Proceedings of the Association for Pathology Informatics Bootcamp 2022.

The Pathology Informatics Bootcamp, held annually at the Pathology Informatics Summit, provides pathology trainees with essential knowledge in the rapidly evolving field of Pathology Informatics. With a focus on data analytics, data science, and data management in 2022, the bootcamp addressed the growing importance of data analysis in pathology and laboratory medicine practice. The expansion of data-related subjects in Pathology Informatics Essentials for Residents (PIER) and the Clinical Informatics fellowship examinations highlights the increasing significance of these skills in pathology practice in particular and medicine in general. The curriculum included lectures on databases, programming, analytics, machine learning basics, and specialized topics like anatomic pathology data analysis and dashboarding.

Machine Learning in Laboratory Medicine: Recommendations of the IFCC Working Group.

BACKGROUND: Machine learning (ML) has been applied to an increasing number of predictive problems in laboratory medicine, and published work to date suggests that it has tremendous potential for clinical applications. However, a number of groups have noted the potential pitfalls associated with this work, particularly if certain details of the development and validation pipelines are not carefully controlled. METHODS: To address these pitfalls and other specific challenges when applying machine learning in a laboratory medicine setting, a working group of the International Federation for Clinical Chemistry and Laboratory Medicine was convened to provide a guidance document for this domain. RESULTS: This manuscript represents consensus recommendations for best practices from that committee, with the goal of improving the quality of developed and published ML models designed for use in clinical laboratories. CONCLUSIONS: The committee believes that implementation of these best practices will improve the quality and reproducibility of machine learning utilized in laboratory medicine. SUMMARY: We have provided our consensus assessment of a number of important practices that are required to ensure that valid, reproducible machine learning (ML) models can be applied to address operational and diagnostic questions in the clinical laboratory. These practices span all phases of model development, from problem formulation through predictive implementation. Although it is not possible to exhaustively discuss every potential pitfall in ML workflows, we believe that our current guidelines capture best practices for avoiding the most common and potentially dangerous errors in this important emerging field.

System Performance Monitoring in Clinical Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS).

Quality assurance (QA) activities enable continuous improvement through ongoing post-implementation monitoring to identify, evaluate, and correct problems. QA for clinical liquid chromatography tandem mass spectrometry (LC-MS/MS) assays should include specific components that address the unique aspects of these methods. This chapter briefly describes approaches for clinical LC-MS/MS system performance monitoring using batch and peak review metrics, largely following CLSI-C62A guidance. Though routine checks ensure the quality of results reported for each run, there is also a need to evaluate metrics between runs over time. Post-implementation performance monitoring of LC-MS/MS methods is typically focused on calibration curves, retention times, peak intensities, and ion ratios.

Quantification of Branched-Chain Amino Acids in Plasma by High-Performance Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS).

Branched-chain amino acids (BCAA), including valine, alloisoleucine, isoleucine, and leucine, play significant roles in a number of metabolic pathways in the body. Deficiency in branched-chain ketoacid dehydrogenase complex, an enzyme required for metabolism of those amino acids, will lead to elevation and accumulation of BCAA and ketoacids in bodily fluids. This results in maple syrup urine disease (MSUD), a condition estimated to affect 1 in 100,000-300,000 births. If MSUD is not diagnosed in the first few days of life, progression of this disease can lead to intellectual disability, coma, irreversible brain damage, seizures, or even death. If diagnosed early, MSUD can be managed by monitoring the blood concentrations of BCAA and adjusting the patient's dietary intake accordingly. Therefore, it is critical to have a rapid, accurate, and reliable BCAA assay for confirmation of MSUD in newborns as well as routine monitoring of MSUD patients. Here, we describe a high-performance liquid chromatography tandem mass spectrometry (LC-MS/MS) method for BCAA measurement which requires only 20 µL of plasma. The sample preparation does not require derivatization and only involves protein precipitation with LC/MS-grade methanol, which contains leucine(13C6;15N), isoleucine(13C6;15N), and valine(13C5;15N) as the internal standards. The final sample extracts do not require dry-down and reconstitution and are readily compatible with the liquid chromatography (LC) method. BCAA are separated using the isocratic gradient method on a mixed-mode Intrada column. Multiple-reaction monitoring (MRM) mode is used for MS/MS detection to monitor the parent-to-daughter transitions m/z 132.2 to 86.4 for leucine, isoleucine, and alloisoleucine; m/z 118.2 to 72.4 for valine; m/z 139.2 to 92.4 for leucine(13C6;15N) and isoleucine(13C6;15N); and m/z 124.2 to 77.4 for valine(13C5;15N).

