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Molecular diagnostics glossary & taxonomy
Evolving Terminologies for Emerging Technologies
Comments? Questions? Revisions?
Mary Chitty MSLS
Last revised January 10, 2020

SCOPE NOTE Diagnostics include biomarkers, circulating cell free DNA, companion diagnostics, pharmacogenomics for clinical trial patient stratification, prenatal diagnostics.  Cancer diagnostics, circulating tumor cells, liquid biopsies appear in the Cancer glossary & taxonomy

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  

Related glossaries include  Biomarkers     Cancer   Clinical trials    Diagnostics overview     Drug safety & Pharmacovigilance    Medical Informatics    Molecular Medicine    Pharmacogenomics    Regulatory    Sequencing    SNPs & other genetic variations    Therapeutic areas including cardiovascular, CNS, immunology, infectious diseases & inflammation   Cancer diagnostics are also in the Cancer overview

Next Generation Diagnostics 2020 Aug 25-27, Washington DC coverage spans cell- and cell-free biopsies, commercialization, reimbursement, biomarkers and companion diagnostics for immunotherapy, point-of-care testing, infectious disease, microfluidics and precision medicine

Molecular Medicine TriConference Precision Health March 2-4, 2020 San Francisco CA key opinion leaders in immunotherapy, liquid biopsy, and cell and gene therapy will discuss the latest tools, clinical advances, and commercial applications of a broad range of new and diverse products for vast improvements in medicine and healthcare.

$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 
Kevin Davies $1,000 genome

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. ASR's that otherwise fall within this definition are not within the scope of subpart E of this part when they are sold to: (1) In vitro diagnostic manufacturers; or (2) Organizations that use the reagents to make tests for purposes other than providing diagnostic information to patients and practitioners, e.g., forensic, academic, research, and other nonclinical laboratories.  FDA, Code of Federal Regulations, Medical Devices

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   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    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 2000  Related terms: clinical specificity and specificity  Compare analytical selectivity.

biopsy: medical test commonly performed by a surgeoninterventional radiologist, or an interventional cardiologist involving extraction of sample cells or tissues for examination to determine the presence or extent of a disease. The tissue is generally examined under a microscope by a pathologist, and can also be analyzed chemically. When an entire lump or suspicious area is removed, the procedure is called an excisional biopsy. An incisional biopsy or core biopsy samples a portion of the abnormal tissue without attempting to remove the entire lesion or tumor. When a sample of tissue or fluid is removed with a needle in such a way that cells are removed without preserving the histological architecture of the tissue cells, the procedure is called a needle aspiration biopsy. Biopsies are most commonly performed for insight into possible cancerous and inflammatory conditions. Wikipedia accessed 2018 Nov 8

capsule endoscopy: a procedure that uses a tiny wireless camera to take pictures of your digestive tract.  Mayo Clinic    Also known as camera pills, video pills.

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

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

clinical chemistry:  (also known as chemical pathologyclinical biochemistry or medical biochemistry) is the area of chemistry that is generally concerned with analysis of bodily fluids for diagnostic and therapeutic purposes. It is an applied form of biochemistry (not to be confused with medicinal chemistry, which involves basic research  for drug development). The discipline originated in the late 19th century with the use of simple chemical reaction tests for various components of blood and urine. In the many decades since, other techniques have been applied as science and technology have advanced, including the use and measurement f  enzyme activities, spectrophotometryelectrophoresis, and immunoassay. Wikipedia accessed 2018 Sept 3

Clinical Chemistry Tests: Laboratory tests demonstrating the presence of physiologically significant substances in the blood, urine, tissue, and body fluids with application to the diagnosis or therapy of disease. MeSH Year introduced: 1998

Clinical NGS Next Generation Sequencing Diagnostics Clinical sequencing is enabling personalized medicine to combat a host of diseases, from cancers to infections, with applications of circulating tumor cells, liquid biopsy utilization, and the technologies and approaches to strategize and optimize processes to bring developments to the clinic and beyond. 

