development for new drugs involves clinical trials that include companion diagnostic tests," asserts Brian Buxton, co-founder of Easton Associates. "These ‘theranostic’ tests are poised to become a major factor in the future worldwide in vitro diagnostic testing market"  BioIT World, March 2006 See also  pharmacodiagnostics

uncertainty: Molecular Medicine

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Bibliography
Abbott Australasia, Abbott Laboratories, Diagnostics Glossary,  http://www.abbottdiagnostics.com/Glossary/index.cfm?alpha=s
Genetics Home Reference Glossary, National Library of Medicine, NIH, US, 2003, 450+ definitions  http://ghr.nlm.nih.gov/ghr/glossary/
Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, US June 2000 http://oba.od.nih.gov/oba/sacgt/reports/oversight_report.pdf 
GeneTests, Children's Hospital, Seattle, US  http://www.genetests.org/  A publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons.
Genetic Alliance http://www.geneticalliance.org/  Includes Online Directory of genetic resources. Coalition of 300+ consumer and health professional organizations.
Genetics Home Reference Glossary, National Library of Medicine, NIH, 2004, 1000+ terms http://ghr.nlm.nih.gov/ghr/glossary/Glossary;jsessionid=1EF1DE69A157E1E 
Intellihealth: guide to diagnostic tests Patient resources
Glossary of Terms, Digital Pathology Association https://digitalpathologyassociation.org/glossary-of-terms_1 
MeSH Medical Subject Headings, PubMed http://www.ncbi.nlm.nih.gov/mesh 
NHGRI (National Human Genome Research Institute), Talking Glossary of Genetic Terms, 100+ definitions. http://www.genome.gov/glossary.cfm Includes extended audio definitions.
Pharmacogenetic tests and genetic tests for inheritable markers: Guidance for Industry and FDA Staff, CDER,  FDA, 2007 http://www.fda.gov/downloads/MedicalDevices/DeviceRegulationandGuidance/GuidanceDocuments/ucm071075.pdf 
Policy  issues associated with undertaking a new large US Population Cohort Study of Genes, Environment and Disease, Report of the Secretary's Advisory Committee on Genetics, Health and Society, March 2007 http://oba.od.nih.gov/oba/sacghs/reports/SACGHS_LPS_report.pdf 
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 Genetic Laws, National Conference of State Legislatures 
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, Glossary, National Cancer Institute, US, http://www.accessexcellence.org/AE/AEPC/NIH/gene27.php 

Other patient and disease related resources: Patient resources

Diagnostics Conferences http://www.healthtech.com/Conferences/Search.aspx?k=&r=&s=BMK
Accelerating Development & Advancing Personalized Therapy ADAPT http://www.adaptcongress.com/
Molecular Medicine Tri Conference http://www.triconference.com/
Next Generation Diagnostics http://www.nextgenerationdx.com/
Next Generation Sequencing NGX http://www.chicorporate.com/sqe?c=6911

Diagnostics CDs, DVDs  http://www.chicorporate.com/Conferences/CompactDiscs.aspx?s=BMK
Diagnostics Short courses http://www.healthtech.com/Conferences_Upcoming_ShortCourses.aspx?s=BMK

Insight Pharma Reports Biomarkers and Diagnostics
http://www.insightpharmareports.com/Biomarker-Diagnostics-Reports/

Alpha glossary index

How to look for other unfamiliar  terms

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.

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