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You are here Biopharmaceutical/ Genomic glossary Homepage > Molecular Medicine > Molecular Diagnostics & Genetic testing
Molecular diagnostics glossary & taxonomy SCOPE NOTE Diagnostics
include biomarkers, circulating cell free DNA, companion diagnostics, pharmacogenomics for
clinical trial patient stratification, prenatal diagnostics
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
Molecular Medicine TriConference Precision Health March 2-4, 2020 San Francisco CA https://www.triconference.com/Precision-Health 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 http://www.bio-itworld.com/2010/09/28/1Kgenome.html 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 https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=864.4020 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://old.iupac.org/reports/provisional/abstract01/vessman_300901.html
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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873211/ 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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873211/ Related terms: clinical specificity and specificity Compare analytical selectivity. biopsy: a medical test commonly performed by a surgeon, interventional 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 https://en.wikipedia.org/wiki/Biopsy capsule endoscopy: a procedure that uses a tiny wireless camera to take pictures of your digestive tract. Mayo Clinic https://www.mayoclinic.org/tests-procedures/capsule-endoscopy/about/pac-20393366 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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873211/ 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 pathology, clinical
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, spectrophotometry, electrophoresis,
and immunoassay.
Wikipedia accessed 2018 Sept 3
https://en.wikipedia.org/wiki/Clinical_chemistry
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 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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873211/ 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; 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. https://www.triconference.com/Companion-Diagnostics
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 https://en.wikipedia.org/wiki/Computer-aided_diagnosis 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 https://en.wikipedia.org/wiki/Cytopathology "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 Diagnostic Innovation Summit 2020 May 19-21 Lisbon Portugal Developing rapid tests and liquid biopsies https://www.dxinnovationsummit.com/ 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 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 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 https://www.mlo-online.com/molecular-diagnostics-automation-and-enhancing-lab-workflow 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. https://www.triconference.com/Digital-Health
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 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
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 genetic
counseling for patients and
their families.
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 Force, Resta R, Biesecker BB, Bennett
RL, Blum
S, Hahn
SE, Strecker
MN, Williams
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 http://www.genome.gov/10002345 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 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? https://ghr.nlm.nih.gov/primer/mutationsanddisorders/predisposition 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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873211/ 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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461364/
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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5033563/ 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 https://www.cancer.gov/publications/dictionaries/cancer-terms/def/germline-mutation 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":
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
http://www.genomenewsnetwork.org/articles/07_00/goodgenes_badgenes.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. 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 https://en.wikipedia.org/wiki/Histopathology 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 https://en.wikipedia.org/wiki/Immunohistochemistry 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
Commercializing Novel IVDs , Harry Glorikian, Insight Pharma
Reports
http://www.insightpharmareports.com/Commercializing-Novel-IVDs-Report/\
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 https://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/LaboratoryDevelopedTests/default.htm
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. See also Laboratory Developed Tests LDTs: Regulatory
liquid
biopsy: Cancer 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
|
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
http://www.nextgenerationdx.com/stream/molecular-biopsy/
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. https://www.amp.org/resources/journal-of-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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873211/
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:
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 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.
https://www.nextgenerationdx.com/microfluidics/
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. https://www.triconference.com/precision-health
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.
https://www.triconference.com/Diagnostics-Technologies
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873211/ 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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873211/ 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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873211/ 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
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.
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, http://bioethics.georgetown.edu/pcbe/topics/sex_index.html
specificity: See analytical specificity, clinical specificity 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 Xie, Seulki
Lee, and Xiaoyuan
Chen tissue
diagnostics: See biopsy, cytopathology, histopathology,
immunohistochemistry
Diagnostics Conferences
http://www.healthtech.com/conferences/upcoming.aspx?s=BMK
IUPAC definitions are reprinted with the permission of
the International Union of Pure and Applied Chemistry. |
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