Informatics Tools in Clinical Diagnostics

Informatics Tools in Clinical Diagnostics | LabLynx Resources

Clinical diagnostics: From the doctor’s office to a more complex organization…

Diagnostic laboratory testing can involve quite a few moving parts: health insurance companies, having the doctor’s orders directed to them and the lab, dealing with forms (or completing them on a computer or smartphone), actually having samples taken, and then waiting for the results. Making all this work and having both the patient and the doctor receive the results involves coordinating systems in the doctor’s office, health insurance, clinical diagnostic lab, and third-party apps that keep you informed about the results, billing, messages, and other items. It’s a lot more than just dropping into your doctor’s office.

The primary purpose of this piece is to look at the role of laboratory informatics in the clinical diagnostics industry and the considerations for the new and/or replacement implementations of a laboratory information management system (LIMS), a variation of which is referred to as a laboratory information system (LIS). Along the way, we’ll look at how the systems noted earlier interact and how that plays into system requirements definitions and selections. We’ll start by looking at the types of clinical laboratories, how the need for clinical testing has changed, and the operations within the clinical diagnostics laboratories.

Clinical laboratory organization

According to a publication by Bayot, Lopes, and Naidoo[1], clinical laboratories can be viewed in different ways:

  • Ownership can be public or private and as part of a medical center or an independent facility;
  • Function includes standard diagnostic tests or specialization into disease-specific and confirmatory tests. These tests can be performed in the doctor’s office lab[2] or in external facilities and
  • Test specialization includes clinical chemistry, Clinical Microbiology, Hematology, Blood banking and Serology (aka Immunohematology, Transfusion Medicine), Clinical Microscopy, Histopathology and Cytopathology, Molecular Biology, and Public Health. Note for a more complete list of common tests, see Appendix 1.

Another approach is to look at their level in the network of labs. The following set of bullets is taken from the previously mentioned publication:

  • Peripheral laboratories – provide routine screening, diagnostics (e.g., conventional and rapid diagnostic tests), and follow up tests for patients; usually situated in the community where people can access their services;
  • Intermediate-level laboratories – can be at the district, provincial [or state], and regional-level facilities; may conduct additional tests than those provided in peripheral laboratories and can serve as referral laboratories for special cases (district-level); aside from performing tests, they carry out management and supervisory tasks under specific areas of jurisdiction (mainly provincial [or state] and regional laboratories);
  • National reference laboratories – also known as the central level, which perform oversight and overall management of the laboratory network in terms of policy and program implementation, training and development, monitoring and evaluation, and research; these facilities also provide a range of routine and highly-specialized laboratory testing, including the introduction and phasing in of new diagnostic tests.

Factors that are changing the clinical diagnostics market and its growth

The need for testing in healthcare is going to continue to grow. The following factors are just a few of those driving the market:

  1. The persistence of concerns with COVID-19 infections and disease transmission, along with flu infections, and respiratory syncytial virus (RSV) will continue to increase the demand for clinical diagnostics testing. The development of new diseases and disease strains – especially as antibiotics overuse leads to resistance – is going to increase the demand for services. While at-home testing is available for some types of detection, lab-based services are going to provide the backup to verify results in case of questions. The growing domestic and international travel rate is just going to fuel the need for more vigilance.
  2. Demographics indicate an aging population. As the number of people in the older population increases, so will the need for testing to keep track of disease progression and development.
  3. The availability and benefits of new drugs and testing services heavily marketed in the media will make people more aware of what is open to them and how to take advantage of their options. This, coupled with an ongoing trend in patient empowerment, will lead people to be more proactive in caring for their health issues.
  4. Research and development into new testing methods and treatments will bring more patients into the clinical lab.

Clinical studies

That last bullet brings us to another dimension in the clinical diagnostics market that affects clinical labs. Therapeutics and diagnostic tests must undergo a series of evaluations before they can be approved by regulatory agencies. Their aim is to determine the safety and effectiveness of treatments and diagnostic tools.

