Search

Background Delay or failure to view test results in a hospital setting can lead to delayed diagnosis, risk of patient harm, and represents inefficiency. Factors influencing this were investigated to identify how timeliness and completeness of test review could be improved through an evidence-based redesign of the use of clinical test review software. Methods A cross-section of all abnormal hematology and biochemistry results which were published on a digital test review platform over a 3-year period were investigated. The time it took for clinicians to view these results, and the results that were not viewed within 30 days, were analyzed relative to time of the week, the detailed type of test, and an indicator of patient record data quality. Results The majority of results were viewed within 90 min, and 93.9% of these results viewed on the digital platform within 30 days. There was significant variation in results review throughout the week, shown to be due to an interplay between technical and clinical workflow factors. Routine results were less likely to be reviewed, as were those with patient record data quality issues. Conclusion The evidence suggests that test result review would be improved by stream-lining access to the result platform, differentiating between urgent and routine results, improving handover of responsibility for result review, and improving search for temporary patient records. Altering the timing of phlebotomy rounds and a review of the appropriateness of routine test requests at the weekend may also improve result review rates.

Background In Korea, the Korean Laboratory Accreditation Program (KLAP) has set minimum standards for verification of clinical test performance. This verification process is time-consuming and labor-intensive when performed manually. We developed a free, statistical software program for KLAP, using the R language (R Foundation for Statistical Computing, Vienna, Austria). Methods We used CLSI guidelines for the algorithm. We built graphic user interfaces, including data input, with Embarcadero Delphi EX4 (Embarcadero Technologies, Inc., Texas, USA). The R Base Package and MCR Package for Method Comparison Regression were used to implement statistical and graphical procedures. Results Our program LaboStats has six modules: parallel test, linearity, method comparison, precision, reference interval, and cutoff. Data can be entered into the field either manually or by copying and pasting from an MS Excel worksheet. Users can print out precise reports. Conclusions LaboStats can be useful for evaluating clinical test performance characteristics and preparing documents requested by KLAP.

Introduction and Objective: In laboratory, the errors related to the total testing process, affecting clinical decision making, may occur in all the phases. Quality Indicators are fundamental tool to assess the laboratory performance. The aim of this study is to observe the error types and rates for analytical and post analytical phase inorder to assess laboratory performance and rectify them. In addition to acrreditate laboratory as per international standards, it would also help to improve patient care and safety. Materials and Methods: For a period of one year, errors were observed, recorded and analyzed at clinical Biochemistry laboratory, SMIMER, Surat by this retrospective study. Data analysis of total 907611 tests carried out on 317212 samples was done. Analytical and post analytical errors were identified; recorded and analysed taking into consideration certain related Quality Indicators. Results: For analytical phase and post analytical phase error rates recorded were 7.51% and 8.57% of total samples respectively while it was observed to be as high as 46.71% and 53.28% respectively against total errors encountered for the phases. Highest (45.9%) error rate of analytical phase error was due to tests not in conformance with External Quality Assurance - Proficiency Testing scheme in a previously treated cause. 17.52% of post analytical phase error was due to low rate of critical call outs to clinicians. No records were maintained pertaining to (1) delayed delivery of reports due to insufficient reagents, (2) critical values call out time (min) and (3) staff training events. Also the laboratory was not equipped with Laboratory Informatics System. Conclusion: Quality Indicators based high error rates warrant active intervention and strict supervision of both the phases of TTP under study. Strategic measures should be initiated to minimize the risk of errors. Ultimately it would be useful for betterment of patient care and safety. Keywords: Total testing pr

Antimicrobial resistance (AMR) is a major threat to human health globally. Surveillance is a key activity to determine AMR burden, impacts, and trends and to monitor effects of interventions. Surveillance systems require efficient capture and onward sharing of high-quality laboratory data. Substantial investment is being made to improve laboratory capacity, particularly in low-income and middle-income countries (LMICs) with high disease burdens. However, building capacity for effective laboratory data management remains an under-resourced area, which, unless addressed, will limit progress towards comprehensive AMR surveillance in LMICs. The lack of a fit-for-purpose and open-source laboratory information management system software is of particular concern. In this Personal View, we summarise the technical requirements for microbiology laboratory data management, provide a snapshot of laboratory data management in LMIC laboratories, and describe the key steps required to improve the situation. Without action to improve information technology infrastructure and data management systems in microbiology laboratories, the ongoing efforts to develop capacity for AMR surveillance in LMICs might not realise their full potential.

DNA-encoded libraries (DELs) have emerged as an efficient and cost-effective drug discovery tool for the exploration and screening of very large chemical space using small-molecule collections of unprecedented size. Herein, we report an integrated automation and informatics system designed to enhance the quality, efficiency, and throughput of the production and affinity selection of these libraries. The platform is governed by software developed according to a database-centric architecture to ensure data consistency, integrity, and availability. Through its versatile protocol management functionalities, this application captures the wide diversity of experimental processes involved with DEL technology, keeps track of working protocols in the database, and uses them to command robotic liquid handlers for the synthesis of libraries. This approach provides full traceability of building-blocks and DNA tags in each split-and-pool cycle. Affinity selection experiments and high-throughput sequencing reads are also captured in the database, and the results are automatically deconvoluted and visualized in customizable representations. Researchers can compare results of different experiments and use machine learning methods to discover patterns in data. As of this writing, the platform has been validated through the generation and affinity selection of various libraries, and it has become the cornerstone of the DEL production effort at Lilly.

Patient based real time Quality Control (PBRTQC) algorithms provide many advantages over conventional QC approaches including lower cost, absence of commutability problems, continuous real-time monitoring of performance, and sensitivity to pre-analytical error. However, PBRTQC is not as simple to implement as conventional QC because of the requirement to access patient data as well as setting up appropriate rules, action protocols, and choosing best statistical algorithms. These requirements need capable and flexible laboratory informatics (middleware). In this document, the necessary features of software packages needed to support PBRTQC are discussed as well as recommendations for optimal integration of this technique into laboratory practice.

