Citations

Abstract Background Beta-quantification (BQ) is the reference method for LDL-C but is not widely available. It is difficult, therefore, for clinical laboratories to independently assess the accuracy of their methods for either calculating or directly measuring LDL-C. Our goal was to investigate if an interrelationship between the tests in the standard lipid panel could be used to compare the performance of different LDL-C methods against BQ, specifically in samples with hypertriglyceridemia, a major cause of bias for LDL-C testing. Methods BQ results from Mayo Medical Labs (n=39,667) and the NIH (n=18,338) were used to identify a linear relationship by least-squares regression analysis between lipid panel test results and LDL-C to facilitate a statistical comparison between different LDL-C methods. Results It is well established that the number of VLDL particles increases as TG increases, because VLDL is the main carrier of TG. As a consequence, the ratio of LDL-C to non-HDL-C is inversely related to TG, which can be made linear by taking the square root of TG (Figure). Nearly identical regression equations were found for this relationship, using two different BQ datasets. When LDL-C was calculated by either Sampson equation, the LDL-C/non-HDL-C regression lines nearly overlapped with the one for BQ. In contrast, the Martin equation showed a positive bias with increasing TG, whereas the Friedewald equation showed a negative bias, consistent with past reports on their LDL-C biases with hypertriglyceridemia. In the UKBiobank, the Beckman direct LDL-C showed a positive bias for TG, which was confirmed in CAP proficiency test surveys. By simulation analysis, approximately 80 samples with high (>200 mg/dL) and low (<100 mg/dL) TG is statistically sufficient to assess if the LDL-C/non-HDL-C regressions lines of LDL-C methods differ from BQ. Conclusions The LDL-C/non-HDL-C ratio method is a simple way to examine LDL-C methods for bias on hypertriglyceridemic samples.

Abstract Background Calculated LDL cholesterol (LDL-C) is a standard component of the lipid panel and an important risk factor in managing atherosclerotic cardiovascular disease (ASCVD). Due to the assumptions in the derivation of the Friedwald formula, fasting (≥8 hours) and triglyceride levels ≤400mg/dL have long been recommended. More recent data have shown that in most cases fasting has minimal effect on results, leading to the endorsement of non-fasting lipid panels for routine evaluation of ASCVD risk in clinical practice guidelines. Furthermore, newer equations (e.g. Sampson-NIH) allow for more accurate estimation of LDL-C even in the presence of hypertriglyceridemia. Mayo Clinic has implemented the Sampson-NIH LDL-C calculation and removed fasting/non-fasting designation from lipid panel orders. We hypothesized that the change to fasting designation would allow more afternoon draws for routine lipid panels and that increased non-fasting collections may increase triglyceride levels, but that the Sampson-NIH equation would prevent bias in LDL-C estimation. In order to test these hypotheses, we analyzed patient data from 1 year prior and 1 year post-implementation. Methods Results of lipid panels performed for one year preceding (n=334,719) and one year after (n=381,804) removal of the fasting/non-fasting designation and implementation of Sampson-NIH equation were collected. Median, 10th, and 90th percentile of draw time, triglyceride, and LDL-C calculated by either Sampson-NIH or Friedwald formulas were compared by quantile regression. Results Draw times shifted post-implementation at the 10th percentile (7:06 vs. 7:10, p<0.0001), median (8:49 vs. 9:08, p<0.0001) and 90th (12:02 vs. 13:46, p<0.0001). No difference in median triglyceride measurement was observed between pre-and post-implementation (110mg/dL), but slight differences were observed in the 10th and 90th percentile values (60 vs 59mg/dL and 224 vs 229mg/dL, p<0.0001). No difference was observed in 10th, 50th, or 90th percentile LDL values when calculated by Sampson-NIH equation (56, 99, 153mg/dL); however, if the Friedwald formula is used, a slight shift is observed in the 10th and 50th percentile LDL values (54 vs. 53, 97 vs. 96; p<0.0001) but not the 90th (150mg/dL). Conclusions Changing to the Sampson/NIH formula for LDL-C and removing fasting vs. non-fasting designation from routine lipid panels had minimal effect on reported triglyceride and LDL-C values, while allowing increased flexibility in draw time and reporting of LDL-C on patients with triglycerides ≥400mg/dL. Patients with TG ≥400mg/dL represented 1.7% of the dataset overall, including 5,387 patients before the change in which LDL-C could not be reported and 6,697 patients in the year post-implementation for whom LDL-C was reported based on the Sampson-NIH formula. Using an equation that is robust in patients with elevated triglyceride levels and removing fasting requirements from routine lipid panels allows greater flexibility and convenience for patients while allowing for more even distribution of phlebotomy workload and reporting of LDL-C results for patients with hypertriglyceridemia without evidence of clinically significant bias in reported results.

