Clinical chemistry最新文献

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Commentary on Progressive Motor Regression in a 3-Year-Old: Dietary Trends Revive an Overlooked Diagnosis. 对3岁儿童进行性运动衰退的评论：饮食趋势使一个被忽视的诊断复苏。

IF 7.1 2区医学 Q1 MEDICAL LABORATORY TECHNOLOGY

Clinical chemistry

Pub Date : 2024-12-02 DOI: 10.1093/clinchem/hvae158

Ravinder Sodi

引用次数: 0

Commentary on Alkaline Phosphatase Activity Inconsistent with Patient's Clinical Presentation: A Cautionary Tale. 碱性磷酸酶活性与患者临床表现不一致的评论：一个警世故事。

IF 7.1 2区医学 Q1 MEDICAL LABORATORY TECHNOLOGY

Clinical chemistry

Pub Date : 2024-12-02 DOI: 10.1093/clinchem/hvae134

Isabelle Piec

引用次数: 0

Validation of Analytical Performance Limits for Accuracy with High-Sensitivity Cardiac Troponin Assays. 高灵敏度心肌肌钙蛋白测定准确度分析性能限的验证。

IF 7.1 2区医学 Q1 MEDICAL LABORATORY TECHNOLOGY

Clinical chemistry

Pub Date : 2024-11-28 DOI: 10.1093/clinchem/hvae198

Peter A Kavsak, Alexander Kumaritakis, Matthew Wong-Fung, Tony Badrick, Michael Knauer

引用次数: 0

Virtual Gene Panels Have a Superior Diagnostic Yield for Inherited Rare Diseases Relative to Static Panels 与静态面板相比，虚拟基因面板对遗传性罕见病的诊断率更高

IF 9.3 2区医学 Q1 MEDICAL LABORATORY TECHNOLOGY

Clinical chemistry

Pub Date : 2024-11-21 DOI: 10.1093/clinchem/hvae183

Massomeh Sheikh Hassani, Ruchi Jain, Sathishkumar Ramaswamy, Shruti Sinha, Maha El Naofal, Nour Halabi, Sawsan Alyafei, Roudha Alfalasi, Shruti Shenbagam, Alan Taylor, Ahmad Abou Tayoun

Background Exome- or genome-based panels—also known as slices or virtual panels—are now a popular approach that involves comprehensive genomic sequencing while restricting analysis to subsets of genes based on patients’ phenotypes. This flexible strategy enables frequent gene updates based on novel disease associations as well as reflexing to analyzing other genes up to the whole exome or genome. With recent improvements addressing limitations associated with virtual panels, the advantages of this approach, relative to static custom-based panels, remain to be systematically characterized. Methods Here we perform slice testing on 1014 patients (50.5% females; average age 17 years) referred from multiple pediatric clinics within a single center in the Middle East (83% Arab population). Results Initial analysis uncovered molecular diagnoses for 235 patients for a diagnostic yield of 23% (235/1014). “On the fly” focused analysis in most negative cases (N = 779) identified clinically significant variants correlating with patients’ presentations in genes outside the originally ordered panel for another 35 patients (3.5% or 35/1024) increasing the overall diagnostic yield to 27%. The pathogenic variants underlying the additional cases (13% of all positive cases) were excluded from the original “panel” gene list, mainly as result of issues related to panel selection, novel gene–disease associations, phenotype spectrum broadening, or gene lists variability. The additional findings led to changes in clinical management in most patients (94%). Conclusions Our findings support slice testing as an efficient and flexible platform that facilitates updates to gene lists to achieve high clinical sensitivity and utility.