The evaluations of new treatments are in the form of clinical trials[3]. Clinical diagnostic laboratories can play a vital role in that work. This work is often performed by contract research laboratories, but clinical diagnostics labs are often used for 3rd-party verification or standard testing that perhaps isn’t a part of the CRO’s capabilities. That work includes, but isn’t limited to:

  • Registering participants in the clinical trial – finding them, evaluating them, devising compensation agreements, taking care of the necessary administrative and legal paperwork, and setting up schedules for the program.
  • Gathering samples to meet the testing needs of the program;
  • Testing and reporting the results; verifying them and
  • Managing the billing and compensation.

This work is often performed with the assistance of software that includes:

  • Electronic data capture systems – to collect, store, and manage data from clinical trials in electronic form;
  • Clinical trial management systems – to help manage the operational aspects of clinical trials, such as tracking milestones, patient enrollment, and site monitoring;
  • Randomization and trial supply management systems – for patient randomization and managing trial supplies;
  • Electronic patient-reported outcome systems – data capture directly from patients via mobile devices or web platforms;
  • Biostatics platforms that assist in data analysis;
  • Regulatory documentation management systems; and
  • Mobile health and wearable devices – may be used for real-time data capture.

Other software and hardware systems may be needed depending on the nature of the work. The bottom line is to ensure that the patients are qualified for the program, that data are being accurately collected and managed, that the necessary reporting mechanisms are in place, and that all of this is being done according to regulatory guidelines.

The effectiveness of new diagnostic tools also gets demonstrated in the form of clinical trials. This involves the creation of pools of samples, some with the disease or condition under concern and others that are clear of it. The testing is done to develop confidence that the diagnostic tools can distinguish between them with a high enough confidence level to be of value. A new test should only be introduced into practice if it has a better chance of improving patient health than existing tools.[4].

Informatics in Clinical Diagnostics

Informatics tools in support of clinical diagnostic systems

Testing is at the heart of clinical laboratory work, and those test protocols are not just a matter of samples but also an interplay of patient-doctor-laboratory-administrative relationships. Patients provide samples, doctors determine the testing protocols that are needed, labs do the work. Administrative services provide access to electronic health records (EHR) and financial services, including making insurance claims, working with doctors to convince insurers that the work is justified, billing patients, and enabling communications between all interested parties with a high level of security and protection for patient records (HIPAA compliance).

The informatics landscape for laboratory work functions at two levels: one is that of patient/physician/administrative functions, and the second is laboratory-specific. The tools are designed to provide the needed communication between patients, physicians, administrators, and labs while providing insulation where appropriate. For example, you’d want patients to have timely access to lab results but be unable to contact the labs themselves to avoid being swamped with patient support calls. All of this is accomplished through the use of patient and physician web portals.


Patient Portal Physician Portal
Purpose This website, or app, gives patients 24-hour secure, HIPAA-compliant access to their personal health information from anywhere with an internet connection.   This portal is tailored for the general public/patients and as a result its design is user-friendly, and it avoids excessive medical jargon. This is designed primarily for healthcare providers to be able to register samples and requested tests/panels, and view test results and histories. It can also allow for printing of barcoded labels to further ensure accurate accessioning at the lab end. It can also have a payment element. Its language can be technical and include medical terminology.
Access The patient portal can be standalone, as in many COVID-testing setups during the recent pandemic, or be in the form of an integration with a healthcare provider’s own patient-facing portal. Patients can view their lab results. Or, if integrated as above, view them along with personal medical records, medications, immunizations, allergies, and more. They can also schedule appointments, communicate with providers, request prescription refills, and even pay bills in some cases. Lab-direct portals often also contain insurance and payment functions. The physician portal is typically accessible by named authorized users at the physician office or healthcare organization, including the physician, nurse, phlebotomist, medical assistant, etc. Their access to HIPAA-protected PHI can be controlled according to their role-based login.
Functionality Offers lab-specific functionality that helps patients to be more actively involved in their healthcare. This is a more comprehensive tool designed for clinical tasks. It may also integrate with electronic health record (EHR) systems, allowing for the sharing of data with specialists, and providing detailed medical histories.
Communications Primarily designed for patient-lab communication. Patients can take control of their own tests and results, where possible. Accurate, documented lab-related communications are enabled for all authorized medical personnel.
Security Both portals prioritize security since they deal with sensitive health information. However, the types of data and functionality available may dictate slightly different security protocols and measures for each portal. In all cases, however, PHI are protected in accordance with HIPAA requirements.