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   Related term: 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  Related term: analytical specificity

combination products: Include (1) A product comprised of two or more regulated components, i.e., drug/device, biologic/device, drug/biologic, or drug/device/biologic, that are physically, chemically, or otherwise combined or mixed and produced as a single entity; (2) Two or more separate products packaged together in a single package or as a unit and comprised of drug and device products, device and biological products, or biological and drug products; (3) A drug, device, or biological product packaged separately that according to its investigational plan or proposed labeling is intended for use only with an approved individually specified drug, device, or biological product where both are required to achieve the intended use, indication, or effect and where upon approval of the proposed product the labeling of the approved product would need to be changed, e.g., to reflect a change in intended use, dosage form, strength, route of administration, or significant change in dose; or (4) Any investigational drug, device, or biological product packaged separately that according to its proposed labeling is for use only with another individually specified investigational drug, device, or biological product where both are required to achieve the intended use, indication, or effect. Definition of a Combination Product, FDA, Office of Combination Products, As defined in 21 CFR § 3.2(e)   See also Biomaterials & Medical Devices

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

Companion Diagnostics and Clinical Biomarkers 2020 March 2-4, San Francisco Clinical biomarkers and companion diagnostics play pivotal roles in clinical development and market access of new therapeutics as well as deliver significant patient benefits, healthcare cost savings, and revenue opportunities. Population genetics and pharmacogenomics became platforms for new drug discovery with NGS enabling sophisticated approaches for target and pathway identification and validation. Pharmaceutical companies are embracing biomarkers as a way to decrease drug failures in the clinic by streamlining patient selection and stratification.

Companion Diagnostics

Related terms:  genetic diagnostics, molecular diagnostics;  /synonym? Pharmacogenomics  pharmacogenomics  

Computer-aided detection (CADe), also called computer-aided diagnosis (CADx), are systems that assist doctors in the interpretation of medical images. Imaging techniques in X-ray, MRI, and ultrasound diagnostics yield a great deal of information that the radiologist or other medical professional has to analyze and evaluate comprehensively in a short time. CAD systems process digital images for typical appearances and to highlight conspicuous sections, such as possible diseases, in order to offer input to support a decision taken by the professional.  CAD also has potential future applications in digital pathology with the advent of whole-slide imaging and machine learning algorithms. So far its application has been limited to quantifying immunostaining but is also being investigated for the standard H&E stain.[1]  CAD is an interdisciplinary technology combining elements of artificial intelligence and computer vision with radiological and pathology image processing. A typical application is the detection of a tumor. For instance, some hospitals use CAD to support preventive medical check-ups in mammography (diagnosis of breast cancer), the detection of polyps in the colon and lung cancer. Wikipedia accessed 2018 Feb 26

cytopathology: (from Greek κύτος, kytos, "a hollow";[1] πάθος, pathos, "fate, harm"; and -λογία, -logia) is a branch of pathology that studies and diagnoses diseases on the cellular level. The discipline was founded by George Nicolas Papanicolaou in 1928. Cytopathology is generally used on samples of free cells or tissue fragments, in contrast to histopathology, which studies whole tissues.  Cytopathology is commonly used to investigate diseases involving a wide range of body sites, often to aid in the diagnosis of cancer, but also in the diagnosis of some infectious diseases and other inflammatory conditions.  Wikipedia accessed 2018 Nov 8

"designer babies":  Steven Pinker, Human Nature and Its Future, 2003  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

Diagnostic Innovation Summit 2020 May 19-21 Lisbon Portugal Developing rapid tests and liquid biopsies  the latest tools, clinical applications, and commercial product launches for liquid biopsies, infectious disease, and point-of-care testing. They will address regulatory changes, implementation challenges, and the path forward for diagnostic innovation.