背景基于外显子组或基因组的基因组分析--又称切片分析或虚拟分析--是目前一种流行的方法，它包括全面的基因组测序，同时根据患者的表型限制对基因子集进行分析。这种灵活的策略可根据新的疾病关联频繁更新基因，并可反射性地分析其他基因，直至整个外显子组或基因组。虽然最近的改进解决了与虚拟面板相关的局限性，但相对于静态的定制面板，这种方法的优势仍有待系统鉴定。方法在这里，我们对中东地区（阿拉伯人口占 83%）一个中心的多个儿科诊所转来的 1014 名患者（50.5% 为女性，平均年龄 17 岁）进行了切片检测。结果初步分析发现了 235 名患者的分子诊断结果，诊断率为 23%（235/1014）。对大多数阴性病例（N = 779）进行的 "即时 "重点分析发现，另有 35 名患者（3.5% 或 35/1024）的临床重要变异与患者表现相关，这些变异的基因不在最初订购的研究小组范围内，从而将总体诊断率提高到 27%。新增病例（占所有阳性病例的 13%）的致病变异基因被排除在最初的 "面板 "基因列表之外，这主要是由于面板选择、新基因与疾病相关、表型谱扩大或基因列表变异等相关问题造成的。额外的发现导致大多数患者（94%）的临床管理发生了变化。结论我们的研究结果表明，切片检验是一种高效灵活的平台，可促进基因列表的更新，从而实现较高的临床灵敏度和实用性。

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引用次数: 0

Xylazine Pharmacokinetics in Patients Testing Positive for Fentanyl and Xylazine. 芬太尼和赛拉嗪检测呈阳性患者的赛拉嗪药代动力学。

IF 7.1 2区医学 Q1 MEDICAL LABORATORY TECHNOLOGY

Clinical chemistry

Pub Date : 2024-11-20 DOI: 10.1093/clinchem/hvae163

Yanchun Lin, Christopher W Farnsworth, Vahid Azimi, David B Liss, Michael E Mullins, Bridgit O Crews

Background: The increasing prevalence of xylazine in the illicit drug supply is a growing concern for major health consequences in individuals who use fentanyl mixed with xylazine, but limited data are available regarding the pharmacokinetics of xylazine in humans.

Methods: Xylazine was quantified in serial remnant plasmas collected from 28 patients starting at the initial patient encounter and continuing for up to 52 h from presentation, using LC-MS/MS to calculate the terminal half-life for xylazine. Xylazine metabolites were identified by product ion scanning, and multiple reaction monitoring was used to estimate the relative abundance of xylazine metabolites in 74 collected plasma samples.

Results: The median terminal half-life for xylazine was calculated to be 12.0 h (range: 5.9-20.8). Oxo-xylazine and sulfone-xylazine metabolites were detected in all plasma specimens that contained xylazine.

Conclusions: The half-life of xylazine in humans is longer than previously observed in animal studies, which furthers the current understanding of the expected duration of effects in individuals who use fentanyl mixed with xylazine and the window of detection. Both oxo-xylazine and sulfone-xylazine appear to circulate in plasma for as long as xylazine.

背景：非法药物供应中的异丙嗪越来越普遍，人们越来越担心使用与异丙嗪混合的芬太尼会对个人健康造成重大影响，但有关异丙嗪在人体中的药代动力学的数据却很有限：使用 LC-MS/MS 对从 28 名患者中收集的连续残余血浆中的恶嗪进行定量，从患者初次就诊开始，持续到就诊后的 52 小时，计算恶嗪的终末半衰期。通过产物离子扫描确定了赛拉嗪代谢物，并使用多重反应监测估算了 74 份收集的血浆样本中赛拉嗪代谢物的相对丰度：结果：据计算，恶嗪的中位终末半衰期为 12.0 小时（范围：5.9-20.8）。在所有含有恶嗪的血浆样本中都检测到了恶嗪和砜类恶嗪代谢物：人类体内的恶嗪半衰期长于之前在动物实验中观察到的时间，这进一步加深了目前对使用与恶嗪混合的芬太尼的个体的预期效应持续时间和检测窗口的理解。氧化恶嗪和磺酮恶嗪在血浆中的循环时间似乎与恶嗪一样长。

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引用次数: 0

Prospective and External Validation of an Ensemble Learning Approach to Sensitively Detect Intravenous Fluid Contamination in Basic Metabolic Panels 前瞻性外部验证组合学习方法，灵敏检测基础代谢面板中的静脉注射液污染

IF 9.3 2区医学 Q1 MEDICAL LABORATORY TECHNOLOGY

Clinical chemistry

Pub Date : 2024-11-15 DOI: 10.1093/clinchem/hvae168

Nicholas C Spies, Leah Militello, Christopher W Farnsworth, Joe M El-Khoury, Thomas J S Durant, Mark A Zaydman