The remainder of any additional communications is managed by websites and/or email or telephone communications to customer support representatives.

Laboratory informatics layers

There are several layers of systems within a laboratory that manage functions such as sample receiving, storage, inventory, sample preparation and processing, and lab operations management. Our primary focus is on one of them:  laboratory operations management. That is carried out with the assistance of a laboratory information system (LIS) or a laboratory information management system (LIMS). Both of those connect to instrument data systems to manage the processing of samples and keep track of results. LIS and LIMS also connect to the portals noted above to be told what work is needed and deliver the results of lab work to either the physician or patient. The LIMS/LIS provides operational management functions for the lab.

The LIMS/LIS is the receiving point for work orders from physicians and the samples that have to be processed. The work is organized by priority, and the samples and worklist requests sorted by the type of testing to be performed, lab analysts and the instruments that will be used. Samples and worklists are sent to those stations, the testing is carried out, and the results are returned to the LIMS/LIS for review and approval. Once approved, those results are made available to the patient or physician through the appropriate portal.

LIMS/LIS are central to organizing and maintaining an orderly workflow within the lab. It’s the place lab personnel go to find outstanding worklists, sample status, test results, work summaries, quality control data, materials inventory, equipment maintenance, etc.

Once, the distinction between a LIS and LIMS was significant, particularly in the early days of informatics development (see LIS vs. LIMS: Does it Matter in Healthcare?).[5] LIS grew out of healthcare and was patient-centric. LIMS was a general industry solution to sample and lab operations management issues. The core of the technologies was essentially the same; the differences were a matter of application. Since that early development, the two product sets have borrowed capabilities from one another to the point where the some of the more general LIMS (including LabLynx) now offer versions incorporating full LIS functionality and terminology. One significant benefit of LIMS to the clinical lab is due to the evolution of clinical testing, which is adopting instrumental techniques common to industrial labs. Clinical labs can take advantage of instrument support facilities built into LIMS.

LIMS is also better positioned to take advantage of industry consolidation and the rise of contract testing laboratories through its ability to support high-volume testing and multi-location organizational structures. And the leading professional systems offer greater flexibility, resulting in longer lifetime and greater return on investment (ROI) than most LIS, which tend to be more narrowly-focused. This is discussed more thoroughly in the previously noted LIS vs. LIMS article.

Introducing LIMS into lab operations

A LIMS can be introduced into a lab in one of two ways: a new system in a laboratory that doesn’t have one, or as a replacement for an existing system that no longer satisfies the lab’s needs. We’ll look at both situations in the following pages.

Adding a first-time LIMS to a laboratory

This can be a daunting prospect for any laboratory, regardless of size. However, the results of the work will be the transformation of an inefficient paper- or spreadsheet-based operation into a more efficient and effective lab operation that will benefit both those working in the lab and those that rely on it for results – as well as those who have investment in the lab.

Most of the equipment in a lab is something you may be familiar with from your educational programs; you’ve used something like them, and the instrumentation you might be buying is a later version of what you may have used. Laboratory informatics is different. It involves hardware, but also software (in some cases, several packages), networks, communications, and things you may not have any direct experience selecting and setting up. How do you start? There are books and many articles on the subject and they are easily found by a web search and talking to several vendors. Our goal here is to give you a means of orienting yourself and seeing the issues.

It would be best to begin by educating yourself and planning for product selection and implementation. The place to start is by determining what problems you want to solve and what your needs are. It’s like buying a car or a house. You can go out and look at what’s available, and you may become overwhelmed with the choices (and prices!). That only gets you somewhere if you have a reference point: what are your lab’s needs, and how do those needs fit into the both the lab’s organization and those you support (physicians and patients)?

Assess your laboratory’s needs
  • Size and Scale: Consider the size of your laboratory and its projected growth. How many people are in the lab now, and how will that change over time? This can affect the license cost of a system. The important thing to consider is what you need to be effective. Just “getting by” will lead to frustration. Your ultimate goal is to be optimal.
  • Type of Tests: Different labs (e.g., molecular diagnostics, pathology, microbiology) might have different requirements.
  • Current Workflow: Understand your existing workflow and identify areas that need improvement. Improving workflow is one of the significant benefits of LIMS. As part of that, consider workflow concerns beyond the lab. What facilities do you need to support physicians, patients, and administrative functions?