Abstract Background Our institution is facing increasing demand for oncology testing that requires high quality DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue. The current DNA extraction workflow involves a time and labor-intensive manual process that limits our ability to accommodate increasing downstream clinical testing volumes. We evaluated the KingFisher (KF) Flex utilizing Autolys M Tubes and the MagMAX FFPE DNA/RNA Ultra Kit as a possible high-throughput, automated DNA isolation workflow option that would decrease hands-on time and be conducive to volume growth without the need for additional staff. Methods DNA from 52 FFPE tissue samples (n=24 unique cases previously extracted by the current “manual method”) were extracted using Autolys M tubes, the MagMAX FFPE DNA/RNA Ultra Kit, and the KF Flex (Thermo Fisher Scientific Waltham, MA) over 4 “automated method” runs. Method modifications to the published procedure were introduced over the runs to determine any effects on DNA quality/quantity. Timings were taken during each run to compare hands-on and total run time against that of the manual method. Precision experiments were performed by extracting 4 replicates of sample on a single run (intra-assay precision) and 2 samples from 2 cases over 2 runs (inter-assay precision). Three cases were processed using varying tissue input levels to assess input-yield correlation. DNA yield was measured using HS dsDNA Qubit (Thermo Fisher Scientific, Waltham, MA). A subset of samples was tested by digital droplet PCR (ddPCR) (n=10), chromosomal microsomal microarray (CMA) (n=1), and next-generation sequencing (NGS) (n=3). Variants and QC metrics of the KF DNA were compared to those of the manual method DNA. Results The average total DNA yield was 3% lower from samples extracted following the manufacturer recommended KF procedure compared to matched samples extracted using the manual method (n=28 samples from 23 unique cases). A CV of 2.8% was observed in an intra-assay experiment (n=4 replicates from 1 case) and 3.0% in an average inter-assay experiment (n=2 replicates from 2 cases). There was a direct correlation between the tissue input amount (4 amounts of varied tissue input) and the total DNA yield (n=3 samples). We observed concordant fractional abundance values for ddPCR samples and concordant variant detection for NGS and CMA samples. We did not see a significant difference in the quality metrics tracked for any of the downstream testing assays. Conclusions This evaluation demonstrated that, as compared to our manual method, the automated method resulted in comparable DNA yields and downstream assay results. The incorporation of this automation would significantly increase our FFPE DNA extraction capacity without requiring additional staff while reducing hands-on time per run by about six hours. We would also be able to reduce ergonomic hazards related to tube cap manipulation, eliminate use of hazardous reagents, and leverage the plate format to better integrate extracted DNA into our clinical sample preparation workflows. These operational benefits highlight the value of automating high-throughput workflows.