Background Eicosanoids are metabolites of arachidonic acid that are rapidly biosynthesized and degraded during inflammation, and their metabolic changes reveal altered enzyme expression following drug treatment. We developed an eicosanoid profiling method and evaluated their changes on drug treatment. Methods Simultaneous quantitative profiling of 32 eicosanoids in liver S9 fractions obtained from rabbits with carrageenan-induced inflammation was performed and validated by liquid chromatography-mass spectrometry coupled to anion-exchange solid-phase purification. Results The limit of quantification for the devised method ranged from 0.5 to 20.0 ng/mg protein, and calibration linearity was achieved (R²>0.99). The precision (% CV) and accuracy (% bias) ranged from 4.7 to 10.3% and 88.4 to 110.9%, respectively, and overall recoveries ranged from 58.0 to 105.3%. Our method was then applied and showed that epitestosterone treatment reduced the levels of all eicosanoids that were generated by cyclooxygenases and lipoxygenases. Conclusions Quantitative eicosanoid profiling combined with in vitro metabolic assays may be useful for evaluating metabolic changes affected by drugs during eicosanoid metabolism.

Drug combination testing in the pharmaceutical industry has typically been driven by late-stage opportunistic strategies rather than by early testing to identify drug combinations for clinical investigation that may deliver improved efficacy. A rationale for combinations exists across a number of diseases in which pathway redundancy or resistance to therapeutics are evident. However, early assays are complicated by the absence of both assay formats representative of disease biology and robust infrastructure to screen drug combinations in a medium-throughput capacity. When applying drug combination testing studies, it may be difficult to translate a study design into the required well contents for assay plates because of the number of compounds and concentrations involved. Dispensing these plates increases in difficulty as the number of compounds and concentration points increase and compounds are subsequently rolled onto additional labware. We describe the development of a software tool, in conjunction with the use of acoustic droplet technology, as part of a compound management platform, which allows the design of an assay incorporating combinations of compounds. These enhancements to infrastructure facilitate the design and ordering of assay-ready compound combination plates and the processing of combinations data from high-content organotypic assays.

Background Recent advances in laboratory information systems have largely been focused on automation. However, the phlebotomy services have not been completely automated. To address this issue, we introduced an automated reception and turnaround time (TAT) management system, for the first time in Korea, whereby the patient's information is transmitted directly to the actual phlebotomy site and the TAT for each phlebotomy step can be monitored at a glance. Methods The GNT5 system (Energium Co., Ltd., Korea) was installed in June 2013. The automated reception and TAT management system has been in operation since February 2014. Integration of the automated reception machine with the GNT5 allowed for direct transmission of laboratory order information to the GNT5 without involving any manual reception step. We used the mean TAT from reception to actual phlebotomy as the parameter for evaluating the efficiency of our system. Results Mean TAT decreased from 5:45 min to 2:42 min after operationalization of the system. The mean number of patients in queue decreased from 2.9 to 1.0. Further, the number of cases taking more than five minutes from reception to phlebotomy, defined as the defect rate, decreased from 20.1% to 9.7%. Conclusions The use of automated reception and TAT management system was associated with a decrease of overall TAT and an improved workflow at the phlebotomy room.

Objectives To identify inappropriate repeats of six common laboratory tests in a population sample of patients, using highly specific criteria based only on repeat time and test value. Methods We used a laboratory informatics database to conduct a retrospective cohort study using a population sample of 103,000 patients in the city of Calgary with an index test in 2010 and uniform follow-up of 1 year. We examined six tests (cholesterol, hemoglobin A1c, thyroid-stimulating hormone, vitamin B12, vitamin D, and ferritin) with consensus-based or easily justified criteria for inappropriate repeats based solely on time to repeat and the index test value. Results The percentages of tests repeated at 3, 6, and 12 months were 11%, 23%, and 41%, respectively. In total, 16% of these six tests were inappropriately repeated, representing an annual internal cost of $0.6 to $2.2 million Canadian dollars and corresponding to population-scaled national estimates for Canada and the United States of $160 million and $2.4 billion, respectively. Conclusions Objective definitions based on repeated testing identified 16% of six studied tests as inappropriate, delineating a subset of inappropriate testing that is well suited to automated identification and intervention and that provides a likely lower bound on the true burden of inappropriate testing.

Background: The identification of in vitro hemolysis (IVH) using a hematology analyzer is challenging because centrifugation of the specimens cannot be performed for cell counts. In the present study, we aimed to develop a scoring system to help identify the presence of hemolysis in anticoagulated blood specimens. Methods: Thirty-seven potassium EDTA anticoagulated blood specimens were obtained, and each specimen was divided into 3 aliquots (A, B, and C). Aliquots B and C were mechanically hemolyzed by aspirating 2 and 5 times, respectively, using a 27-gauge needle and then tested; aliquot A was analyzed immediately without any hemolysis. After the cells were counted, aliquots B and C were centrifuged and the supernatants were tested for the hemolytic index and lactate dehydrogenase levels. Results: The 4 hematologic parameters were selected and scored from 0 to 3 as follows

Harmonization initiatives in laboratory medicine seek to eliminate or reduce illogical variations in service to patients, clinicians and other healthcare professionals. Significant effort will be required to achieve consistent application of terminology, units and reporting across laboratory testing providers. Current variations in practice for nomenclature, reference intervals, flagging, units, standardization and traceability between analytical methods, and presentation of cumulative result data are inefficient and inconvenient, or worse yet, patient safety risks. All aspects of laboratory service across the “total testing process” ultimately depend on concise, reliable communication. Clinical terminologies (e.g. SNOMED-CT, LOINC, IFCC/IUPAC NPU) provide a mechanism to correctly identify an analyte or panel of tests within a request for testing and communicate the results back to the clinician or electronic health record (EHR). Electronic systems for requesting and reporting laboratory testing are said to be interoperable when reliable connection and communication of content occur. Modern electronic reports and EHRs will provide greater flexibility and functionality, but also require effective guidelines or standards to ensure consistent representation of laboratory data. Programs to harmonize service in these areas require ongoing local, national and international efforts and should incorporate stakeholders from laboratories, medical staff, information technology and informatics specialists, patient representatives and government. The process of identifying harmonized best practice, then ensuring uptake across many laboratory testing providers, is generally iterative rather than “one off”. New opportunities for additional harmonization will be generated as analytical performance, standardization and traceability, and diagnosis and treatment continue to evolve.

