Background: Inborn errors of metabolism comprise a set of more than 2000 known disorders which can result in significant morbidity and may be rapidly fatal. Diagnosing these disorders at birth and treating immediately, however, may often result in a normal to near-normal life for the affected infant. Thus, newborn screening (NBS) has saved or improved the lives of countless individuals since its inception in the 1960s.
Content: This review covers NBS, from its early beginnings up to the current day practice. We follow the evolution of NBS, as well as describe the need and how disorders are added to NBS programs, the testing and how its performance is monitored, and the follow-up to the testing. We also briefly touch on NBS outside the United States.
Summary: Newborn screening in the United States is a major public health success story and it continues to grow and evolve to cover more disorders and utilize new technological advances.
{"title":"Newborn Screening: Current Practice and Our Journey over the Last 60 Years.","authors":"Jing Cao, Marzia Pasquali, Patricia M Jones","doi":"10.1093/jalm/jfae020","DOIUrl":"10.1093/jalm/jfae020","url":null,"abstract":"<p><strong>Background: </strong>Inborn errors of metabolism comprise a set of more than 2000 known disorders which can result in significant morbidity and may be rapidly fatal. Diagnosing these disorders at birth and treating immediately, however, may often result in a normal to near-normal life for the affected infant. Thus, newborn screening (NBS) has saved or improved the lives of countless individuals since its inception in the 1960s.</p><p><strong>Content: </strong>This review covers NBS, from its early beginnings up to the current day practice. We follow the evolution of NBS, as well as describe the need and how disorders are added to NBS programs, the testing and how its performance is monitored, and the follow-up to the testing. We also briefly touch on NBS outside the United States.</p><p><strong>Summary: </strong>Newborn screening in the United States is a major public health success story and it continues to grow and evolve to cover more disorders and utilize new technological advances.</p>","PeriodicalId":46361,"journal":{"name":"Journal of Applied Laboratory Medicine","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140177070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Beomki Lee, Go Eun Bae, In Hwa Jeong, Jong-Hun Kim, Min-Jung Kwon, Jayoung Kim, Byoungguk Kim, June-Woo Lee, Jeong-Hyun Nam, Hee Jin Huh, Eun-Suk Kang
Background: Although age negatively correlates with vaccine-induced immune responses, whether the vaccine-induced neutralizing effect against variants of concern (VOCs) substantially differs across age remains relatively poorly explored. In addition, the utility of commercial binding assays developed with the wild-type SARS-CoV-2 for predicting the neutralizing effect against VOCs should be revalidated.
Methods: We analyzed 151 triple-vaccinated SARS-CoV-2-naïve individuals boosted with BNT162b2 (Pfizer-BioNTech). The study population was divided into young adults (age < 30), middle-aged adults (30 ≤ age < 60), and older adults (age ≥ 60). The plaque reduction neutralization test (PRNT) titers against Delta (B.1.617.2) and Omicron (B.1.1.529) variants were compared across age. Antibody titers measured with commercial binding assays were compared with PRNT titers.
Results: Age-related decline in neutralizing titers was observed for both Delta and Omicron variants. Neutralizing titers for Omicron were lower than those against Delta in all ages. The multiple linear regression model demonstrated that duration from third dose to sample collection and vaccine types were also significant factors affecting vaccine-induced immunity along with age. The correlation between commercial binding assays and PRNT was acceptable for all age groups with the Delta variant, but relatively poor for middle-aged and older adults with the Omicron variant due to low titers.
Conclusions: This study provides insights into the age-related dynamics of vaccine-induced immunity against SARS-CoV-2 VOCs, corroborating the need for age-specific vaccination strategies in the endemic era where new variants continue to evolve. Moreover, commercial binding assays should be used cautiously when estimating neutralizing titers against VOCs, particularly Omicron.