The Impact of COVID-19 on Laboratory Test Utilization at a Pediatric Medical Center.

BACKGROUND: The epidemiology and clinical manifestation of coronavirus disease 2019 (COVID-19) in the pediatric population is different from the adult population. The purpose of this study is to identify effects of the COVID-19 pandemic on laboratory test utilization in a pediatric hospital. METHODS: We performed retrospective analysis on test utilization data from Ann & Robert H. Lurie Children's Hospital of Chicago, an academic pediatric medical center. Data between two 100-day periods prior to (prepandemic) and during the pandemic (mid-pandemic) were analyzed to evaluate changes in test volume, lab utilization, and test positivity rate. We also evaluated these metrics based on in- vs outpatient testing and performed modeling to determine what variables significantly impact the test positivity rate. RESULTS: During the pandemic period, there was an expected surge in COVID-19 testing, while over 84% of lab tests studied decreased in ordering volume. The average number of tests ordered per patient was not significantly different during the pandemic for any of the laboratories (adjusted P value > 0.05). Thirty-three studied tests showed significant change in positivity rate during the pandemic. Linear modeling revealed test volume and inpatient status as the key variables associated with change in test positivity rate. CONCLUSIONS: Excluding severe acute respiratory syndrome coronavirus 2 tests, the COVID-19 pandemic has generally led to decreased test ordering volume and laboratory utilization. However, at this pediatric hospital, the average number of tests performed per patient and test positivity rates were comparable between pre- and mid-pandemic periods. These results suggest that, overall, clinical test utilization at this site remained consistent during the pandemic.

A rapid LC-MS/MS assay for detection and monitoring of underivatized branched-chain amino acids in maple syrup urine disease.

Introduction: Quantitation of the isomeric branched-chain amino acids (BCAA; valine, alloisoleucine, isoleucine, leucine) is a challenging task that typically requires derivatization steps or long runtimes if a traditional chromatographic method involving a ninhydrin ion pairing reagent is used. Objectives: To develop and perform clinical validation of a rapid, LC-MS/MS-based targeted metabolomics assay for detection and monitoring of underivatized BCAA in human plasma. Methods: Various columns and modes of chromatography were tested. The final optimized method utilized mixed mode chromatography with an Intrada column under isocratic condition. Sample preparation utilized the 96-well format. Briefly, extraction solvent containing the internal standard is added to 20 uL of sample, followed by shaking and positive pressure filtering, and the resulting extracted sample is analyzed. The assay was validated based on accepted quality standards (e.g., CLIA and CLSI) for clinical assays. Results: The method is linear over a wide range of concentrations, 2.0-1500 µM, with LOD of 0.60 µM and LOQ of 2.0 µM. The precision of the assay was 4-10% across analytes. The method was also validated against reference laboratories via blinded split-sample analysis and demonstrated good agreement with accuracy: 89-95% relative to the external group mean. Conclusion: We have developed a method that is accurate, rapid, and reliable for routine clinical testing of patient sample BCAA, which is used in the diagnosis and management of maple syrup urine disease (MSUD). The assay also has desirable characteristics, such as short run time, small sample volume requirement, simple sample preparation without the need for derivatization, and high throughput.

Create laboratory business intelligence dashboards for free using R: A tutorial using the flexdashboard package.

This tutorial described use of the R flexdashboard package and its possibilities for customization to develop a dashboard to monitor critical result reporting in a clinical laboratory. Several examples of interactive components were demonstrated. Sample code and exercises were provided to facilitate learning.