Next, we’ll look at what features the system needs to support the lab’s work.

Features and Functionality
  • Sample Tracking: Ensure the system can track samples from receipt to reporting. This is a primary purpose of a LIMS. You need to ensure that the LIMS can take work orders from a physician portal, allow you to see their progress at any time, and release approved results in a timely, efficient and accurate fashion.
  • Integration: The system should integrate seamlessly with other hospital or clinic systems, such as Electronic Health Records (EHR) or billing systems, as well as instruments and reporting authorities such as state public health departments. The system needs to be able to communicate using HL7 and other industry standards/formats.
  • Automation: Look for features that automate repetitive tasks to reduce manual errors.[6]  Moving from manual to electronic data entry (e.g., barcodes, instrument data systems) will increase productivity. And features like alerts based on deadlines, out-of-calibration instruments and more help raise overall quality.
  • Reporting: Ensure the system can generate customizable reports as required. Are there reports that you’d like to provide, but can’t currently because of time or formatting constraints?
  • Data Security: Given the sensitive nature of clinical data and PHI, ensure the system has robust security features that fully support HIPAA compliance.
  • User Interface: A user-friendly interface can reduce the learning curve and increase efficiency. How easy and intuitive is the system to work with?
  • Training: Consider how much training will be required and if the vendor provides it. Two levels of training will be needed: administrative and user. On-premise systems (see Implementation and Transition) may require IT training.
  • Support: Ensure the vendor offers timely technical support. Is the support outsourced or provided by the vendor’s personnel? Will you have consistent access to a group of people or will every call be to someone new?
Scalability and Flexibility
  • Modular Design: Some systems allow you to add modules as your lab grows or as new tests are introduced.
  • Customization: The ability to customize the system to your lab’s specific needs can be beneficial. Understand the difference between configuration and customization. Is this something the system administrator can do through the application itself (configuration), or are all modifications done by the vendor’s developers (customization, requiring coding)? How much support does the vendor provide, and how are costs determined?
Regulatory Compliance
  • Ensure the system meets all necessary regulatory standards, such as those set by the Clinical Laboratory Improvement Amendments (CLIA), Health Insurance Portability and Accountability Act (HIPAA), and others relevant to your region or range of testing.

The following sections move from lab and product concerns to those of a project management or business standpoint.

  • Budget: Determine your budget and consider both the initial investment and ongoing costs. This should include project management costs and some provision for unexpected items. Always factor in a 10-20% buffer.
  • Return on Investment (ROI): Consider how the system might increase efficiency and reduce errors, leading to cost savings in the long run. See “Justifying LIMS Acquisition and Deployment within Your Organization: First Edition” for a discussion of this subject.[7] Remember, the longer the usable lifetime of the system, the more ROI. And flexibility, based on widely-used, proven technology platform foundations, means longer system life.
Vendor Reputation
  • References: Ask for references from other labs that have implemented the system.
  • Experience: Consider how long the vendor has been in the market and their experience with clinical diagnostic laboratories specifically.
  • Updates: Ensure the vendor regularly updates the system to keep up with technological advancements and changing regulations. Note: the type of implementation will have a major impact of this topic. This is covered below.
  • Hands-on Experience: Before making a decision, request a demo to get a feel for the system in a real-world setting. Most vendors will be happy to do multiple demos for you if necessary, and configure them to address your specific requirements, or at least show clearly how they can be addressed.
  • Feedback: Gather feedback from staff who will be using the system daily. A successful system implementation depends on the buy-in of your team. Listen closely to their input.
Implementation and Transition
  • Data Migration: Discuss how existing data will be migrated to the new system (see the material on records retention below). This can be a significant time and cost component, especially if the condition of your legacy data is less than optimal. In many cases, it’s ok to leave the data where they are if they aren’t necessary for operations going forward, as long as they are accessible if needed.
  • Downtime: Understand how much downtime, if any, will be required during the transition, and plan accordingly. This also includes planning your resources, especially staff training, and implementation project management and communications, meetings and collaboration.
  • Implementation: There are two methods of implementing LIMS systems: on-premise and cloud-based. An on-premise system means that the software and hardware run within your lab and that you, or someone you designate (possibly IT) are responsible for updates, maintenance, etc. Cloud-based systems are maintained by the vendor, and don’t require any maintenance on your part nor any involvement by IT. Cloud-based systems are faster to implement and get into production, potentially at a lower cost. For more details see “Choosing a LIMS technology: Cloud-based or on-premises?”[8]

