Book:Laboratory Informatics Buyer's Guide for Medical Diagnostics and Research/Introduction to medical diagnostics and research laboratories/Medical diagnostics lab
1. Introduction to medical diagnostics and research laboratories
Those who work in a medical diagnostics or research laboratory have a lot on their plate. (Or is that "on their slides"? "In their blood collection tubes"?) From small- to high-volume laboratories, the analysts in them must follow strict workflows and procedures in order to produce timely and accurate results for the best possible patient health outcomes. Many of those analysts will also have additional ancillary roles within the laboratory, including controlling quality, managing regulatory and cybersecurity requirements, and managing and updating documentation. Particularly in medical labs with significant volume, the chance for human error to impact operations and patient health may increase, requiring systematic and continual improvement approaches to collecting, analyzing, and protecting patient data. The introduction of laboratory informatics solutions and other information technology within the medical diagnostic and research fields has made those approaches easier to adopt, resulting in smoother procedures and improved patient safety.
Evaluating, selecting, implementing, and maintaining a laboratory informatics solution is no simple task, however. The laboratory team (or individual) taking these actions must consider their laboratory's business goals, current and future workflows, and the regulations that affect them, as well as the budget for the lab, its technology requirements, and its cybersecurity goals. And then of course there's the matter of understanding the options available and working with vendors to make the theoretical solution a reality, backed up with updates to training, business processes, and responsibilities within the organization. This can, for some, lead to a state of anxiety.
But the acquisition and implementation of a laboratory informatics solution doesn't have to be painful. With advance preparation and a full understanding of both how your lab's internal processes work and how acquiring a system should ideally occur, you'll be better prepared to take the leap.
This guide aims to assist you in that preparation, providing referenced information about the various processes and details of putting a laboratory informatics solution to work for you and your medical lab. We begin below by providing background on a variety of medical diagnostic and research laboratories, from pathology and public health labs to genetic diagnostic and central labs. Afterwards, the second chapter covers a wide array of considerations to make when evaluating, selecting, implementing, and maintaining an informatics solution, including an introduction to the benefits of a user requirements specification (URS) for that process. The third, fourth, and fifth chapters offer a wealth of resources for putting chapter two's information to use, including vendor lists, service providers, organizations, conferences, and other information sources. It also introduces LIMSpec, an ever-evolving software URS for laboratory informatics systems. The sixth chapter then gets into the nuts and bolts of the value of a URS, and more specifically LIMSpec, as well as how to get the most out of it. We provide closing comments afterwards, followed by an appendix that contains a blank version of the LIMSpec for medical diagnostic and research labs, along with a downloadable Microsoft Word version of the same document.
1.1 Medical diagnostics lab
Often referred to as simply a medical or clinical laboratory, the medical diagnostics lab performs tests on clinical specimens in order to get information about the health of a patient as it pertains to the diagnosis, treatment, and prevention of disease. An additional definition is provided by the Clinical Laboratory Improvement Amendments (CLIA) program, as "a facility that performs testing on materials derived from the human body for the purpose of providing information for the diagnosis, prevention, or treatment of any disease or impairment of, or assessment of the health of, human beings."
At a basic level, the medical laboratory, whether chemistry or pathology, operates like many other analytical testing laboratories. However, there are a few nuances between the medical laboratory and other analytical laboratories. Aside from handling human and animal specimens, one of these differences is the need to have a specific unidirectional workflow. This is intended to both minimize the risk of biohazard contamination and to establish assurance that sample cross contamination is minimized. Another major difference concerns the regulations governing the management of patient data (e.g., the Health Insurance Portability and Accountability Act [HIPAA] in the U.S. and General Data Protection Regulation [GDPR] in Europe). This creates a significant challenge not generally experienced by other types of analytical laboratories.