Rise of the Machines: Artificial Intelligence and the Clinical Laboratory.

BACKGROUND: Artificial intelligence (AI) is rapidly being developed and implemented to augment and automate decision-making across healthcare systems. Being an essential part of these systems, laboratories will see significant growth in AI applications for the foreseeable future. CONTENT: In laboratory medicine, AI can be used for operational decision-making and automating or augmenting human-based workflows. Specific applications include instrument automation, error detection, forecasting, result interpretation, test utilization, genomics, and image analysis. If not doing so today, clinical laboratories will be using AI routinely in the future, therefore, laboratory experts should understand their potential role in this new area and the opportunities for AI technologies. The roles of laboratorians range from passive provision of data to fuel algorithms to developing entirely new algorithms, with subject matter expertise as a perfect fit in the middle. The technical development of algorithms is only a part of the overall picture, where the type, availability, and quality of data are at least as important. Implementation of AI algorithms also offers technical and usability challenges that need to be understood to be successful. Finally, as AI algorithms continue to become available, it is important to understand how to evaluate their validity and utility in the real world. SUMMARY: This review provides an overview of what AI is, examples of how it is currently being used in laboratory medicine, different ways for laboratorians to get involved in algorithm development, and key considerations for AI algorithm implementation and critical evaluation.

Soft, skin-interfaced sweat stickers for cystic fibrosis diagnosis and management.

The concentration of chloride in sweat remains the most robust biomarker for confirmatory diagnosis of cystic fibrosis (CF), a common life-shortening genetic disorder. Early diagnosis via quantitative assessment of sweat chloride allows prompt initiation of care and is critically important to extend life expectancy and improve quality of life. The collection and analysis of sweat using conventional wrist-strapped devices and iontophoresis can be cumbersome, particularly for infants with fragile skin, who often have insufficient sweat production. Here, we introduce a soft, epidermal microfluidic device ("sweat sticker") designed for the simple and rapid collection and analysis of sweat. Intimate, conformal coupling with the skin supports nearly perfect efficiency in sweat collection without leakage. Real-time image analysis of chloride reagents allows for quantitative assessment of chloride concentrations using a smartphone camera, without requiring extraction of sweat or external analysis. Clinical validation studies involving patients with CF and healthy subjects, across a spectrum of age groups, support clinical equivalence compared to existing device platforms in terms of accuracy and demonstrate meaningful reductions in rates of leakage. The wearable microfluidic technologies and smartphone-based analytics reported here establish the foundation for diagnosis of CF outside of clinical settings.

7 Is the New 8: Improving Adherence to Restrictive PRBC Transfusions in the Pediatric ICU.

Up to 30%-40% of children admitted to the pediatric intensive care unit (PICU) have anemia, and approximately 15% receive packed red blood cell (pRBC) transfusions. Current literature supports a pRBC transfusion threshold of hemoglobin less than or equal to seven for most PICU patients. Our objective was to determine pRBC transfusion rates, assess compliance with transfusion guidelines, understand patient-level variables that affect transfusion practices, and use cross-industry innovation to implement a practice strategy. This was a pre-post study of pediatric patients admitted to our PICU. We collected baseline data on pRBC transfusion practices. Next, we organized an innovation platform, which generated multi-industry ideas and produced an awareness campaign to effect pRBC ordering behavior. Innovative educational interventions were implemented, and postintervention transfusion practices were monitored. Statistical analysis was performed using linear mixed models. A p value < .05 was considered statistically significant. At baseline, 41% of pRBC transfusions met restrictive transfusion guidelines with a pretransfusion hemoglobin less than or equal to 7 g/dl. In the postintervention period, 53% of transfusions met restrictive transfusion guidelines (odds ratio 1.66, 95% confidence interval 1.21-2.28). Implementation of a behavioral campaign using multi-industry innovation led to improved adherence to pRBC transfusion guidelines in a tertiary care PICU.

Automation of chromatographic peak review and order to result data transfer in a clinical mass spectrometry laboratory.