Background: Hemolysis, icterus, and lipemia (HIL) cause preanalytical interference and vary unpredictably with different analytical equipments and measurement methods. We developed an integrated reporting system for verifying HIL status in order to identify the extent of interference by HIL on clinical chemistry results. Methods: HIL interference data from 30 chemical analytes were provided by the manufacturers and were used to generate a table of clinically relevant interference values that indicated the extent of bias at specific index values (alert index values). The HIL results generated by the Vista 1500 system (Siemens Healthcare Diagnostics, USA), Advia 2400 system (Siemens Healthcare Diagnostics), and Modular DPE system (Roche Diagnostics, Switzerland) were analyzed and displayed on physicians’ personal computers. Results: Analytes 11 and 29 among the 30 chemical analytes were affected by interference due to hemolysis, when measured using the Vista and Modular systems, respectively. The hemolysis alert indices for the Vista and Modular systems were 0.1-25.8% and 0.1-64.7%, respectively. The alert indices for icterus and lipemia were

This perspective article considers the strategy, design and implementation of an electronic bioanalytical laboratory working to GLP and/or GCP regulations. There are a range of available automated systems and laboratory informatics that could be implemented and integrated to make an electronic laboratory. However, which are the appropriate ones to select and what is realistic and cost-effective for an individual laboratory? The answer is to develop an overall automation strategy that is updated periodically after each system or application has been implemented to assess if the strategy is still valid or needs to be changed. As many laboratory informatics applications have functional overlap or convergence, for example, Laboratory Information Management System, Electronic Laboratory Notebook, and Instrument and Chromatography Data Systems, the decision of which application performs a specific task needs to be carefully considered in the overall strategy. Ensuring data integrity and regulatory compliance, especially in light of a number of recent falsification cases, is a mandatory consideration for the overall strategy for an electronic bioanalytical laboratory submitting data to regulatory authorities.

Effective integration of data and laboratory informatics tools promises the ability for organizations to make better informed decisions about resource allocation during the drug discovery and development process, and for more informed decisions to be made with respect to the market opportunity for compounds. There are technologies on the horizon that could dramatically change how informatics organizations design, develop, deliver, and support applications and data infrastructures to deliver maximum value to drug discovery organizations. There are numerous benefits of integrating laboratory informatics tools like Laboratory Information Management System (LIMS), Chromatographic Data Systems (CDS), Electronic Laboratory Notebooks (ELN), and Analytical Instrumentation and Scientific Data Management Systems (SDMS) for drug discovery processes, but there is no well-established path for effective integration of these tools. We propose in this article four new integration models for effective integration of labor...

Background Documentation is very important; a considerable number of documents exist for use in accreditation inspection. However, most laboratories do not effectively manage the processes of documentation, organization, and storage. The purpose of this study was to facilitate the establishment of a strategically effective and sustainably standardized document management system. Methods A document code formatting system was modified by comparing the document list data received from 3 major university hospitals. In addition, a questionnaire regarding document code standardization was created and sent to 268 institutes to establish document classifications and generate a standard coding scheme. A computerized document management system was developed. Results Only 32% (8 out of 25 institutes) answered that they were able to identify all of the document types and their numbers. In total, 76% of institutes (19 out of 25) answered that a systematic document management system was necessary. Disorganized document files were systemized by classifying them into 8 major groups according to their characteristics: patient test records (T), test quality control (Q), manuals (M), equipment and environment management (E), statistics (S), division administration (A), department administration (R), and others (X). Conclusions Our documentation system may serve as a basis for the standardization of documents and the creation of a document management system for all hospital laboratories.

Electronic laboratory notebooks (ELNs) are increasingly replacing paper notebooks in life science laboratories, including those in industry, academic settings, and hospitals. ELNs offer significant advantages over paper notebooks, but adopting them in a predominantly paper-based environment is usually disruptive. The benefits of ELN increase when they are integrated with other laboratory informatics tools such as laboratory information management systems, chromatography data systems, analytical instrumentation, and scientific data management systems, but there is no well-established path for effective integration of these tools. In this article, we review and evaluate some of the approaches that have been taken thus far and also some radical new methods of integration that are emerging.

There are technologies on the horizon that could dramatically change how informatics organizations design, develop, deliver, and support applications and data infrastructures to deliver maximum value to drug discovery organizations. Effective integration of data and laboratory informatics tools promises the ability of organizations to make better informed decisions about resource allocation during the drug discovery and development process and for more informed decisions to be made with respect to the market opportunity for compounds. We propose in this article a new integration model called ELN-centric laboratory informatics tools integration.

Objective The objectives of this case report are as follows: to describe the process of establishing a national laboratory information management system (LIMS) program for clinical and public health laboratories in Vietnam; to evaluate the outcomes and lessons learned; and to present a model for sustainability based on the program outcomes that could be applied to diverse laboratory programs. Methods This case report comprises a review of program documentation and records, including planning and budgetary records of the donor, monthly reports from the implementer, direct observation, and ad-hoc field reports from technical advisors and governmental agencies. Additional data on program efficacy and user acceptance were collected from routine monitoring of laboratory policies and operational practices. Results LIMS software was implemented at 38 hospital, public health and HIV testing laboratories in Vietnam. This LIMS was accepted by users and program managers as a useful tool to support laboratory processes. Implementation cost per laboratory and average duration of deployment decreased over time, and project stakeholders initiated transition of financing (from the donor to local institutions) and of system maintenance functions (from the implementer to governmental and site-level staff). Collaboration between the implementer in Vietnam and the global LIMS user community was strongly established, and knowledge was successfully transferred to staff within Vietnam. Conclusion Implementing open-sourced LIMS with local development and support was a feasible approach towards establishing a sustainable laboratory informatics program that met the needs of health laboratories in Vietnam. Further effort to institutionalize IT support capacity within key government agencies is ongoing.