Abstract Background In complex automated clinical laboratory Next Generation Sequencing (NGS) workflows, numerous opportunities exist for contamination events to occur. For oncology testing applications, detection of these events is crucial for accurate results reporting. A contamination detection module (MICon) using microhaplotype (MH) regions and an in-house designed analysis model was developed for use in a NGS assay for myeloid neoplasms (NGSHM) [1]. Variant detection for NGSHM has a validated analytical sensitivity of 2% variant allele frequency (VAF). Gross contamination events can potentially cause erroneous false positive variant detection whereas true low VAF mutations may be masked and evade detection. The following study was performed to evaluate MICon module performance on samples processed over the course of a year. Methods MH regions contain highly conserved tandem single nucleotide polymorphisms (SNPs) with high global heterogeneity occurring within a 300-nucleotide span. From the work of Kidd et al [2], 27 MH regions covering 92 SNPs and spanning 16 chromosomes were selected for inclusion in the 47 gene NGSHM target-capture panel. Sequencing was performed on a NovaSeq 6000 and analyzed through an internal bioinformatics pipeline, which incorporates the MICon module. MICon uses a binary classification model incorporating VAFs from MH regions, number of MH genotypes, and the contamination estimation score from verifyBamID to compute a single value on a 0-100 scale. Scores <50 are classified as non-contaminated and scores ≥50 require further investigation. Results The dataset was comprised of 10,990 samples. A total of 10,232 patient cases (93.1%) had non-contaminated MICon scores <50. Control replicates accounted for 261 samples (2.4%). There were 497 patient cases (4.5%) with MICon scores ≥50. Of the 497 patient cases, 137 (27.6%) had undergone hematopoietic stem cell transplantation (HSCT) and 114 (22.9%) contained gross chromosomal abnormalities, representing iatrogenic or tumor biological factors. An additional 135 (27.2%) of cases were contaminated from laboratory processing errors, 45 (9.1%) occurred due to chemistry failures during run processing, and 66 (13.2%) had an undetermined cause for a high score, representing laboratory-related and unknown factors. Overall, the 135 laboratory processing errors detected accounted for 1.3% of patient cases analyzed by the laboratory. These cases were repeated, and the non-contaminated results were accurately reported. Conclusions Herein it was shown the implementation of MICon has improved patient safety over the course of a year. The 1.3% of patient cases identified as arising from laboratory processing errors were successfully reprocessed. While the overall rate of laboratory processing errors appears low, the absolute number can be significant in a high-volume test setting, despite reliance on highly automated processes. Value is added by MICon through identifying errors that could result in the release of inaccurate patient results. By detecting previously unrealized errors, MICon has become an invaluable asset to the NGSHM assay by enhancing patient laboratory testing safety. References: [1] Balan J, et al. MICon Contamination Detection Workflow for Next-Generation Sequencing Laboratories Using Microhaplotype Loci and Supervised Learning. J Mol Diagn. 2023;25(8):602-610. doi:10.1016/j.jmoldx.2023.05.001. [2] Kidd KK, et al. Selecting microhaplotypes optimized for different purposes. Electrophoresis. 2018;39(21):2815-2823. doi:10.1002/elps.201800092.

Abstract Background Hemoglobin S (HbS) causes sickling disorders. In the laboratory, confirmation of HbS in patient samples with varying percentages is essential. Assessment is routinely performed using capillary electrophoresis (CE) and/or high-performance liquid chromatography. Sickle solubility (SS) exploits decreased solubility of HbS under reducing conditions and is a confirmatory test. SS is unreliable with low HbS, elevated HbF, severe anemia, erythrocytosis, hyperglobulinemia, extreme leukocytosis, hyperlipidemia, or increased serum proteins. Infant samples commonly have low percentages of HbS, high HbF, and limited sample volume. Intact globin chain Mass Spectrometry (MS) is used to identify abnormal hemoglobin variants by detecting the mass change (normal α/β/γ mass =15127/15867/15996 amu), respectively). MS has potential advantages in sensitivity and efficiency over SS and requires lower input sample volume. Herein we compare the utility of MS versus SS for confirmation of HbS. Methods Twenty-three EDTA-anticoagulated blood samples containing low percentages of HbS were identified. SS was performed on 30μL washed packed cells (requires 200μL whole blood) per standard methods. Intact Quadrupole Time-of-Flight MS (Accurate-Mass Q-TOF LC/MS 6520, Agilent Technologies, California) was performed using 10μL whole blood sample in acetonitrile solution reagent and results were compared. HbS and HbF levels were assayed by capillary electrophoresis (Sebia, France) per standard methods. Results Select results are summarized in Table 1. SS detected HbS percentages to 4.8% when HbF was low but not 6% HbS when Hb F is high. MS showed no HbF interference and identified HbS peaks (at 15837 amu) down to 3.1%. HbS percentages <3.1 were undetected by both methods. Conclusions Overall, MS was superior to SS for confirming HbS, particularly in samples with low variant percentage and/or elevated HbF. MS is also optimal when sample volume is minimal, such as for infants. Percentages of HbS <3% require methods such as IEF or DNA sequencing for confirmation.