In most parts of the world, the medical laboratory is either attached to a hospital, performing tests on their patients, or acts as a private (or public) laboratory that receives analysis requests and samples from physicians, insurance companies, clinical research sites, and other health clinics for analysis. In cases where a particularly specialized analysis is required and a standard medical laboratory is not equipped to handle it, a research laboratory with the appropriate equipment and expertise may be employed. In other cases, a laboratory may decide it's simply more cost effective to contract more specialized, less common analyses out to specialized medical labs rather than heavily invest in the equipment and training to perform such analyses. Examples include the molecular diagnostics and cytogenetics laboratory, which provide diagnoses and treatment options for genetic or cancer-related disorders.
Like other analytical laboratories, regulations, laws, and standards typically drive how vital aspects of the laboratory operate. In the United States, clinical laboratories are primarily regulated by the Department of Health and Human Services. Inside that infrastructure are sub-entities like the Centers for Disease Control and Prevention (CDC) and the Centers for Medicare and Medicaid Services (CMS) to apply standards and regulations through their respective Laboratory Quality Assurance and Standardization Programs, and the Clinical Laboratory Improvement Amendments. Although generally not as strict as the regulations regarding pharmaceutical and diagnostic manufacturers, the regulations affecting the medical laboratory nonetheless act as a significant hurdle to managing the overall operations of the laboratory, from acquiring customers and samples, to testing, reporting results, and handling billing for the completed tests.
Internationally, regulatory bodies vary from country to country. However, organizations like the not-for-profit Clinical and Laboratory Standards Institute (CLSI) and associations like the Research Quality Association (RQA) exist to promote a more global approach to regulations and guidance affecting medical diagnostic and research laboratories. Additionally, a set of Good Clinical Laboratory Practice standards—originally developed in 2002 and since adopted by the World Health Organisation (WHO), non-governmental organizations (NGOs), and research institutions worldwide—provide guidance on implementing laboratory practices that are critical for laboratory operations around the world.
Pathology is at the heart of a medical laboratory's operations. In the context of modern medical treatment, the laboratory practice of pathology involves analytical workflow, which falls within the contemporary medical field of "general pathology," and the associated determination of the causes and effects of disease and other medical ailments. General pathology is broadly composed of a number of distinct but inter-related medical specialties that involve the analysis of tissue, cell, and body fluid specimens to better understand the cause, pathogenesis, morphologic changes, and clinical manifestations of a disease. In common medical practice, general pathology is mostly concerned with analyzing known clinical abnormalities that are markers or precursors for both infectious and non-infectious disease and is conducted by experts in one of two major specialties: anatomical pathology and clinical pathology. Additional subspecialties of pathology may further specialize in specific diseases (such as cancer) or situational focuses (such as cause of death).
188.8.131.52 Anatomical vs. clinical pathology
Anatomical (or "anatomic") pathology is a medical specialty of pathology that is concerned with the gross, microscopic, chemical, immunologic, and molecular examination of organs, tissues, and whole bodies (as in autopsy) to determine the presence of disease. Its subspecialties include surgical pathology (e.g., neuropathology, dermatopathology, etc.), cytopathology, and forensic pathology. Clinical pathology, however, is concerned with the diagnosis of disease based on the laboratory analysis of bodily fluids such as blood, urine, and tissues using the tools of chemistry, microbiology, hematology, and molecular analysis. Its subspecialties include hematopathology, immunopathology, and molecular pathology. Both anatomical and clinical pathologists work in close collaboration with clinical scientists (i.e., clinical biochemists, clinical microbiologists, etc.), medical technologists, surgeons, hospital administrators, and referring physicians to ensure the accuracy and optimal utilization of laboratory testing. Yet some argue the distinction between anatomic and clinical pathology is increasingly blurred by the introduction of molecular technologies that require new expertise and the need to provide patients and referring physicians with integrated diagnostic reports.
Regardless, some differences between anatomical and clinical pathology remain distinct:
- Specific dictionary-driven tests are found in clinical pathology environments, but not so much in anatomic pathology environments.
- Ordered anatomic pathology tests typically require more information than clinical pathology tests.
- A single anatomic pathology order may be comprised of several tissues from several organs; clinical pathology orders usually do not.
- Anatomic pathology specimen collection may be a procedural, multi-step process, while clinical pathology specimen collection is routinely more simple.