Background: Many laboratories use 4 delta check methods: delta difference, delta percent change, rate difference, and rate percent change. However, guidelines regarding decision criteria for selecting delta check methods have not yet been provided. We present new decision criteria for selecting delta check methods for each clinical chemistry test item. Methods: We collected 811,920 and 669,750 paired (present and previous) test results for 27 clinical chemistry test items from inpatients and outpatients, respectively. We devised new decision criteria for the selection of delta check methods based on the ratio of the delta difference to the width of the reference range (DD/RR). Delta check methods based on these criteria were compared with those based on the CV% of the absolute delta difference (ADD) as well as those reported in 2 previous studies. Results: The delta check methods suggested by new decision criteria based on the DD/ RR ratio corresponded well with those based on the CV% of the ADD except for only 2 items each in inpatients and outpatients. Delta check methods based on the DD/RR ratio also corresponded with those suggested in the 2 previous studies, except for 1 and 7 items in inpatients and outpatients, respectively. Conclusions: The DD/RR method appears to yield more feasible and intuitive selection criteria and can easily explain changes in the results by refl ecting both the biological variation of the test item and the clinical characteristics of patients in each laboratory. We suggest this as a measure to determine delta check methods.

Sociedade Brasileira de Patologia Clinica/Medicina Laboratorial (SBPC/ML) annually holds a Brazilian congress on its specialty. But why? The reasons are innumerable. At a scientific congress one can keep up-to-date and meet colleagues from other regions of the country and of the world. Technical scientific updating in the medical area is fundamental, considering that significant modifications rapidly occur in diagnostic procedures, with the development of more robust methods, and the exploitation of novel resources of automation and computing. It is in congresses that novelties are presented, either by well-qualified speakers, in lectures, conferences and round-table discussions, or by input and equipment companies. During such events, the possibilities are huge for exchange and acquisition of knowledge, directly from the generating sources, by the presence of eminent researchers.Meeting colleagues is always a reason for satisfaction and rejoicing; it strengthens friendship ties, and allows the sharing of everyday experiences. Interaction, though for just three or four days, with professionals from different areas of laboratory diagnosis, and from other medical specialties that make frequent use of the clinical laboratory, creates a highly productive setting where benefits and limitations can be clearly and informally discussed.Companies, manufacturers or distributers of input and equipment actively participate in the success of the congress by organizing a trade fair, where they display state-of-the-art devices, systems and methodologies. It is the opportunity not only to learn what is being presented, but to negotiate trade agreements.Soon, from September 29 to October 2, in Fortaleza, Ceara, the 49th Brazilian Congress of Clinical Pathology/Laboratory Medicine and the 1st Brazilian Congress of Laboratory Informatics will be held. The choice of Fortaleza as their seat was a dream come true for clinical pathologists and laboratory workers from the whole Northeast region of Brazil.The main theme of the Laboratory Medicine Congress will be “Integration for diagnosis”. It is the view that currently guides Laboratory Medicine, prizing integration among professionals from different areas and reflecting the reality of our days, with growing integration among the several diagnostic tools.The 1st Brazilian Congress of Laboratory Informatics will convene activities related to information technology in its own and simultaneous meeting, lasting one day, when participants will improve their knowledge without missing the scientific program of the event as a whole. For both congresses, 170 Brazilian and 10 foreign speakers are invited. A total of 24 conferences will be held, besides 45 round-table discussions, covering all areas of Laboratory Medicine. Approximately 122 companies, including manufacturers and distributors of clinical laboratory products, governmental entities of education and health, and private laboratories will be present, actively participating in all the activities.The chosen place, Centro de Eventos do Ceara (CEC), opened in 2012, is considered the most modern and well-equipped venue for events of this nature. The center has the ideal infrastructure for the congress, with a wide area for technical-scientific exhibitions, rooms, auditoriums, lounges and circulation areas that ensure participants’ comfort.In addition, the capital of Ceara, with many tourist attractions, has excellent hotel and restaurant facilities to host big events. The increased frequency of direct flights between Fortaleza (Aeroporto Internacional Pinto Martins) and European countries encouraged the participation of many foreign guests.Welcome and enjoy Fortaleza.

Biomedicine and health today are supported by a tightly woven interdisciplinary braid of (1) the discovery and use of information content, (2) its storage, management, and retrieval by information science (including the practice of librarianship) enabled by (3) the tools of information technology. Few specialists in one strand of the braid can work without some understanding of the other two strands. None have a monopoly on any one strand. Professional titles in research, education, and practice often are inadequate descriptions of the cross-disciplinary roles of their holders, or the actual practice of the professions. Some are medical librarians, health information managers, biomedical informaticists, and clinical informationists. Others work with controlled vocabularies, imaging and radiation therapy informatics, or business information systems. Biomedical informatics and bioinformatics related to human health include biosignals (including patient monitoring), laboratory informatics, pharmaceu...