Abstract Background Alpha fetoprotein (AFP) is a circulating tumor marker utilized clinically to detect liver cirrhosis, liver cancer and testicular seminomas. AFP molecule contains one single N-glycosylation site, with highly variable glycan structures, resulting in diverse AFP glycoforms in circulating blood. The core fucosylation of AFP (AFP-L3) is a clinical biomarker to monitor and predict risks of liver cancer progression and recurrence. Clinical testing for AFP-L3 utilizes lectin-binding and gel-shift electrophoresis. We developed a novel method to measure AFP glycoforms, based on immune-enrichment and liquid chromatography with high resolution mass spectrometry (LC-HRMS). Methods Immune enrichment of AFP was achieved by anti-AFP antibody, immobilized to magnetic beads. After binding and enrichment, the magnetic beads were washed, AFP was eluted, and the samples were analyzed by LC-HRMS (Exploris 480 MS and Vanquish UHPLC, Thermo Fisher Scientific), using full scan, positive polarity acquisition mode. Chromatographic separation was performed on PLRP column (Agilent); flow rate 200 µL/min. The HRMS data were processed and deconvoluted with intact mass analysis workflow in Biopharma Finder 5.1 (Thermo Fisher Scientific) to derive the intact AFP masses. The method’s sensitivity and imprecision were assessed by replicate analysis of serial diluted patient serum samples. AFP and its associated glycoforms were matched and identified with an in-house developed bioinformatics workflow. The deconvoluted intact masses and the sum intensity of detected charged species for each AFP glycoform were used to quantify relative abundance of AFP glycoforms. Results The method specificity for AFP was confirmed by bottom-up analysis after immune-enrichment with observed peptide sequence coverage over 35%. The recovery of the immune enrichment was shown to be independent of the AFP glycoform compositions. The identified AFP glycoforms and their relative abundance were consistent among replicates between AFP concentration 100 ng/mL and 5000 ng/mL. Analysis of authentic serum specimens from patients with different chronic liver diseases and liver cancer (n=102), revealed multiple complex biantennary branched AFP glycan modifications, with different numbers of terminal sialic acid and core fucose. Four AFP glycoforms were identified in over 60% patient samples with elevated AFP concentrations. Although occurring consistently, relative abundance of these AFP glycoforms varied significantly among patients. Assessment of the AFP fucosylation and sialylation features suggested that the two are orthogonal processes. Clinical correlations suggested that fewer terminal sialic acids were associated with impaired liver functions, while the fucosylation was linked to inflammatory responses and presence of liver malignancy. Strong linear correlation (Spearman’s rs=0.952, N=35) was observed between AFP-L3% quantitated by the LC-HRMS method, and AFP-L3% determined by the lectin-binding based isotachophoresis assay (Wako Diagnostics). Discrepancies between the two methods were observed in specimens containing < 400 ng/mL of AFP, in which the LC-HRMS method detected only a single predominant glycoform. Conclusions We developed and evaluated the LC-HRMS method for profiling circulating AFP glycoforms in patients with chronic liver diseases and liver cancer. The detected AFP glycoforms and their relative abundance were used to establish glycan features, which can be further linked to cancer development, impaired liver function, and inflammation.