{"title":"Age-Related Differences in Neutralizing Antibody Responses against SARS-CoV-2 Delta and Omicron Variants in 151 SARS-CoV-2-Naïve Metropolitan Residents Boosted with BNT162b2.","authors":"Beomki Lee, Go Eun Bae, In Hwa Jeong, Jong-Hun Kim, Min-Jung Kwon, Jayoung Kim, Byoungguk Kim, June-Woo Lee, Jeong-Hyun Nam, Hee Jin Huh, Eun-Suk Kang","doi":"10.1093/jalm/jfae014","DOIUrl":"10.1093/jalm/jfae014","url":null,"abstract":"<p><strong>Background: </strong>Although age negatively correlates with vaccine-induced immune responses, whether the vaccine-induced neutralizing effect against variants of concern (VOCs) substantially differs across age remains relatively poorly explored. In addition, the utility of commercial binding assays developed with the wild-type SARS-CoV-2 for predicting the neutralizing effect against VOCs should be revalidated.</p><p><strong>Methods: </strong>We analyzed 151 triple-vaccinated SARS-CoV-2-naïve individuals boosted with BNT162b2 (Pfizer-BioNTech). The study population was divided into young adults (age < 30), middle-aged adults (30 ≤ age < 60), and older adults (age ≥ 60). The plaque reduction neutralization test (PRNT) titers against Delta (B.1.617.2) and Omicron (B.1.1.529) variants were compared across age. Antibody titers measured with commercial binding assays were compared with PRNT titers.</p><p><strong>Results: </strong>Age-related decline in neutralizing titers was observed for both Delta and Omicron variants. Neutralizing titers for Omicron were lower than those against Delta in all ages. The multiple linear regression model demonstrated that duration from third dose to sample collection and vaccine types were also significant factors affecting vaccine-induced immunity along with age. The correlation between commercial binding assays and PRNT was acceptable for all age groups with the Delta variant, but relatively poor for middle-aged and older adults with the Omicron variant due to low titers.</p><p><strong>Conclusions: </strong>This study provides insights into the age-related dynamics of vaccine-induced immunity against SARS-CoV-2 VOCs, corroborating the need for age-specific vaccination strategies in the endemic era where new variants continue to evolve. Moreover, commercial binding assays should be used cautiously when estimating neutralizing titers against VOCs, particularly Omicron.</p>","PeriodicalId":46361,"journal":{"name":"Journal of Applied Laboratory Medicine","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140294941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Joseph H Blommel, Matthew M Roforth, Calvin R Jerde, Carley A Karsten, Amber R Bridgeman, Jesse S Voss, Luigi Boccuto, Diana S Ivankovic, Sara M Sarasua, Benjamin R Kipp, Stephen J Murphy
Background: The COVID-19 pandemic emphasized an urgent need for devices used in the self-collection of biospecimens in an evolving patient care system. The mailing of biospecimen self-collection kits to patients, with samples returned via mail, provides a more convenient testing regimen, but could also impart patient sampling variabilities. User compliance with device directions is central to downstream testing of collected biospecimens and clear instructions are central to this goal.
Methods: Here, we performed an evaluation of 10 oral DNA collection devices involving either swab or saliva self-collection and analyzed ease of use and comfort level with a device, as well as DNA recovery quantity/quality and sample stability.
Results: We show that while these DNA quality/quantity metrics are comparable between devices, users prefer direct saliva collection over swab-based devices.
Conclusions: This information is useful in guiding future experiments including their use in human RNA, microbial, or viral sample collection/recovery and their use in clinical testing.