 Future-proofing. Your lab’s needs are going to change over time. More users, new techniques, requirements for new reports, and increased regulatory oversight are possibilities. Will the system and/or vendor have the capabilities to support those changes?

For another perspective on the subject, see “20 Key Features to Look for in a Modern LIMS”.[9]

One point you will have to plan for is the transition from the existing lab processes to those using the LIMS. Making sure people are fully educated on the use of the system is an initial step, followed by systems testing and validation. Once that work is done and the system is accepted for use, it’s a matter of setting up a schedule and process to make the transition.

One concern that must be addressed is handling the data from the previous processes. Whether they are paper-based or in spreadsheets the data will still be there. Regulations will prohibit their deletion, but you’ll have to determine how much active work will be transferred to the LIMS. In-process work may be left as is, with new requests entering the LIMS. At some point, all active work will be through the LIMS, and the previous data will be kept available for reference purposes.

Replacing an existing LIMS with a new updated/upgraded software package

In the previous section, we transformed a lab’s operations using LIMS to manage and improve the execution of many lab functions. Here we will upgrade an existing lab operation with a new system, making improvements where needed. There will be considerable benefits; however, effort must be applied to make the transition as smooth as possible so that in-lab and customer support functions are only beneficially affected.

Three key issues need to be addressed: selecting a replacement system, planning for its installation, and the transition from the previous system to the new LIMS.

Product selection would follow the same process and concerns noted in the previous section.  One of the benefits of a replacement process is that you and your team are already familiar with technology and its capabilities. Your primary concern is looking at issues the current system doesn’t handle well, the future growth path for the lab, and how its work will evolve. These items will add to the needs analysis for product selection.

Transitioning from the existing system to the new implementation will take a significant planning effort. One key to your success is formulating a plan and discussing it with those in the lab and those directly affected by it. This will flush out issues you may have yet to be aware of, and keep everyone aware of what is going on and how it will affect them. It also brings everyone onto the same team, pulling together for a common goal. You will be replacing a significant component of a lab’s operating structure, and many connections will be impacted, including instrumentation and any other systems or portals that access the systems. The primary considerations are shown in the following tables.

Data Migration
  • Identify all data that need to be transferred from the old system to the new one.
  • Plan for data cleaning, as there might be inconsistencies or errors in the old system.
  • Ensure that the new system can accommodate the data formats from the old system or plan for data conversion.
Records Retention
The regulations for records retention vary from one country to another, and within the U.S. from one state to another. Here are some guidelines.

  1. Health Insurance Portability and Accountability Act (HIPAA) in the U.S. sets the standard for protecting sensitive patient data. Any organization that deals with protected health information (PHI) must ensure that all the required physical, network, and process security measures are in place and followed. A Business Associate Agreement (BAA) will be necessary for any outside parties, including the LIMS vendor’s implementation team, who will access PHI.
  2. General Data Protection Regulation (GDPR) in the European Union: This regulation protects individuals regarding their personal data, and applies to healthcare data. Laboratories must ensure data privacy and security, and demonstrate compliance with the GDPR.
  3. Access Controls: Access to client data should be restricted to authorized personnel only. This often includes implementing user authentication, role-based access controls, and maintaining access logs.
  4. Retention Policies: Many jurisdictions require that medical records be retained for a specific period, depending on the record type and the patient’s age. After that period, the data usually must be securely destroyed, with documentation.
  5. Patient Consent: In many jurisdictions, patient consent is required for specific data handling or sharing types. This may also include informing patients of their rights regarding their data, such as the right to access or correct information.
  6. Collaboration with Third Parties: If the laboratory collaborates with third parties, contracts must clearly define the responsibilities regarding data protection, and the third parties must comply with the same regulations that apply to the laboratory. If the LIMS is changing, the contract should be reviewed to see if any conditions need to be updated.
  7. Local and Industry-Specific Regulations: Different jurisdictions and even specific regions within countries may have additional regulations and guidelines. Furthermore, industry-specific standards, such as those set by professional associations, might apply.
  8. Ethical Considerations: Beyond legal requirements, many organizations adopt ethical guidelines that may include additional client privacy and autonomy protections.