The differences between the two may appear to be small, but a differentiation in laboratory workflow between the two is apparent, to the point that developers of laboratory information systems (LIS) and anatomic pathology computer systems used in the pathology fields have created different functionality for them. Specimen collection, receipt, and tracking; work distribution; and report generation may vary–sometimes significantly–between the two, requiring targeted functionality in the utilized software.
184.108.40.206 Forensic pathology
Typically associated with a medical examiner or coroner, forensic pathology is focused on identifying and determining the cause of death of an individual. This includes not only the analysis of wounds and injuries but also full tissue specimens, identifying traumas—as well as chemical, biological, and solid foreign bodies and contaminates—that may have played a role in the individual's death. Anatomic pathology plays an important part of the examiner's analyses—represented by the forensic pathologist's required training—though clinical pathology also plays a role. Outside the gross examination of a body, the forensic pathologist will rely on the lab to conduct a variety of analyses. Whole organs and slides containing cross-sectional slivers of organs, as well as blood, urine, bile, and vitreous humor may be analyzed for toxicology, DNA typing, infectious diseases, disorders, or other chemical tests. In particular, maintaining chain of custody for such specimens is vital to ensure analyses are correct and evidence is not compromised. Though a medical laboratory, the forensic pathology laboratory isn't held to the same CLIA standards; they must be accredited by a related organization such as The American Society of Crime Laboratory Directors/Laboratory Accreditation Board to ensure the lab operates at prescribed standards.
1.1.2 Physician office lab
The physician office lab, or POL, is a physician-, partnership-, or group-maintained laboratory that performs medical diagnostic tests or examines specimens in order to diagnose, prevent, and/or treat a disease or impairment in a patient as part of the physician practice. The POL shows up in primary care physician offices as well as the offices of specialists like urologists, hematologists, gynecologists, and endocrinologists. In many countries like the United States, the POL is considered a clinical laboratory and is thus regulated by federal, state, and/or local laws affecting such laboratories. In October 2021, the Centers for Medicare and Medicaid Services (CMS) reported 41% of all CLIA-approved laboratories in the United States (130,335) were physician office laboratories. However, as of 2014, POLs were estimated to be processing only about nine percent of all clinical laboratory tests.
Testing and reporting at a POL, at least in the U.S., is largely concentrated on the realm of waived CLIA testing. As of October 2021, 68% of the POLs in the United States were primarily running CLIA waived tests. CLIA test complexity has three levels: high, moderate, and waived. Waived tests are simple to perform and have a relatively low risk of an incorrect test result. Moderately complex tests include tests like provider performed microscopy (PPM), which requires the use of a microscope during the office visit. Providers that want to perform PPM tests must be qualified to do so under CLIA regulations. High-complexity tests require the most regulation. These tests are the most complicated and run the highest risk of an inaccurate result, as determined during the Food and Drug Administration (FDA) pre-market approval process. Tests may come from the manufacturer with their complexity level on them, or one can search the FDA database to determine the complexity of the test.
Commonly performed tests include:
- urine analysis
- urine pregnancy
- blood occult
- glucose blood
- pathology consultation during surgery
- crystal identification by microscope
- sperm identification and analyses
- bilirubin total
- blood gasses
- complete blood count
- bone marrow smear
- blood bank services
- transfusion medicine
1.1.3 Integrative medicine lab
Dr. Ralph Snyderman, Director of the Center for Personalized Health Care at Duke University, defines integrative medicine as a process that creates and encourages "a seamless engagement by patients and caregivers in the full range of physical, psychological, social, preventive, and therapeutic factors known to be effective and necessary for the achievement of optimal health over the course of one's life." This type of personalized healthcare takes a more holistic approach to the causes of illnesses, including the biological, behavioral, psychosocial, and environmental contributors. Some medical laboratories such as those found within Duke Integrative Medicine, as well as Harvard Medical School's Contemplative Neuroscience and Integrative Medicine Laboratory, include an integrative medicine approach to their medical diagnostic and research activities. Laboratories associated with integrative medicine approaches are quite similar to standard medical laboratories, though, broadly speaking, they may focus more on nutritional, metabolic, and toxicity test types.
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