Background Intravenous (IV) fluid contamination within clinical specimens causes an operational burden on the laboratory when detected, and potential patient harm when undetected. Even mild contamination is often sufficient to meaningfully alter results across multiple analytes. A recently reported unsupervised learning approach was more sensitive than routine workflows, but still lacked sensitivity to mild but significant contamination. Here, we leverage ensemble learning to more sensitively detect contaminated results using an approach which is explainable and generalizable across institutions. Methods An ensemble-based machine learning pipeline of general and fluid-specific models was trained on real-world and simulated contamination and internally and externally validated. Benchmarks for performance assessment were derived from in silico simulations, in vitro experiments, and expert review. Fluid-specific regression models estimated contamination severity. SHapley Additive exPlanation (SHAP) values were calculated to explain specimen-level predictions, and algorithmic fairness was evaluated by comparing flag rates across demographic and clinical subgroups. Results The sensitivities, specificities, and Matthews correlation coefficients were 0.858, 0.993, and 0.747 for the internal validation set, and 1.00, 0.980, and 0.387 for the external set. SHAP values provided plausible explanations for dextrose- and ketoacidosis-related hyperglycemia. Flag rates from the pipeline were higher than the current workflow, with improved detection of contamination events expected to exceed allowable limits for measurement error and reference change values. Conclusions An accurate, generalizable, and explainable ensemble-based machine learning pipeline was developed and validated for sensitively detecting IV fluid contamination. Implementing this pipeline would help identify errors that are poorly detected by current clinical workflows and a previously described unsupervised machine learning-based method.

背景临床标本中的静脉注射液（IV）污染一旦被检测到，就会给实验室带来操作负担，而如果未被检测到，则可能对患者造成伤害。即使是轻度污染，也往往足以对多种分析物的检测结果造成有意义的改变。最近报道的一种无监督学习方法比常规工作流程更灵敏，但对轻微但严重的污染仍然缺乏敏感性。在这里，我们利用集合学习来更灵敏地检测污染结果，这种方法可以在不同机构之间进行解释和推广。方法在真实世界和模拟污染的基础上，对通用模型和特定液体模型进行了基于集合的机器学习管道训练，并进行了内部和外部验证。性能评估基准来自硅学模拟、体外实验和专家评审。特定流体回归模型估计了污染严重程度。通过计算 SHapley Additive exPlanation（SHAP）值来解释标本级预测，并通过比较不同人群和临床亚群的标记率来评估算法的公平性。结果内部验证集的灵敏度、特异性和马修斯相关系数分别为 0.858、0.993 和 0.747，外部验证集的灵敏度、特异性和马修斯相关系数分别为 1.00、0.980 和 0.387。SHAP 值为葡萄糖和酮症酸中毒相关的高血糖提供了合理的解释。流水线的标记率高于当前工作流程，对超出测量误差和参考变化值允许范围的污染事件的检测能力也有所提高。结论为灵敏检测静脉输液污染，开发并验证了一种准确、可推广且可解释的基于集合的机器学习管道。实施该管道将有助于识别当前临床工作流程和之前描述的基于无监督机器学习方法难以检测到的错误。

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引用次数: 0

Proteinuria, Blinded by Bright Light. 蛋白尿、强光致盲。

IF 7.1 2区医学 Q1 MEDICAL LABORATORY TECHNOLOGY

Clinical chemistry

Pub Date : 2024-11-04 DOI: 10.1093/clinchem/hvae111

Mirthe Ubink, Judith Y M N Derijks-Engwegen, Miranda van Berkel, Harm Westdorp, Joannes F M Jacobs

引用次数: 0

Commentary on Mosaic Copy Number Variation in a Patient with Cerebral and Pulmonary Arteriovenous Malformations and Recurrent Epistaxis. 关于一名脑和肺动静脉畸形及复发性鼻衄患者的马赛克拷贝数变异的评论。

IF 7.1 2区医学 Q1 MEDICAL LABORATORY TECHNOLOGY

Clinical chemistry

Pub Date : 2024-11-04 DOI: 10.1093/clinchem/hvae113

Anne B S Giersch

引用次数: 0

Alzheimer Disease Blood-Based Biomarkers: Translation from Research into Clinical Use. 阿尔茨海默病血基生物标记物：从研究转化为临床应用。