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

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 

diagnostics automation: Automation of the total testing process allows precise time-stamping and error-free, legible entries that can be easily retrieved for future reference. Zero tolerance of data entry duplications and immediate transmission of results to electronic medical records (EMRs) are other advantages of automation. Automated laboratory testing, synchronized with hospital data management systems, results in efficient disease/health management workflow. The automatic population of the data and the ability to retrospectively analyze the test ordering pattern and results are major benefits of the adoption of laboratory information systems (LIS) into the diagnostic workflow. The interoperability of the LIS and the hospital information system avoids test over-utilization and redundant or incorrect test ordering and ensures follow-up of results and better management of the reflex testing per guidelines. Web-based electronic health records and ordering options offer simple and flexible solutions for information gathering and transfer within the shortest possible time to ensure physician adherence, and better and timely patient management.  Molecular Diagnostics Automation and Enhancing Lab Workflow, MLO Medical Laboratory Observer 2016 Feb

Digital Health, Sensors, Wearable and IOT Clinical Utility and Emerging Applications in Drug Development, Diagnostics, and Healthcare MARCH 11-13, 2019,  San Francisco CA   Digital Health is promising to revolutionize healthcare delivery, optimize personalized and precision medicine, and offer new tools for drug and diagnostic development. The applications of biosensors, mobile devices and wearables, Internet of Things, mobile health platforms, artificial intelligence, and digital biomarkers are quickly expanding into all areas of patient monitoring and disease management, point-of-care diagnostics, and digital endpoints in clinical trials. Cambridge Healthtech Institute’s Inaugural Digital Health: Sensors, Wearables, and IoT meeting will bring together leading experts and thought leaders in digital health to discuss the latest technologies and implementation of digital tools into drug development, diagnostics and healthcare.

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 

Digital Pathology 
The first digital pathology platform receiving FDA approval has been introduced to the market and is leading to expanded deployment of hardware solutions, along with accompanying software tools and applications. These include slide-free imaging, enterprise-wide solutions and algorithms that use machine learning and AI to improve diagnoses, guide treatment, and address medical challenges across a variety of diseases. The merging of different fields including radiology and pathology is leading to ways of creating digital platforms and streamlining workflows.   See also molecular pathology

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

GeneReviews, an international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and  for patients and their families.    
GeneReviews glossary

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.

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

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 

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 
Genetic discrimination  genetic discrimination in health insurance, NHGRI

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 
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 

genetic predisposition A genetic predisposition (sometimes also called genetic susceptibility) is an increased likelihood of developing a particular disease based on a person's genetic makeup. A genetic predisposition results from specific genetic variations that are often inherited from a parent. These genetic changes contribute to the development of a disease but do not directly cause it. Some people with a predisposing genetic variation will never get the disease while others will, even within the same family. Genetic variations can have large or small effects on the likelihood of developing a particular disease. US NLM NIH, Genetic home Reference What does it mean to have a genetic predisposition?   

genetic privacy:  

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  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

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 

genetic testing clinical Genetic testing has grown from a niche speciality for rare disorders to a broad scope of applications for complex disease and personal use17,18. Not surprisingly, the definition of a genetic test has changed as the applications have evolved. Applications of clinical genetic testing span medical disciplines, including: newborn screening for highly penetrant disorders; diagnostic and carrier testing for inherited disorders; predictive and pre-symptomatic testing for adult-onset and complex disorders; and pharmacogenetic testing to guide individual drug dosage, selection and response (TABLE 1). Currently, genetic tests may be indicated in different clinical contexts and ordered by multiple health-care providers Katsanis SH, Katsanis N. Molecular genetic testing and the future of clinical genomics. Nature reviews Genetics. 2013;14(6):415-426. doi:10.1038/nrg3493.

genetic testing regulatory issues: Genetic testing is in an area with substantial knowledge gaps; both regulators and providers have acknowledged this issue. While CMS is in the best position to address these gaps using the existing CLIA framework, it has shown a reluctance to do so and the FDA has stepped in.25 Nonetheless, it is hard to believe that the tools available to the FDA are a better fit for the task. While the FDA's goals are admirable in trying to bring regulatory coherence to the genetic testing industry, the FDA is imposing an undue regulatory burden that will change the industry in a way that harms providers and patients while not addressing the greatest problems. These problems are best solved by better clinical guidelines from medical associations, increased proficiency testing from laboratories (through CMS and self-regulation), and reliance on the latest peer-reviewed research which will allow this industry to stay innovative, agile, and open. The FDA and genetic testing: improper tools for a difficult problem. J Law Biosci. 2015;2(1):158-166. Published 2015 Feb 7. doi:10.1093/jlb/lsv002

germ cells: The reproductive cells in multicellular organisms at various stages during GAMETOGENESIS MeSH