Abstract Background Factitious hypoglycemia, a deliberate attempt to induce low blood glucose levels occurring secondary to the surreptitious administration of exogenous insulin, can be difficult to diagnose due to a variety of factors including the increased use of synthetic insulin analogs in clinical practice. Traditional insulin immunoassays demonstrate variable cross-reactivity with commonly prescribed insulin analogues and their metabolites, making it difficult to measure specific analogs. The development of liquid chromatography high resolution accurate mass (LC-HRAM)-mass spectrometry (MS) assays has largely circumvented the limitations of traditional immunoassays for detection and quantitation of insulin analogs. Analytical challenges remain, however, specifically in differentiating lispro, an isomeric human insulin analog formed by the transposition of proline and lysine near the C-terminal end of the B chain, from human insulin in patient samples due to the equivalent mass-to-charge ratios of their precursor ions. Methods Immunoaffinity purification of insulin from calibrators and quality control material prepared by spiking insulin-depleted serum with pharmaceutical insulin preparations, as well as patient samples, was performed using tips coupled with anti-insulin monoclonal antibody. An automated liquid handler was programmed to perform aspiration and dispense cycles. Eluate from the purification protocol was submitted for analysis using a TLX-2 multiplex LC system paired with a Thermo Scientific Q Exactive Plus mass spectrometer. Various HPLC column chemistries were evaluated, a column passivation procedure was established, and column heater temperature was optimized to identify a combination of parameters yielding the best chromatographic separation of human insulin and lispro. Additionally, parallel reaction monitoring (PRM) targeted tandem mass spectrometry (MS/MS) analysis was utilized in combination with the full scan data to increase specificity through the monitoring of fragment ions produced from human insulin and each insulin analog. Results We found that a 1000 Å Diphenyl, 2.7 µm, 2.1 x 100 mm analytical column in a column heater maintained at a temperature of 80°C allowed for human insulin and lispro to be differentiated as two chromatographically separated extracted ion chromatographic peaks (XICs) and quantified down to 2.5 mcIU/mL with near-baseline separation. Before use, the column required passivation with a high protein buffer (0.05% bovine serum albumin in 20% acetonitrile [ACN] + 0.2% acetic acid) followed by increasingly organic buffers (20% ACN + 0.2% acetic acid and 50% ACN + 0.2% acetic acid). MS/MS was used to confirm the presence of analogs detected. Conclusions The LC-HRAM-MS method described here, coupled with optimized column chemistry, column passivation, and proper column temperature control allows for chromatographic separation of human insulin and lispro. Incorporating a PRM scan into the mass spectrometry full scan method provides confirmation of the insulin detected in the XICs. The results obtained from preliminary studies suggest this method is appropriate for use to facilitate the clinical investigation of suspected factitious hypoglycemia with the ability to differentiate isomeric compounds, such as human insulin and lispro.

Abstract Background Our established method for measuring plasma catecholamines utilized a Shimadzu HPLC coupled to an ESA Coulochem III electrochemical detector. Chromatographic run times were long, resulting in slow turnaround times. Instrument maintenance was labor intensive, and the assay was prone to interferences. To overcome these limitations, we changed the method to liquid chromatography-tandem mass spectrometry (LC-MS/MS) measurements. Methods After the addition of a labeled internal standard for each analyte, samples are loaded onto 50 mg of activated alumina at pH 8.6, utilizing a Tris-HCl, sodium carbonate and EDTA buffer. After incubation the alumina is then washed with 50% acetonitrile followed by water. Elution off the alumina is performed with 2% acetic acid. Derivatization is then performed on the eluate utilizing acetaldehyde and a cyanoborohydride buffer. Following derivatization, the samples are analyzed for epinephrine, norepinephrine, and dopamine by LC-MS/MS using a Sciex 7500 coupled to a ThermoFisher Scientific TLX-4 equipped with Vanquish pumps. Chromatographic separation was obtained using a Phenomenex Kinetex 2.6 um BiPhenyl 50x3 mm analytical column. Results Runtimes were significantly shorter than with the previous method, and no interferences were observed. Assay validation consisted of: intra/inter assay precision, accuracy, recovery, linearity, carryover, limit of detection (LOD), and interferences. Three levels were assessed for intra assay precision and each of the analytes monitored yielded %CVs of less than 6%. Four levels were assessed for inter assay precision and each of the analytes monitored yielded %CVs of less than 10%. When using linear regression analysis to compare results with the previous clinical assay, the slope, y-intercept and R2 were the following; dopamine: 1.06, 2.74, 0.978; epinephrine: 0.905, 2.20, 0.989; norepinephrine: 0.919, 9.75, 0.953. Spike and recovery from five samples yielded a mean average recovery of 93.4% for dopamine, 100% for epinephrine and 98.1% for norepinephrine. For linearity 4 samples were diluted and the mean % difference from expected was -1.66% for dopamine, -0.25% for epinephrine and 1.78% for norepinephrine. Blanks were injected following the high standard and carryover was negligible. LOD was determined by running a low sample pool along with a blank over 20 assays. The LOD was determined to be less than the LLOQ. Sixty-two common drugs/vitamins along with varying levels of hemolysis, lipemia, and bilirubin were also tested to ensure no interferences were seen. Conclusions The LC-MS/MS method exceeded the performance of the historical Shimdazu HPLC system with ESA Coluochem III electrochemical detector method. We anticipate that the better analytical performance will improve the testing quality of our patients.