Korea is known as a hepatitis B virus-endemic area with a high incidence of hepatocellular carcinoma (HCC) [1]. Alpha-fetoprotein (AFP) is the most widely used tumor marker for monitoring HCC in clinical practices. The serum AFP level is 400 ng/mL) [3, 4]. Tyson et al. [5] reported that 29% of patients with hepatitis C-related HCC had elevated AFP levels of >1,000 ng/mL. AFP levels are currently determined by immunoassay in most clinical laboratories. As the analytical measurement range (AMR) of AFP assay reagents cannot cover all the clinically important range of AFP levels, it is necessary to dilute and retest the specimens with high AFP levels. At our institution, we measure AFP levels by using the chemiluminescent microparticle immunoassay (ARCHITECH i2000SR system; Abbott Laboratories, Abbott Park, IL, USA) with the ARCHITECT AFP Reagent kit (Abbott Laboratories). The AMR of the assay reagent is 0.4-350 ng/mL. However, the manufacturer has made the following recommendation: if the AFP level of the original samples is >200 ng/mL, the original samples are automatically retested by the instrument with a fixed-dilution ratio of 1:16.7 to rule out "hook effect." In addition, if the AFP levels of auto-diluted samples are >5,845 ng/mL (350×16.7), the original samples are manually diluted. These dilution processes not only waste assay reagents but increase turnaround time (TAT) as well. Therefore, we developed an auto-dilution and manual dilution algorithm by using the laboratory information system (LIS) to minimize the number of AFP dilution analyses and reduce TAT. We developed an auto-dilution and manual dilution algorithm, taking into consideration both the measurement range of the AFP reagent and the fixed-dilution rate of the instrument (Fig. 1). When previous AFP results were not available or the previous AFP results were 5,000 ng/mL, corresponding sample racks were immediately ejected from the instrument with a particular flag sign, and the tests were subsequently performed following the manual dilution procedure conducted by laboratory personnel. Fig. 1 Flow chart of the auto-dilution and manual dilution algorithm for the alpha-fetoprotein (AFP) assay. The upper linearity limit of AFP assay without dilution is 200 ng/mL for the ARCHITECT AFP reagent kit. The 5,000 ng/mL is an arbitrary value that is ... In total, 11,297 samples were ordered for AFP assay from June to September 2012. Among them, the developed algorithm was evaluated using 10,947 samples, excluding 350 samples for prenatal screening. Previous AFP assay results were available for 8,745 of the total 10,947 samples (79.9%). Of these 8,745 samples, 479 (479/8,745; 5.5%), and 169 (169/8,745; 1.9%) had previous AFP assay results that were 200-5,000 ng/mL and >5,000 ng/mL, respectively. By applying the developed auto-dilution algorithm, one assay step could be omitted by automatically diluting the original samples with previous AFP results of 200-5,000 ng/mL (i.e., 479 samples). Starting from the time of aspiration of the sample in the instrument, it takes approximately 29 min to obtain the result of an AFP assay. As the original samples were not analyzed, the TAT could be shortened by more than 29 min in these samples. In no cases were the AFP values obtained by dilution analysis lower than the lowest limit of detection. Similarly, 2 assay steps, including the measurement of the original sample and the auto-dilution assay, could be omitted by manual dilution in samples with previous AFP results of >5,000 ng/mL (i.e., 169 samples). The TAT was shortened by more than 58 min in these cases. Consequently, 8.4% of the reagents could be conserved, and the TAT was shortened by 29 to 58 min by applying the auto-dilution algorithm in patients with previous AFP results. In conclusion, the LIS-based auto-dilution and manual dilution algorithm for the AFP assay shortened the TAT and conserved reagents. Application of this auto-dilution and manual dilution algorithm based on the patient's previous results to the automated immunoassay system could allow for more cost-effective laboratory practices in clinical laboratories.

Aim Our aim is to evaluate the performance of a computerized virtual crossmatch within the Duke University Medical Center HLA laboratory. Our HLA lab has used virtual crossmatch (vXM) to select deceased donors for heart and lung transplantations for more than ten years, which has allowed us to accept donors from outside of our Organ Procurement Organization territory. The virtual crossmatches were done by manually checking the recipient’s HLA antibody profiles within our lab database against the potential donor’s HLA typing to identify if the recipient has any donor-specific antibodies (DSA) in the most recent serum tested and in historical sera. To ensure no DSA was missed, the vXM was manually done by multiple transplant professionals at different stages for each sensitized recipient when a donor offer was available. Laboratory informatics vendor HLA Data Systems, developers of the mTilda Lab Management System, has developed a stand-alone software program which performs a computerized vXM (cVXM) under the product name VxMatch. The VxMatch program directly connects to any HLA lab database to query required data for analysis. Methods We performed 56 cVXMs by using the new program for patients who had previously received manual vXMs (mVXM) over the past few months. 35 of the 56 patients have calculated panel reactive antibodies (cPRA) = >80%. Results We found a 100% concordance for identification of DSA between cVXM and mVXM. It took less than 5 min to complete the cVXM while the conventional mVXM took 30 min on average. For each identified unacceptable antigen, the cVXM program provides detailed information, including antibody specificities, mean fluorescence intensity (MFI), serum date and a graph showing the MFI changes of DSA over time. The mTilda cVXM can operate in two different modes: a technologist’s level and supervisory level. The supervisory module allows us to review each individual bead carrying potential unacceptable HLA antigen at alpha chain, beta chain, or allele level. This cVXM can also be used to identify the sera (for example the serum with peak DSA) for final XM and the ability to track the change of DSA post-transplant. Conclusion Our evaluation suggests that this new computerized vXM program is a user-friendly, reliable and powerful tool for HLA testing and management.

A transformation affecting the workflow and information management in microbiology laboratories is the shift from diagnostic testing based on culture, antigen detection, antibody detection, and microscopy to a greater dependence upon molecular technologies. The responsibilities of the microbiology laboratory leadership team are becoming more informatics-centric as well. This chapter reviews the principles of laboratory informatics and the architecture of information system. A laboratory information system (LIS) consists of one or more servers that provide the array of services, and the information entered into, stored within, and reported from the LIS is directly or indirectly related to laboratory testing. Typically encountered interfaces between the LIS and other information systems include admission/discharge/transfer (ADT) interface and order-entry interface. Long-term storage and retrieval of laboratory data can be easily accommodated by a suitably configured LIS. The current emphasis by payors and healthcare accrediting agencies on utilization review of laboratory services and quality assurance analysis of laboratory testing requires that laboratory activity be evaluated on a regular basis. The chapter discusses the manner in which the LIS can serve to enhance the cost-effectiveness and accuracy of microbiology testing. The clinical laboratory, including the microbiology laboratory, is an ideal candidate for lean/Six Sigma reorganization. Leveraging the capabilities of the LIS to track bar-coded specimens, to connect with testing instruments to improve error-free data flow, and to display laboratory productivity snapshots on workstation dashboards are all important components of a program to pursue excellence in laboratory testing.

With the recent results of promising cancer vaccines and immunotherapy 1 – 5 , immune monitoring has become increasingly relevant for measuring treatment-induced effects on T cells, and an essential tool for shedding light on the mechanisms responsible for a successful treatment. Flow cytometry is the canonical multi-parameter assay for the fine characterization of single cells in solution, and is ubiquitously used in pre-clinical tumor immunology and in cancer immunotherapy trials. Current state-of-the-art polychromatic flow cytometry involves multi-step, multi-reagent assays followed by sample acquisition on sophisticated instruments capable of capturing up to 20 parameters per cell at a rate of tens of thousands of cells per second. Given the complexity of flow cytometry assays, reproducibility is a major concern, especially for multi-center studies. A promising approach for improving reproducibility is the use of automated analysis borrowing from statistics, machine learning and information visualization 21 – 23 , as these methods directly address the subjectivity, operator-dependence, labor-intensive and low fidelity of manual analysis. However, it is quite time-consuming to investigate and test new automated analysis techniques on large data sets without some centralized information management system. For large-scale automated analysis to be practical, the presence of consistent and high-quality data linked to the raw FCS files is indispensable. In particular, the use of machine-readable standard vocabularies to characterize channel metadata is essential when constructing analytic pipelines to avoid errors in processing, analysis and interpretation of results. For automation, this high-quality metadata needs to be programmatically accessible, implying the need for a consistent Application Programming Interface (API). In this manuscript, we propose that upfront time spent normalizing flow cytometry data to conform to carefully designed data models enables automated analysis, potentially saving time in the long run. The ReFlow informatics framework was developed to address these data management challenges.