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 

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

GINA Genetic Information Nondiscrimination Act: 

"good genes", "bad genes": a recurring theme that is emerging as researchers probe the genetics of disease: genes are probably only rarely unidimensionally good or bad. "Genes can act differently in different environments," says James Hixson, of the University of Texas in Houston. Several studies are showing that genes can be beneficial or harmful depending on the tissue and time in which they are active, the presence or absence of other genes, as well as the gender and life history of the individual in whom they reside. Genome News Network Good Genes Bad Genes 2000
Genetic Literacy Project Is it time to retire “good genes” “bad genes” distinction? 2016

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.

histopathology: (compound of three Greek words: ἱστός histos "tissue", πάθος pathos "suffering", and -λογία -logia "study of") refers to the microscopic examination of tissue in order to study the manifestations of disease. Specifically, in clinical medicine, histopathology refers to the examination of a biopsy or surgical specimen by a pathologist, after the specimen has been processed and histological sections have been placed onto glass slides. In contrast, cytopathology examines (1) free cells or (2) tissue micro-fragments (as "cell blocks"). Wikipedia accessed 2018 Nov 8  

immunohistochemistry (IHC): involves the process of selectively imaging antigens (proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues.[1] IHC takes its name from the roots "immuno", in reference to antibodies used in the procedure, and "histo," meaning tissue (compare to immunocytochemistry). Albert Coons conceptualized and first implemented the procedure in 1941.[2] Immunohistochemical staining is widely used in the diagnosis of abnormal cells such as those found in cancerous tumors. Specific molecular markers are characteristic of particular cellular events such as proliferation or cell death (apoptosis).[3] Immunohistochemistry is also widely used in basic research to understand the distribution and localization of biomarkers and differentially expressed proteins in different parts of a biological tissue. Wikipedia accessed 2018 Nov 8  

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 

Draft Guidance for Industry, Clinical Laboratories and FDA Staff, In Vitro Diagnostic Multivariate Index Assays, CDRH, FDA, 2007 

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 

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   

Commercializing Novel IVDs , Harry Glorikian, Insight Pharma Reports\   Executive Summary    The process of developing a successful in vitro diagnostic (IVD) relies on the expertise of a diverse group of individuals, including the scientists who identify the biomarkers of significance, engineers and assay developers who translate those ideas into a tangible product, and the sales and marketing staff who get the product into the market. Global and regional trends have a tremendous effect on the IVD industry. Rising healthcare costs have led to a greater emphasis on evidence-based medicine and a focus on improved patient outcomes. An aging population along with the growing epidemic of chronic diseases and (re)emergence of infectious diseases are creating a demand for diagnostic devices for a variety of conditions. The growth of emerging economies and the push for decentralized healthcare are opening the IVD market to a wider audience. Healthcare delivery systems are changing, with growing numbers of integrated delivery networks and accountable care organizations, while smaller physician and hospital networks are being acquired by larger corporations and/or are aligning themselves with other small groups

Laboratory Developed Tests LDTs: A laboratory developed test (LDT) is a type of in vitro diagnostic test that is designed, manufactured and used within a single laboratory. ... For example, some tests can detect many DNA variations from a single blood sample, which can be used to help diagnose a genetic disease.  FDA, LDTs

However, currently, patients and providers cannot uniformly rely on all tests offered for clinical use as some are not subject to active premarket oversight to ensure they provide accurate measurements and valid claims.  Discussion paper on LDTs 2017,