背景:COVID-19 大流行突显了在不断发展的病人护理系统中对用于自我采集生物样本的设备的迫切需求。向患者邮寄生物样本自助采集包,并通过邮件将样本寄回,提供了一种更方便的检测方案,但也可能造成患者采样差异。方法:在此,我们对 10 种涉及拭子或唾液自采集的口腔 DNA 采集设备进行了评估,并分析了设备的易用性和舒适度,以及 DNA 回收数量/质量和样本稳定性:结果:我们发现,虽然不同设备的 DNA 质量/数量指标相当,但用户更喜欢直接采集唾液,而不是基于拭子的设备:这些信息有助于指导未来的实验,包括用于人类 RNA、微生物或病毒样本的采集/回收,以及用于临床测试。
{"title":"Evaluating User Experience and DNA Yield from Self-Collection Devices.","authors":"Joseph H Blommel, Matthew M Roforth, Calvin R Jerde, Carley A Karsten, Amber R Bridgeman, Jesse S Voss, Luigi Boccuto, Diana S Ivankovic, Sara M Sarasua, Benjamin R Kipp, Stephen J Murphy","doi":"10.1093/jalm/jfae030","DOIUrl":"10.1093/jalm/jfae030","url":null,"abstract":"<p><strong>Background: </strong>The COVID-19 pandemic emphasized an urgent need for devices used in the self-collection of biospecimens in an evolving patient care system. The mailing of biospecimen self-collection kits to patients, with samples returned via mail, provides a more convenient testing regimen, but could also impart patient sampling variabilities. User compliance with device directions is central to downstream testing of collected biospecimens and clear instructions are central to this goal.</p><p><strong>Methods: </strong>Here, we performed an evaluation of 10 oral DNA collection devices involving either swab or saliva self-collection and analyzed ease of use and comfort level with a device, as well as DNA recovery quantity/quality and sample stability.</p><p><strong>Results: </strong>We show that while these DNA quality/quantity metrics are comparable between devices, users prefer direct saliva collection over swab-based devices.</p><p><strong>Conclusions: </strong>This information is useful in guiding future experiments including their use in human RNA, microbial, or viral sample collection/recovery and their use in clinical testing.</p>","PeriodicalId":46361,"journal":{"name":"Journal of Applied Laboratory Medicine","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Farida Almarzooqi, Amir Karin, Andre Mattman, Alexander Easton, Christopher Lee, Anthony Gador
{"title":"Resolved Myositis, Normal Creatine Kinase, and Peaking Cardiac Troponin T.","authors":"Farida Almarzooqi, Amir Karin, Andre Mattman, Alexander Easton, Christopher Lee, Anthony Gador","doi":"10.1093/jalm/jfae026","DOIUrl":"10.1093/jalm/jfae026","url":null,"abstract":"","PeriodicalId":46361,"journal":{"name":"Journal of Applied Laboratory Medicine","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140868487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kenneth J Hampel, Diana L Gerrard, Denise Francis, Jordan Armstrong, Margaret Cameron, Alexa Ostafin, Briege Mahoney, Miles Malik, Nikoletta Sidiropoulos
Background: During the COVID-19 pandemic, many molecular diagnostic laboratories performed high-throughput SARS-CoV-2 testing often with implementation of automated workflows. In parallel, vaccination campaigns resulted increasingly in specimens from fully vaccinated patients, with resultant clinical inquiries regarding positive results in this patient population. This prompted a quality improvement initiative to investigate the semi-automated testing workflow for false-positive results. The troubleshooting workflow is described and procedural improvements are outlined that serve as a resource for other molecular diagnostic laboratories that need to overcome testing anomalies in a semi-automated environment.
Methods: This workflow utilized the MagMax-96 Viral RNA kit and the CDC 2019-nCoV RT-qPCR Panel on the Agilent Bravo Liquid-Handler (Bravo). Screening of the environment, personnel, and the mechanical performance of instrumentation using low Ct checkerboard challenges was executed to identify sources of cross-contamination. Evaluation of the assay and reporting design was conducted.
Results: Specimen contamination was observed during the viral extraction process on the Bravo. Changes to the program reduced plate contamination by 50% and importantly revealed consistent hallmarks of contaminated samples. We adjusted the reporting algorithm using these indicators of false positives. False positives that were identified made up 0.11% of the 45 000+ tests conducted over the following 8 months.
Conclusions: These adjustments provided confident and quality results while maintaining turnaround time for patients and pandemic-related public health initiatives. This corrected false-positive rate is concordant with previously published studies from diagnostic laboratories utilizing automated systems and may be considered a laboratory performance standard for this type of testing.