Background: Laboratory data can provide a wide range of information to estimate adherence to guidelines and proper utilization of genetic testing. The methylene tetrahydrofolate reductase (MTHFR) C677T variant has been demonstrated to have negligible utility in patient management. However, the testing of this variant remains pervasive. The purpose of this study was to develop methods to analyze concordance of clinician ordering practices with national guidelines. Methods: We used laboratory data to extract specific data elements including patient demographics, timestamps, physician ordering logs and temporal relationship to chemistry requests to examine 245 consecutive MTHFR tests ordered in 2011 at an academic tertiary center. A comprehensive chart review was used to identify indications for testing. These results were correlated with a retrospective analysis of 4,226 tests drawn at a range of hospitals requesting testing from a national reference laboratory over a 2-year period. MTHFR ordering practices drawn from 17 institutions were examined longitudinally from 2002 to 2011. Results: Indications for testing included cerebrovascular events (40.0%) and venous thrombosis (39.1%). Family history prompted testing in eight cases. Based on acceptable hypercoagulability guidelines recommending MTHFR C677T testing only in the presence of elevated serum homocysteine, 10.6% (22/207) of adult patients met an indicated threshold at an academic tertiary center. Among 77 institutions, 14.5% (613/4226) of MTHFR testing met recommendations. Conclusion: We demonstrate an effective method to examine discreet elements of a molecular diagnostics laboratory information system at a tertiary care institution and to correlate these findings at a national level. Retrospective examination of clinicians′ request of MTHFR C677T genetic testing strongly suggests that clinicians have failed to adjust their ordering practices in light of evolving scientific and professional organization recommendations.

Graphical dot-matrix plots can provide the most complete and detailed comparison of two sequences. Presented here is DOTTER2, a dot-plot program for X-windows which can compare DNA or protein sequences, and also DNA versus protein. The main novel feature of DOTTER is that the user can vary the stringency cutoff interactively, so that the dot-matrix only needs to be calculated once. This is possible thanks to a ‘Greyramp tool’ that was developed to change the displayed stringency of the matrix by dynamically changing the greyscale rendering of the dots. The Greyramp tool allows the user to interactively change the lower and upper score limit for the greyscale rendering. This allows exploration of the separation between signal and noise, and fine-grained visualization of different score levels in the dot-matrix. Other useful feature are dot-matrix compression, mouse-controlled zooming, sequence alignment display and saving/loading of dot-matrices. Since the matrix only has to be calculated once and since the algorightm is fast and linear in space, DOTTER is practical to use even for sequences as long as cosmids. DOTTER was integrated in the gene-modelling module of the genomic database system ACEDB. This was done via the homology viewer BLIXEM in a way that also allows segments from the BLAST suite of searching programs to be superimposed on top of the full dot-matrix. This feature can also be used for very quick finding of the strongest matches. As examples, we analyse a Caenorhabditis elegans cosmid with several tandem repeat families, and illustrate how DOTTER can improve gene modelling.

Directing a cytology laboratory is one of the most complex jobs in the laboratory. The workflow is complex due to the extensive quality assurance and other regulatory requirements imposed by the clinical laboratory improvement Act of 1988 (CLIA 1988) in addition to the usual tasks of accessioning, processing, routing different specimen types appropriately, and reporting. The advent of the CLIA 1988 regulations made it virtually mandatory that cytology laboratories be computerized to effectively manage their workflow and efficiently compile and summarize the quality assurance data necessary to meet the CLIA 1988 mandates. Practical informatics for cytopathology is a brief (204 pages), informative book which provides a succinct introduction to all aspects of informatics pertinent to cytology laboratories. It will be most helpful to the cytotechnologist or cytopathologist who has a directorial or supervisory role and who has the task of interfacing with the computer professionals in a clinic or hospital, or representing the cytology section when a laboratory is evaluating and comparing candidate systems to replace an existing system. It is not a comprehensive textbook covering the topic in sufficient detail for someone training to be a laboratory informatics professional. However, the reader of this book will have a basic understanding of the terminology and concepts of informatics in discussions with information technology professionals. While all of the chapters provide suitable introductions to their topics, several are especially useful for those who are seeking to quickly familiarize themselves with the basic concepts that are relevant to a specific topic. The introductory chapter gives a short overview of the field, mentions the major federal regulatory acts that pertain to laboratory informatics and provides the names and websites of the major professional societies and other resources. The next two chapters cover basic principles of computing and networking at a very basic level, but with enough detail to allow the informatics beginner to have an idea about what is happening “under the hood” in a computer, and to be able to follow the conversation in a system planning meeting with the institution's informatics team. The next chapter discusses various types of databases. This chapter clarifies the distinction between spreadsheets (which are “flat” databases) and other types of databases that are commonly used in laboratories such as hierarchical and relational. This chapter also provides explanations of data warehouses and data mining, both terms which are likely to be heard in discussions of laboratory informatics. The next four chapters address “laboratory information systems (LISs),” “LIS operations and regulations,” “reporting,” and “quality management.” In the aforementioned context of a cytology supervisor or laboratory director who needs to quickly familiarize him or herself with basic concepts of laboratory informatics pertinent to cytopathology, these four chapters are probably the most useful in the book. Chapter 6 covers most of the important concepts necessary for understanding the architecture of LISs. Chapter 7 addresses the regulatory requirements pertinent to LISs, and the basic concepts pertinent to ongoing maintenance of a system. Chapter 8 briefly discusses the building of reports in an LIS, a topic with more complexity than one might think. Chapter 9 addresses quality management. The introduction of the CLIA regulatory requirements over the two decades ago adds such complexity to quality management that computerization of the laboratory is all but required. Helpful examples are provided such as for cytology–histology correlation. The relation between reporting, quality management, and database architecture is not discussed, but admittedly such a discussion might have been beyond the scope of this work. The quality management chapter also provides a brief list of references which will be of interest to many readers. The other chapters lack such a reference list and although there is a short and well-chosen list of references at the end of the book, the reader who wishes to dig deeper into a particular area will need to search on their own. Fortunately, with online search tools, this will not be terribly difficult. Other chapters of general interest are devoted to telecytology, coding (CPT, ICD10, and SNOMED), barcoding, and digital imaging. Telecytology is of increasing relevance due to the increasing requests for rapid onsite evaluation for specimen adequacy of specimens procured by endoscopists, radiologists, or other clinicians. Telecytology allows such evaluations to be performed remotely, and thus utilizes the cytopathologists’ time more efficiently. Many cytologists will already have some familiarity with coding; however, barcoding is a “black box” to many, and the chapter on that topic shines a little light inside it. The chapter on digital imaging provides a good explanation of the basics principles of digital imaging including whole slide imaging as well as some direction on how to improve suboptimal images, but additional detail would have been helpful in this section and would not have been beyond the scope of the book. There are also chapters on project management, informatics projects, research informatics, bioinformatics, Lean Six Sigma, electronic medical records, automated cytology, and online cytology resources. At the end of the book, there is a listing of key definitions and recommended readings. In summary, practical informatics for cytopathology provides an introduction to informatics as applied to cytopathology. Cytologists who are not conversant with informatics will find it informative, and some will be inspired to delve deeper into the topic after reading this book.