See also Laboratory Developed Tests LDTs: Regulatory 

liquid biopsy: Cancer

medical genetics :
the branch of medicine that involves the diagnosis and management of hereditary disorders. Medical genetics differs from human genetics in that human genetics is a field of scientific research that may or may not apply to medicine, while medical genetics refers to the application of genetics to medical care. For example, research on the causes and inheritance of genetic disorders would be considered within both human genetics and medical genetics, while the diagnosis, management, and counselling people with genetic disorders would be considered part of medical genetics. .. Genetic medicine is a newer term for medical genetics and incorporates areas such as gene therapy, personalized medicine, and the rapidly emerging new medical specialty, predictive medicine.  Wikipedia accessed 2018 Feb 26
American College of Medical Genetics
American Society of Medical Genetics

medical genomics:  Term that is sometimes used interchangeably with clinical genomics, may refer 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 could therefore be considered a type of clinical genomics.

Microfluidics and Lab-on-a-Chip  |  Recent advances in MEMS technology and nanotechnology brought to life a series of next generation micro and nanofluidic devices with potential of cheaper, faster and more accurate point-of-care testing (POCT). Lab-on-a chip devices enable automation and sample-to-result solutions while being millimeters to a few square centimeters in size.  The miniaturization technology greatly impacted not only handheld devices but also compact comprehensive bench top analyzers.

molecular biopsy: Advances in sequencing technologies and data analytics has brought about a new era in understanding and interpreting cells, DNA, RNA, and exosomes, which in turn has rapidly advanced our capabilities in diagnostics and therapeutics. The Molecular Biopsy stream at Next Generation Dx Summit gathers leaders, researchers, and experts in cell and DNA capture and microdissection, sequencing, data analysis, and interpretation to explore applications of molecular biopsy in clinical applications, their impact on the healthcare system, and future directions for diagnostic assay research and development.of advances in sequencing

molecular 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.  Is this changing?

The Journal of Molecular Diagnostics, the official publication of the Association for Molecular Pathology, co-owned by the American Society for Investigative Pathology, publishes 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.

Molecular Diagnostics 

molecular diagnostics - cancer  Cancer

Molecular Diagnostics for Infectious Disease March 2-4, San Francisco, CA  Advancing Molecular Diagnostics to Improve Detection and Patient Outcome  The role of advanced molecular diagnostics for infectious disease continues to grow – not only are these assays moving into the clinic, but they are being used for infection surveillance and outbreak control, appearing in the pharmacy, and continuing to improve care in resource-limited settings, the latest in NGS and metagenomics, the latest regulatory and reimbursement challenges, and updates in the public health sphere. We’ll further examine the role of host response vs. pathogen detection in the clinic, the potential for microbiome analysis, and other novel approaches to infectious disease diagnosis. Special attention will be paid to antimicrobial resistance, from the clinical challenges to the emerging technologies, and novel technologies being developed specifically for resource-limited settings. We will also address the state of the industry from the point-of-view of numerous stakeholders: industry, regulatory, investment, technology, and clinical.

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

molecular diagnostics non-invasive:  See liquid biopsy, prenatal diagnostic testing

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. 

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

Next Generation Diagnostics 2020 Aug 25-27, Washington DC coverage spans cell- and cell-free biopsies, commercialization, reimbursement, biomarkers and companion diagnostics for immunotherapy, point-of-care testing, infectious disease, microfluidics and precision medicine.

patient stratification: Early patient stratification is critical to enable effective and personalized drug discovery and development
See also Pharmacogenomics

point of care diagnostics: Point-of-Care Diagnostics March 2-4, 2020 • San Francisco, CA  | It is without argument that the point-of-care market is one of the fastest growing markets in life sciences – POC diagnostics are quicker and more efficient, can reach more patients, can eliminate follow-up visits, and ultimately will save money in the healthcare system.