{"title":"When False-Positives Arise: Troubleshooting a SARS-Coronavirus-2 (SARS-CoV-2) Detection Assay on a Semi-Automated Platform.","authors":"Kenneth J Hampel, Diana L Gerrard, Denise Francis, Jordan Armstrong, Margaret Cameron, Alexa Ostafin, Briege Mahoney, Miles Malik, Nikoletta Sidiropoulos","doi":"10.1093/jalm/jfae016","DOIUrl":"10.1093/jalm/jfae016","url":null,"abstract":"<p><strong>Background: </strong>During the COVID-19 pandemic, many molecular diagnostic laboratories performed high-throughput SARS-CoV-2 testing often with implementation of automated workflows. In parallel, vaccination campaigns resulted increasingly in specimens from fully vaccinated patients, with resultant clinical inquiries regarding positive results in this patient population. This prompted a quality improvement initiative to investigate the semi-automated testing workflow for false-positive results. The troubleshooting workflow is described and procedural improvements are outlined that serve as a resource for other molecular diagnostic laboratories that need to overcome testing anomalies in a semi-automated environment.</p><p><strong>Methods: </strong>This workflow utilized the MagMax-96 Viral RNA kit and the CDC 2019-nCoV RT-qPCR Panel on the Agilent Bravo Liquid-Handler (Bravo). Screening of the environment, personnel, and the mechanical performance of instrumentation using low Ct checkerboard challenges was executed to identify sources of cross-contamination. Evaluation of the assay and reporting design was conducted.</p><p><strong>Results: </strong>Specimen contamination was observed during the viral extraction process on the Bravo. Changes to the program reduced plate contamination by 50% and importantly revealed consistent hallmarks of contaminated samples. We adjusted the reporting algorithm using these indicators of false positives. False positives that were identified made up 0.11% of the 45 000+ tests conducted over the following 8 months.</p><p><strong>Conclusions: </strong>These adjustments provided confident and quality results while maintaining turnaround time for patients and pandemic-related public health initiatives. This corrected false-positive rate is concordant with previously published studies from diagnostic laboratories utilizing automated systems and may be considered a laboratory performance standard for this type of testing.</p>","PeriodicalId":46361,"journal":{"name":"Journal of Applied Laboratory Medicine","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140177115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: The clinically significant Factor V Leiden (FVL) point mutation (1691 G/A) causes replacement of Arg with Gln (glutamine), preventing activated protein C from inactivating Factor V leading to a lengthened clotting process. Individuals with the Factor V Leiden mutations have an increased risk for venous thrombosis. The aim of this study is to compare an unlabeled probe high-resolution melting analysis (HRMA) assay for Factor V Leiden mutation to a TaqMan hydrolysis assay (fluorogenic 5' nuclease PCR hydrolysis assay). HRMA is a post-PCR, homogenous, closed-tube system for the detection of sequence variants. Post-PCR, the amplicons are heated gradually until the melting temperature is reached and the fluorescent dye unbinds from the amplicon and exhibits low fluorescence. A melt-curve analysis is generated that is characteristic of a particular sequence variant. Therefore, HRMA allows for comparison of one base changes in genetic sequences based on their differences in melting rate.
Methods: Blood samples were collected in EDTA tubes and DNA extracted using the Roche MagNaPure. Reactions of both HRMA and TaqMan were carried out on 3 controls (1691 G/G, 1691 G/A, and 1691 G/G and G/A) and 20 samples.
Results: The genotypes for 3 reference controls purchased from Coriell (F5 1691 G/G, FVL 1691 G/A, and Heterozygote 1691 G/G and G/A) were confirmed by both the HRMA and TaqMan FVL assays. All 20 samples were confirmed to be F5 1691 G/G by both HRMA and TaqMan assays.
Conclusions: Comparing the results of the unlabeled probe HRMA FVL assay with a real-time TaqMan probe end point genotyping assay resulted in 100% sensitivity and 100% specificity for both assays.