Over 70% of clinical decisions are based on laboratory data, according to some surveys. Given the critical role that laboratory information plays in patient care, it is imperative that laboratories have effective systems for collecting, managing, storing, analyzing, and distributing this data. This article first provides a general overview of the flow of information to and from the laboratory and the steps involved in laboratory testing. Next, it describes the key role that information systems play in each of these steps. Subsequent sections describe some of the “behind-the-scenes” aspects of laboratory informatics, providing an outline of the data structures and standards that support laboratory information management, as well as providing an overview of exciting emerging technologies, including medical language processing and digital image analysis. Keywords: clinical informatics; laboratory informatics; laboratory information system; medical vocabulary; medical language processing; digital microscopy; digital image; quality control; resource utilization; provider order entry

George Gallatig and John Petrakis Introducing a standardized enterprise-wide solution can lower the total cost of ownership (TCO) for laboratory information management systems (LIMSs). Electronic notebooks (ELNs) can improve the personal productivity of analysts working in research and quality-control laboratories. Data management and data warehouse systems provide ready access to information, and can help reduce search time and duplication of effort by knowledge workers. Providing integrated analytical tool kits and training for scientists can reduce some of the chaos, support costs for research, and provide new opportunities for sharing and building on innovative ideas. We intuitively know that there is value in implementing these laboratory informatics solutions. These solutions help companies in all industries to produce better products with shorter development cycle times and at lower cost. However, business decisions to acquire them have to be based on the review of a business case including a cost justification. This presentation will present ideas and a model for calculating the benefits for laboratory informatics solutions. The model will include rules of thumb based on industry experience for projecting productivity improvements resulting from the introduction of technology to replace functions typically performed manually like data entry, data access, or compilation of reports. However, projections of productivity improvement are only part of the story. These need to be translated into actual benefits that are measurable by the corporation in terms of speed, productivity, or cost. The author will describe strategies for accomplishing this. These will be supported by examples. This will be a valuable presentation for anyone involved in looking at the impact of the introduction of laboratory informatics technology, whether developing a business case or looking at benefits being captured by systems that have been implemented.

Laboratory informatics is the application of computers and information systems to information management in the pathology laboratory. Effective information management is crucial to the success of pathologists and laboratorians. Informatics has become one of the key pillars of pathology, and the requirement for skilled informaticists in the laboratory has quickly grown. This article provides a wide-ranging review of pertinent aspects of laboratory informatics, and deals with important technical and management processes. Topics covered include personal computing, networks, databases, fundamentals and advanced functions of the laboratory information system, interfaces and standards, digital imaging, coding, hospital information systems and electronic medical records.

The LabBase and LabFlow systems described in this chapter are the latest in a series of systems we have built to tackle the problems of data management and workflow management for large scale biological research projects. We and our colleagues have used the predecessor systems for several projects at the Whitehead/MIT Center for Genome Research and are beginning to use the current systems for projects there and elsewhere. Though the software is incomplete in many ways, it is proven technology that in our hands, at least, greatly reduces the work of creating laboratory informatics systems.

The primary objective of clinical laboratorians is to provide the highest possible quality of service to patients and those who care for patients. High-quality service encompasses accurate and precise analysis, timely, clear, and concise reporting, and delivery of the service to a location in a format most valuable to the user of the service. Quality has also come to include elements of efficiency, effectiveness, analysis of diagnostic utility, and decision support.1,2 Delivery of the service has come to mean that integration into a comprehensive electronic medical record (EMR) is to be expected.3,4 Although it is widely accepted that about 70% of the information used in the management of patients comes from the clinical and anatomical pathology laboratories,5 in one large medical center in which information flow is tracked, about 94% of requests to the EMR are for laboratory results.4 In addition, a critical quality feature is the transformation of laboratory data into information.2,5,6–8

Aim The Hema-Quebec HLA laboratory and stem cell donor registry performs HLA typing and donor search for more than 250 patients per year. We also do HLA typing for our cord blood registry (2000/year) and our stem cell donor registry (2000/year). Before February 2012, all the results from these activities and the follow up were done by paper work without informatics system support, thus increasing the risks for file loss and errors. In 2011, decision was taken to introduce a laboratory informatics system (LIS) to improve security and efficiency of the HLA laboratory and the cord blood and donor registries. Methods A French company, Inlog, was chosen to develop informatics modules which suit our needs. Three modules were developed: EdgeLab for the patient, donor, and cord blood unit HLA files; EdgeCell for the patient and donor files, the search activities, the data bank for donors, and the data bank and processing file for cord blood units; and EdgeLink to get these two first modules connected together and allow the transfer of information and results. The laboratory instruments have been interfaced and the majority of the laboratory forms have been integrated to reduce transcription. Results The EdgeLab module was implemented at the end of February 2012, following the EdgeCell module. The adaptation period for the staff extended through June 2012 where modifications to the system were needed. After this point, we could observe a clear decrease in unnecessary analysis repeats, non-conformance reports, paper work, and most of all in our turnaround time. Our delays for urgent typing could be reduced to almost half the time. A reorganization of the workflow was possible and allows us to increase our volume of HLA typing by more than 40%. Conclusions The benefit of a LIS implementation is obvious. Better control and turnaround time is achieved while the capacity of the HLA lab is increased.