Abstract Background Patients with sporadic or hereditary Medullary Thyroid Carcinoma (MTC) often undergo total thyroidectomy and lymph node dissection, with postoperative surveillance relying on serum calcitonin levels and ultrasound examinations. According to American Thyroid Association (ATA) guidelines, detectable levels of serum calcitonin and Carcinoembryonic Antigen (CEA) post-thyroidectomy suggest potential disease persistence or recurrence, necessitating frequent monitoring for early detection. This study sought to reassess the role of postoperative calcitonin levels in identifying possible tumor recurrence. Methods A retrospective analysis was conducted using Siemens Atellica to test calcitonin levels in 562 samples collected between 09/27/2022 and 08/11/2023, at least 3 months post-total thyroidectomy. Imaging studies performed within 6 months of the calcitonin assessment were also reviewed. Sample pools with calcitonin concentrations near 3.00 and 5.00 pg/mL were utilized to determine the limit of quantification (LoQ). CEA results were included for comparison. Additionally, 16 serum samples were analyzed using the Roche Cobas system at a reference laboratory. Results Precision analysis around 3.00 and 5.00 pg/mL revealed coefficients of variation (CVs) of 16.49% and 8.87%, respectively. Comparison of calcitonin levels between Siemens Atellica and Roche Cobas systems demonstrated consistent levels < 5.00 pg/mL in 15 out of 16 samples, indicating alignment and reliability between the platforms. A calcitonin cutoff of 1.89 pg/mL yielded 43% sensitivity and 67% specificity, while a cutoff of 5.00 pg/mL resulted in 0% sensitivity and 100% specificity. Conclusions Our findings suggest that a 5 pg/mL calcitonin cutoff on the Siemens Atellica platform may be suitable for identifying tumor persistence or recurrence in post-thyroidectomy patients within our institution. However, individual laboratories should establish their LoQ criteria when interpreting calcitonin levels for postoperative monitoring of tumor recurrence.

Stenosis of the left main coronary artery (LM stenosis) is associated with significant mortality and morbidity due to the large area of affected myocardium. Evidence on the use of percutaneous coronary intervention (PCI) for the treatment of LM stenosis is growing. However, the role of Western guidelines on patients in the Asian-Pacific region is unclear due to anatomical variations, substantial heterogeneity in healthcare resources and infrastructure, and the lack of consensus on the optimal management of LM stenosis in the Asia-Pacific region. Hence, an Asian Pacific Society of Cardiology (APSC) working group developed consensus recommendations on the use of PCI in the management of LM stenosis in the Asia-Pacific region. The APSC expert panel reviewed and appraised the available evidence using the Grading of Recommendations Assessment, Development, and Evaluation system. Consensus recommendations were developed and put to an online vote. Consensus was reached when 80% of votes for a given recommendation were in support of ‘agree’ or ‘neutral’. The resulting 12 statements provide guidance for clinical practitioners in the region on the use of PCI in the treatment of patients with LM stenosis.