IF 7.1 2区医学 Q1 MEDICAL LABORATORY TECHNOLOGY

Clinical chemistry

Pub Date : 2024-11-04 DOI: 10.1093/clinchem/hvae144

Lance A Ladic, Mari L DeMarco, Nicholas J Ashton, Andrew J Saykin, Louis B Jacques

引用次数: 0

Deconvolution of Human Urine across the Transcriptome and Metabolome. 人类尿液转录组和代谢组的解卷积。

IF 7.1 2区医学 Q1 MEDICAL LABORATORY TECHNOLOGY

Clinical chemistry

Pub Date : 2024-11-04 DOI: 10.1093/clinchem/hvae137

Sevahn K Vorperian, Brian C DeFelice, Joseph A Buonomo, Hagop J Chinchinian, Ira J Gray, Jia Yan, Kathleen E Mach, Vinh La, Timothy J Lee, Joseph C Liao, Richard Lafayette, Gabriel B Loeb, Carolyn R Bertozzi, Stephen R Quake

Background: Early detection of the cell type changes underlying several genitourinary tract diseases largely remains an unmet clinical need, where existing assays, if available, lack the cellular resolution afforded by an invasive biopsy. While messenger RNA in urine could reflect the dynamic signal that facilitates early detection, current measurements primarily detect single genes and thus do not reflect the entire transcriptome and the underlying contributions of cell type-specific RNA.

Methods: We isolated and sequenced the cell-free RNA (cfRNA) and sediment RNA from human urine samples (n = 6 healthy controls and n = 12 kidney stone patients) and measured the urine metabolome. We analyzed the resulting urine transcriptomes by deconvolving the noninvasively measurable cell type contributions and comparing to plasma cfRNA and the measured urine metabolome.

Results: Urine transcriptome cell type deconvolution primarily yielded relative fractional contributions from genitourinary tract cell types in addition to cell types from high-turnover solid tissues beyond the genitourinary tract. Comparison to plasma cfRNA yielded enrichment of metabolic pathways and a distinct cell type spectrum. Integration of urine transcriptomic and metabolomic measurements yielded enrichment for metabolic pathways involved in amino acid metabolism and overlapped with metabolic subsystems associated with proximal tubule function.

Conclusions: Noninvasive whole transcriptome measurements of human urine cfRNA and sediment RNA reflects signal from hard-to-biopsy tissues exhibiting low representation in blood plasma cfRNA liquid biopsy at cell type resolution and are enriched in signal from metabolic pathways measurable in the urine metabolome.

背景：早期检测几种泌尿生殖道疾病的细胞类型变化在很大程度上仍是一项尚未满足的临床需求，现有的检测方法（如果有的话）缺乏侵入性活检所提供的细胞分辨率。虽然尿液中的信使 RNA 可以反映有助于早期检测的动态信号，但目前的测量主要检测单个基因，因此不能反映整个转录组和细胞类型特异性 RNA 的潜在贡献：我们从人类尿液样本（6 个健康对照组和 12 个肾结石患者）中分离出了无细胞 RNA（cfRNA）和沉积物 RNA，并对其进行了测序，同时测量了尿液代谢组。我们通过对非侵入性可测量的细胞类型贡献进行解旋，并将其与血浆中的 cfRNA 和测量的尿液代谢组进行比较，从而分析得出了尿液转录组：尿液转录组细胞类型解旋主要得出了泌尿生殖道细胞类型的相对贡献率，此外还有来自泌尿生殖道以外的高周转实体组织的细胞类型。与血浆 cfRNA 相比，代谢途径和细胞类型谱更加丰富。尿液转录组和代谢组测量的整合富集了涉及氨基酸代谢的代谢途径，并与近端肾小管功能相关的代谢子系统重叠：人体尿液 cfRNA 和沉积物 RNA 的无创整体转录组测量反映了难以活检组织的信号，这些组织在血浆 cfRNA 液体活检中的细胞类型分辨率较低，并且富含尿液代谢组中可测量的代谢途径信号。

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Clinical chemistry

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