{"title":"Comparison of an Unlabeled Probe High-Resolution Melting Analysis Assay (HRMA) for Factor V Leiden 1691 G/A Mutation to a Fluorogenic 5' Nuclease PCR Hydrolysis Assay.","authors":"Heping Han, Sally Lewis","doi":"10.1093/jalm/jfae039","DOIUrl":"10.1093/jalm/jfae039","url":null,"abstract":"<p><strong>Background: </strong>The clinically significant Factor V Leiden (FVL) point mutation (1691 G/A) causes replacement of Arg with Gln (glutamine), preventing activated protein C from inactivating Factor V leading to a lengthened clotting process. Individuals with the Factor V Leiden mutations have an increased risk for venous thrombosis. The aim of this study is to compare an unlabeled probe high-resolution melting analysis (HRMA) assay for Factor V Leiden mutation to a TaqMan hydrolysis assay (fluorogenic 5' nuclease PCR hydrolysis assay). HRMA is a post-PCR, homogenous, closed-tube system for the detection of sequence variants. Post-PCR, the amplicons are heated gradually until the melting temperature is reached and the fluorescent dye unbinds from the amplicon and exhibits low fluorescence. A melt-curve analysis is generated that is characteristic of a particular sequence variant. Therefore, HRMA allows for comparison of one base changes in genetic sequences based on their differences in melting rate.</p><p><strong>Methods: </strong>Blood samples were collected in EDTA tubes and DNA extracted using the Roche MagNaPure. Reactions of both HRMA and TaqMan were carried out on 3 controls (1691 G/G, 1691 G/A, and 1691 G/G and G/A) and 20 samples.</p><p><strong>Results: </strong>The genotypes for 3 reference controls purchased from Coriell (F5 1691 G/G, FVL 1691 G/A, and Heterozygote 1691 G/G and G/A) were confirmed by both the HRMA and TaqMan FVL assays. All 20 samples were confirmed to be F5 1691 G/G by both HRMA and TaqMan assays.</p><p><strong>Conclusions: </strong>Comparing the results of the unlabeled probe HRMA FVL assay with a real-time TaqMan probe end point genotyping assay resulted in 100% sensitivity and 100% specificity for both assays.</p>","PeriodicalId":46361,"journal":{"name":"Journal of Applied Laboratory Medicine","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141076425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Illegal Drug Use or Not-The Role of the Laboratory in Helping to Interpret Drug Test Results.","authors":"Jeanne Carr, Jeffrey Hurst, Larry A Broussard","doi":"10.1093/jalm/jfae008","DOIUrl":"10.1093/jalm/jfae008","url":null,"abstract":"","PeriodicalId":46361,"journal":{"name":"Journal of Applied Laboratory Medicine","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140289195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sara Ho, Jacqueline Darrow, Francesca De Simone, Amanda Calabro, Sara Gannon, Rianne Esquivel, Parmi Thakker, Kristina Khingelova, Aruna Rao, Yifan Zhang, Abhay Moghekar
Background: Standardizing cerebrospinal fluid (CSF) laboratory protocols will improve the reliability and availability of clinical biomarker testing required for prescription of novel Alzheimer disease (AD) therapies. This study evaluated several preanalytical handling and storage factors common to β-amyloid1-42 (Aβ1-42), β-amyloid1-40 (Aβ1-40), and phosphorylated tau (pTau181) concentrations including storage at different temperatures, extended cap contact, various mixing methods, and multiple freeze-thaw cycles.
Methods: Aβ1-42, Aβ1-40, and pTau181 concentrations were measured using LUMIPULSE G1200 automated assays. Samples were collected in polypropylene tubes of various volumes. Sample cap-contact was evaluated by storing samples in upright and inverted positions at either 4°C for 1 week or -80°C for 1 month. To assess mixing methods, samples were freeze-thawed and mixed by inversion, vortex, horizontal roller, or unmixed prior to assay sampling. The impact of successive freeze-thaw cycles was assessed through freezing, thawing, and analyzing CSF samples.
