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American Journal of Clinical Pathology May 2024Tumor mutational burden (TMB) is a significant biomarker for predicting immune checkpoint inhibitor response, but the clinical performance of whole-exome sequencing...
OBJECTIVES
Tumor mutational burden (TMB) is a significant biomarker for predicting immune checkpoint inhibitor response, but the clinical performance of whole-exome sequencing (WES)-based TMB estimation has received less attention compared to panel-based methods. This study aimed to assess the reliability and comparability of WES-based TMB analysis among laboratories under routine testing conditions.
METHODS
A multicenter study was conducted involving 24 laboratories in China using in silico reference data sets. The accuracy and comparability of TMB estimation were evaluated using matched tumor-normal data sets. Factors such as accuracy of variant calls, limit of detection (LOD) of WES test, size of regions of interest (ROIs) used for TMB calculation, and TMB cutoff points were analyzed.
RESULTS
The laboratories consistently underestimated the expected TMB scores in matched tumor-normal samples, with only 50% falling within the ±30% TMB interval. Samples with low TMB score (<2.5) received the consensus interpretation. Accuracy of variant calls, LOD of the WES test, ROI, and TMB cutoff points were important factors causing interlaboratory deviations.
CONCLUSIONS
This study highlights real-world challenges in WES-based TMB analysis that need to be improved and optimized. This research will aid in the selection of more reasonable analytical procedures to minimize potential methodologic biases in estimating TMB in clinical exome sequencing tests. Harmonizing TMB estimation in clinical testing conditions is crucial for accurately evaluating patients' response to immunotherapy.
PubMed: 38733635
DOI: 10.1093/ajcp/aqae056 -
Talanta Jun 2024In this study, we established a versatile and simple magnetic-assisted microfluidic method for fast bacterial detection. Quantum dots (QDs) were loaded onto magnetic...
In this study, we established a versatile and simple magnetic-assisted microfluidic method for fast bacterial detection. Quantum dots (QDs) were loaded onto magnetic beads (MBs) to construct performance enhanced on-chip capture of bacteria. Escherichia coli (E. coli), as a model bacterium was studied. CdSe QDs were deposited onto the surface of FeO MBs through layer-by-layer self-assembly to enhance the loading of antibodies (Abs). MBs functionalized with anti-E. coli antibody molecules in a micropillar-based microfluidic chip were utilized to capture E. coli, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used for characterization of captured bacteria. This method was found capable of specifically isolating E. coli within the range of 1.0 to 1.0 × 10 CFU/mL, having a detection limit (LOD) of 10 CFU/mL. The average similarity score among mass spectra for the bacterial capture obtained in independent experiments is calculated as 0.97 ± 0.01 (n = 3), which shows this work's excellent reproducibility for bacterial capture. Bacterial growth on ready-to-eat (RTE) foods during its time of storage was successfully monitored. The present protocol has promising potential for microbial control and pathogen detection in the food industry.
Topics: Escherichia coli; Quantum Dots; Reproducibility of Results; Bacteria; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Magnetic Phenomena
PubMed: 38484499
DOI: 10.1016/j.talanta.2024.125880 -
Food Additives & Contaminants. Part A,... Jun 2024This study developed a highly sensitive microbiological method utilizing a novel microtiter plate to screen 10 sulfonamides in chicken muscles, eggs, and prawns. This...
This study developed a highly sensitive microbiological method utilizing a novel microtiter plate to screen 10 sulfonamides in chicken muscles, eggs, and prawns. This plate was fabricated from agar incorporating trimethoprim and spread with . After residue detection by bioassay, the same test solutions were analyzed by LC-MS/MS for accurate identification and quantification. It also proved eco-friendly compared to using other quantitative methods. The residual drugs were extracted with McIlvaine buffer and purified using an Oasis MCX cartridge. A triethylamine/methanol/water (0.5:75:24.5, v/v/v) mixture was used as the eluate. The obtained LOD values of the bioassay ranged from 5 to 25 µg kg- allowing the detection of the target drugs at the MRLs established in Japan. Adhering to ISO/IEC 17025 standards, the performance of the bioassay was evaluated. Based on the inhibition zone size in bioassay results, quality control yielded a Z score within ±2, indicating reasonable control over the screening process. Proficiency testing of a chicken muscle sample spiked with sulfadimidine demonstrated the inhibition zone detection of the bioassay and quantified value alignment of LC-MS/MS with reference values. In a surveillance study of 91 samples, sulfamethoxazole was detected in one prawn sample.
PubMed: 38913845
DOI: 10.1080/19440049.2024.2368903