Sir, Pathology informatics is now recognized as an important component of pathology training.[1,2] Learning objectives and rotations in informatics have been established in an effort to train pathology residents.[3,4] Educated residents and formally trained informatics fellows play an important role in the future of this specialty. However, the success of pathology informatics also relies on the competencies of their allies (pathology assistants, cytotechnologists, medical technologists) in informatics. While the American Society of Clinical Pathologists (ASCP) offers some informatics training to medical technologists through its “Qualification in Laboratory Informatics” program, unfortunately insufficient attention has been dedicated toward training the various technologists in the field of pathology. The Anisa I. Kanbour School of Cytotechnology at the University of Pittsburgh Medical Center (UPMC) recently updated their curriculum to include a course in informatics for its cytotechnology students. The hospital-based, 12-month program for postbaccalaureate biology graduates has traditionally been based mainly on training in morphology and limited to ancillary studies. However, in order to keep abreast with changes in the practice of cytopathology (e.g., molecular pathology and informatics),[5,6] modifications of the curriculum were deemed necessary to reflect current practices. In addition to keeping pace with evolving technologies in the field, impetus for this change in cytotechnology student training was partially market driven. Demands for new graduates who have a more diverse technical background than just morphologic skills are more desirable first-hires. In response to changing skill requirements, the American Society of Cytopathology (ASC) published a white paper in 2010 regarding the future needs of the profession.[7] The ASC commissioned the Forbes group whose findings outlined forces that might lead to the emergence of new professions or roles in cytology. The group emphasized the need to create new skills and expanding traditional roles merging morphologic skills with new technologies for the profession's survival. Professional predictions of traditional microscopy obsolescence, new guidelines calling for less frequent Pap testing, and the digitization of proficiency testing[8] necessitated course modernization. As a result, eight cytotechnology students were exposed to pathology informatics practices and technologies in the form of an interactive 2-day course. To the best of our knowledge, the school of cytotechnology at UPMC is currently the first of 31 accredited programs in the USA to offer a structured, formal informatics course. The course was provided by the collaborative effort between the school of cytotechnology and informatics division in the department of pathology. The goals of this course were to introduce the students to the fundamentals of pathology informatics (e.g., terminology, basic computing, coding, data management, etc.), explain and demonstrate to them various information technologies (e.g., laboratory information systems, digital imaging, telecytology, etc.), and offer them “hands-on” experiences (e.g., scanning glass slides to create whole slide images, perform internet literature searches). Students were required to construct a presentation of an interesting case in which they inserted both static and virtual images into the final report. The course was well received by the students who completed a questionnaire about it. The course evaluations indicated the participants’ overall satisfaction, with only slight reservation concerning the impact informatics will play in their future practices. Following the course, students were more comfortable with digital imaging, and even able to access the institution's digital slide teaching sets in preparation for their final examinations [Figure 1]. While informatics training may be considered important by many technologist training programs, inadequate resources and lack of formal, structured programs may limit training. Therefore, we recommend that programs begin to partner with pathology departments who have informatics resources to leverage their faculty and equipment such as whole slide scanners. In the near future we can anticipate that well-trained cytotechnologists will begin to fill a niche for informatics within pathology departments. Figure 1 Example of a digital slide teaching set for cytotechnology students

Genetic medicine is poised to revolutionise healthcare. No medical specialty field will be more transformed by the use of genetic technology and genetic knowledge than pathology and laboratory medicine. To help pathologists and laboratory professionals understand the strategic implications of these developments, this presentation will provide an overview of how health system dynamics, financial considerations, and advances in genetic technology will drive forward the clinical acceptance and use of molecular technologies in pathology testing services. Themes to be discussed include how new genetic technologies will be incorporated into diagnostic testing services, market adoption paths for personalised medicine and companion diagnostics, and the role of laboratory informatics in linking laboratories with referring clinicians. Opportunities for pathology to participate as a collaborative diagnostic service will be identified. Pathologists will gain a strategic understanding of the major trends in healthcare and how these trends will support advancements in molecular diagnostics. Information and concepts presented will complement the presentations which follow during this session.

The mouse N-ethyl-N-nitrosourea (ENU) mutagenesis program at the Genomics Institute of the Novartis Research Foundation (GNF) uses MouseTRACS to analyze phenotype screens and manage animal husbandry. MouseTRACS is a Web-based laboratory informatics system that electronically records and organizes mouse colony operations, prints cage cards, tracks inventory, manages requests, and reports Institutional Animal Care and Use Committee (IACUC) protocol usage. For efficient phenotype screening, MouseTRACS identifies mutants, visualizes data, and maps mutations. It displays and integrates phenotype and genotype data using likelihood odds ratio (LOD) plots of genetic linkage between genotype and phenotype. More detailed mapping intervals show individual single nucleotide polymorphism (SNP) markers in the context of phenotype. In addition, dynamically generated pedigree diagrams and inventory reports linked to screening results summarize the inheritance pattern and the degree of penetrance. MouseTRACS displays screening data in tables and uses standard charts such as box plots, histograms, scatter plots, and customized charts looking at clustered mice or cross pedigree comparisons. In summary, MouseTRACS enables the efficient screening, analysis, and management of thousands of animals to find mutant mice and identify novel gene functions. MouseTRACS is available under an open source license at http://www.mousetracs.sourceforge.net. Electronic Supplementary Material Electronic Supplementary material is available for this article at http://dx.doi.org/10.1007/s00335-005-1145-1 and accessible for authorised users.