It is recommended that you check the requirements in your location. One reference worth noting is “CLIA Laboratory Record Retention Requirements” that can be found at

Integration and Pilot Testing
  • Ensure that the new LIMS can integrate seamlessly with other systems in the laboratory, such as billing systems, electronic health records, and instrumentation.
  • Before fully transitioning, run a pilot test where a subset of the laboratory’s operations is managed through the new LIMS.
  • Identify any issues or challenges and address them before full implementation.
Post-Implementation Review
  • After a few weeks or months of using the new system, gather user feedback.
  • Address any challenges or issues that have arisen. Make necessary adjustments or customizations based on user feedback.

In addition, backup and contingency planning should be reviewed to see if any changes are required in light of the new system’s implementation. Throughout the process, those affected by the changes being made need to be informed of the project progress, when key milestones are being approached, and your success in meeting them. They must also be prepared for the final changeover from one system to another.

In closing…

The clinical diagnostic lab is a unique environment for laboratory informatics. Not only does it have to meet the challenges of laboratory management and instrument communications, but it also has to do it while interacting with patients, physicians, insurance companies and administrative systems through standardized interfaces. Because of the recognition of the importance of automation in keeping clinical labs economically viable, lab informatics is both a mature and developing set of systems. LIMS provides a pivotal role in its operations, managing testing and distributing data as needed. LabLynx, with its Elab LIMS, is well suited to addressing the needs of this application and assisting your lab in successfully integrating its products into your operations.


Appendix 1 – Common Tests in Clinical Diagnostic Laboratories

  • Complete Blood Count (CBC), CBC Morphology
  • Hemoglobin and hematocrit
  • Blood clotting tests (e.g., prothrombin time, partial thromboplastin time, internal normalized ratio)
Biochemistry/Clinical Chemistry & Comprehensive Metabolic Testing
  • Blood glucose
  • Blood urea nitrogen (BUN) and creatinine
  • Liver function tests (e.g., ALT, AST, bilirubin)
  • Lipid profile (e.g., cholesterol, LDL, HDL, triglycerides)
  • Electrolytes (e.g., sodium, potassium, chloride)
  • Bacterial culture and sensitivity testing
  • Antigen or antibody detection tests
  • PCR for the detection of specific pathogens
  • Note: Covid-19 testing falls into this category
  • Tests for autoimmune disorders (e.g., ANA, RF)
  • Allergy testing
  • HIV serology
  • Pap smears
  • Biopsy tissue examination
Molecular Diagnostics
  • Detection of genetic mutations
  • Oncology markers
  • Infectious agent genotyping
  • Thyroid function tests (e.g., TSH, T3, T4)
  • Insulin and C-peptide levels
  •  Testosterone, estrogen, and progesterone levels
  • Drug screenings
  • Alcohol levels
  • Heavy metal assays
  • Factor assays
  • Thrombin time
Urinalysis Examination of the urine for various constituents to help diagnose renal diseases, diabetes, and urinary tract infections among others.
Clinical Microscopy
  • Examination of body fluids (e.g., cerebrospinal fluid)
  • Parasite examinations
Point-of-Care Testing (POCT) These are diagnostic tests conducted outside the laboratory, near to where the patient is receiving care. Examples include glucose meters and rapid strep tests.

 This is far from a comprehensive list. New tests are continually added. For a more thorough list please see and

Not all testing is available from all laboratories.



[1] Bayot ML, Lopes JE, Naidoo P. Clinical Laboratory. [Updated 2022 Dec 19]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from:

[2] See

[3] For more information, see

[4]  See

[5] See


[7] See

[8] See

[9] See

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