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 

point of care technologies: AUGUST 26-27, 2020, Washington DC Point-of-care technologies (POCT) provide actionable information at the location and time of care. This can mean by the hospital bedside, on the battlefield, or even at home versus conventional laboratory-based testing. This requires diagnostic testing to be done in a way where sample preparation is automated, the assay or sensor is accurate with a simple read out, having the whole platform should be easy to bring to locations outside of a laboratory or a hospital, and the cost to manufacture should be low. Some POC tests can utilize a smart phone or other mobile device to provide data analysis and is useful for sending data to the cloud. Creating an accurate, sensitive, reliable diagnostics that anyone can use is difficult, and there are many challenges to overcome.

population genetics, population genomics: SNPs and other genetic variations

precision health: March 2-4 2020 San Francisco CA Molecular diagnostics and devices along with point-of-care tools, AI, and companion diagnostics are enabling prediction, prevention, and precise treatment of cancer, infectious disease and will expand to include many other disease areas.

precision medicine and diagnostics advanced technologies for March 2-4, 2020 San Francisco CA Recent technological advances and scientific breakthroughs have improved our understanding of disease pathogenesis. These improvements in sequencing, computing, and much more allow for more precise and faster diagnosis and treatments.

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

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  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

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  Related terms: carrier testing, molecular genetic screening

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

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

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.   

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.

Sample prep resources
IUPAC Poole, C., Mester, Z., Miró, M., et al. (2016). Glossary of terms used in extraction (IUPAC Recommendations 2016). Pure and Applied Chemistry, 88(5), pp. 517-558.  doi:10.1515/pac-2015-0903

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 Toxicology   Related terms: analytical sensitivity, clinical sensitivity

sex selection:  President's Council on Bioethics, 

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

susceptibility:  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: The term “theranostics” was coined to define ongoing efforts in clinics to develop more specific, individualized therapies for various diseases, and to combine diagnostic and therapeutic capabilities into a single agent. The rationale arose from the fact that diseases, such as cancers, are immensely heterogeneous, and all existing treatments are effective for only limited patient subpopulations and at selective stages of disease development. The hope was that a close marriage of diagnosis and therapeutics could provide therapeutic protocols that are more specific to individuals and, therefore, more likely to offer improved prognoses. Nanoparticle-based theranostic agents Jin XieSeulki Lee, and Xiaoyuan Chen  Adv Drug Deliv Rev. Author manuscript; available in PMC 2011 Aug 30.   Related term:  pharmacodiagnostics

tissue diagnostics: See biopsy, cytopathology, histopathology, immunohistochemistry

uncertainty: Molecular Medicine

Diagnostics Resources
Genetics Home Reference Glossary, National Library of Medicine, NIH, US, 2003, 450+ definitions
Enhancing the oversight of genetic tests: Recommendations of the SACGT, Secretary's Advisory Committee on Genetic Testing, US June 2000  
Gene Reviews glossary
GeneTests, Children's Hospital, Seattle, US  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  Includes Online Directory of genetic resources. Coalition of 300+ consumer and health professional organizations.
Genetics Home Reference Glossary, National Library of Medicine, NIH  
Glossary of Terms, Digital Pathology Association 
UPAC International Union of Pure and Applied Chemistry, Glossary of Terms in Quantities and Units in Clinical Chemistry, Biochim Clin 1995; 19: 471-502. Around 300 definitions Pure & Applied Chemistry 68: 957- 1000, 1996 
IUPAC International Union of Pure and Applied Chemistry, GLOSSARY FOR CHEMISTS OF TERMS USED IN TOXICOLOGY Clinical Chemistry Division, Commission on Toxicology, Recommendations. Pure and Appl. Chem., 65 ( 9):  2003-2122, 1993. 1200+ definitions. 


NCI Dictionary of Genetics Terms
NHGRI (National Human Genome Research Institute), Talking Glossary of Genetic Terms, 250+ definitions.  Includes extended audio definitions.
Pharmacogenetic tests and genetic tests for inheritable markers: Guidance for Industry and FDA Staff, CDER,  FDA, 2006 
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 
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 2008
State of the art of genetic testing in the US: Survey of biotechnology companies and nonprofit clinical laboratories (1994-1995) has some interesting observations.
Other patient and disease related resources: Patient resources

Diagnostics Conferences
Molecular Medicine Tri Conference Diagnostics
Next Generation Diagnostics

Insight Pharma Reports Biomarkers and Diagnostics

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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