INTRODUCTION: Mass spectrometry-based assays have increasingly been implemented in clinical laboratories for their multiplexing capacity and high specificity and sensitivity. However, these methods are often associated with labor-intensive and error-prone data-related workflows, due to the volume of data generated that is often manually reviewed and resulted. We aimed to establish a system within our clinical mass spectrometry laboratory to facilitate data 'flow' from electronic medical record order to result and to automate processes for chromatogram peak review. The processes and validation are described for a 25-hydroxyvitamin D assay. METHODS: Automating chromatogram review and order to result data transfer required flat file interfacing, file transfers of standardized data formats, barcode scanning, and software for peak processing and review. Validation of the automated workflow involved (1) correlation of quantified results generated by two chromatogram analysis methods: Waters TargetLynx and Indigo Bioautomation ASCENT, (2) manual verification of quality assurance flags applied in ASCENT, and (3) testing data flow and integrity across all the systems from order to result. Efficiency and quality improvements were assessed through calculation of batch review times and rates for autoverification and manual manipulations. RESULTS: The correlation of TargetLynx and ASCENT quantitation methods for 25-hydroxyvitamin D2 in patient samples yielded slope of 0.99 (95% CI: 0.989 to 0.996), intercept of 0.46 (95% CI: 0.363 to 0.565), with r = 0.999. The correlation for the D3 fraction showed Deming regression slope of 0.98 (95% CI: 0.969 to 0.989), intercept of 0.06 (95% CI: -0.115 to 0.313), and r = 0.995. Results from both quantitation approaches were also compared to the assigned value in CDC reference samples. The mean bias relative to the CDC was 4.6% for ASCENT and 2.5% for TargetLynx. The median time for chromatogram review of a full 96-well plate of vitamin D results is reduced from approximately 2 h to 14 min and 80% of batches were reviewed within 30 min. Instead of 100% peak review, technologists review only the peaks that have been flagged by the system based on applied rules. Analysis of full plate batches showed that 2-20% of peaks per batch were flagged for manual review. Manipulations made by technologists during chromatogram review were reduced by 75% when using the automated versus manual system. CONCLUSIONS: We describe a system to facilitate data 'flow' from electronic order to result and to automate chromatogram peak review in a clinical liquid chromatography mass spectrometry assay for 25-hydroxyvitamin D. This eliminated manual result entry, repetitive transcription, and unnecessary review of high quality data while enabling systematic evaluation of data quality indicators. The new processes were accurate, improved the data review and processing times, and helped to reduce manual manipulations during chromatogram review.

Contribution of symmetric dimethylarginine to GFR decline in pediatric chronic kidney disease.

BACKGROUND: In pediatric chronic kidney disease (pCKD), traditional factors (proteinuria, etiology, and race) do not fully explain disease progression. The levels of methylated arginine derivatives (MADs: asymmetric and symmetric dimethylarginine, respectively) rise in CKD and increase with CKD progression. The impact of MADs on glomerular filtration rate (GFR) decline has not been examined in pCKD. The aim of this study was to examine the additive impact of baseline (BL) levels of MADs on directly measured GFR (mGFR) decline per year (ml/min/1.73 m2/year) for a period of up to 4 years. METHODS: Plasma and data, including mGFR by plasma iohexol clearance, were provided by the prospective, observational Chronic Kidney Disease in Children study. BL MADs were analyzed by high-performance liquid chromatography-tandem mass spectrometry. RESULTS: For 352 pCKD subjects, the median [interquartile range] BL mGFR was 45 [35, 57] ml/min/1.73 m2. The levels of BL MADs were inversely related to the initial mGFR and its decline over time (p < 0.0005) but not to the rate of decline. Covariates, non-glomerulopathy and Tanner stage of ≥ 3 demonstrated weaker relationships between BL levels and beginning mGFR (p = 0.004 and p = 0.002, respectively). CONCLUSIONS: In pCKD, higher concentrations of BL MADs were inversely related to BL mGFR. MADs did not affect the CKD progression rate. Quantification of this relationship is novel to the pCKD literature.