Results: Short-term storage at 4°C did not affect Aβ1-42, Aβ1-40, or pTau181 measurements in any tube type. Tube cap contact affected Aβ1-42 in 2.5 mL tubes and pTau181 levels in 10 mL tubes. No difference was observed between mixing methods. After 4 freeze-thaw cycles, Aβ1-42 significantly decreased but Aβ1-40 remained unchanged. Utilizing the Aβ1-42/Aβ1-40 ratio, Aβ1-42 values normalized, maintaining ratio values within ±5% of baseline measurements.
Conclusions: Storage of CSF at 4°C for 1 week or -80°C for 1 month did not significantly affect Aβ1-42, Aβ1-40, pTau181, or associated ratio measurements. Tube cap-contact impacted pTau181 and pTau181/Aβ1-42 values in larger tubes. Mixing methods are equivalent. The Aβ1-42/Aβ1-40 ratio compensates for freeze-thaw variability up to 4 cycles.
{"title":"Assessment of Preanalytical Cerebrospinal Fluid Handling and Storage Factors on Measurement of Aβ1-42, Aβ1-40, and pTau181 Using an Automated Chemiluminescent Platform.","authors":"Sara Ho, Jacqueline Darrow, Francesca De Simone, Amanda Calabro, Sara Gannon, Rianne Esquivel, Parmi Thakker, Kristina Khingelova, Aruna Rao, Yifan Zhang, Abhay Moghekar","doi":"10.1093/jalm/jfae033","DOIUrl":"10.1093/jalm/jfae033","url":null,"abstract":"<p><strong>Background: </strong>Standardizing cerebrospinal fluid (CSF) laboratory protocols will improve the reliability and availability of clinical biomarker testing required for prescription of novel Alzheimer disease (AD) therapies. This study evaluated several preanalytical handling and storage factors common to β-amyloid1-42 (Aβ1-42), β-amyloid1-40 (Aβ1-40), and phosphorylated tau (pTau181) concentrations including storage at different temperatures, extended cap contact, various mixing methods, and multiple freeze-thaw cycles.</p><p><strong>Methods: </strong>Aβ1-42, Aβ1-40, and pTau181 concentrations were measured using LUMIPULSE G1200 automated assays. Samples were collected in polypropylene tubes of various volumes. Sample cap-contact was evaluated by storing samples in upright and inverted positions at either 4°C for 1 week or -80°C for 1 month. To assess mixing methods, samples were freeze-thawed and mixed by inversion, vortex, horizontal roller, or unmixed prior to assay sampling. The impact of successive freeze-thaw cycles was assessed through freezing, thawing, and analyzing CSF samples.</p><p><strong>Results: </strong>Short-term storage at 4°C did not affect Aβ1-42, Aβ1-40, or pTau181 measurements in any tube type. Tube cap contact affected Aβ1-42 in 2.5 mL tubes and pTau181 levels in 10 mL tubes. No difference was observed between mixing methods. After 4 freeze-thaw cycles, Aβ1-42 significantly decreased but Aβ1-40 remained unchanged. Utilizing the Aβ1-42/Aβ1-40 ratio, Aβ1-42 values normalized, maintaining ratio values within ±5% of baseline measurements.</p><p><strong>Conclusions: </strong>Storage of CSF at 4°C for 1 week or -80°C for 1 month did not significantly affect Aβ1-42, Aβ1-40, pTau181, or associated ratio measurements. Tube cap-contact impacted pTau181 and pTau181/Aβ1-42 values in larger tubes. Mixing methods are equivalent. The Aβ1-42/Aβ1-40 ratio compensates for freeze-thaw variability up to 4 cycles.</p>","PeriodicalId":46361,"journal":{"name":"Journal of Applied Laboratory Medicine","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140869243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vishnu A Aravind, Valentina L Kouznetsova, Santosh Kesari, Igor F Tsigelny
Background: Esophageal cancer (EC) remains a global health challenge, often diagnosed at advanced stages, leading to high mortality rates. Current diagnostic tools for EC are limited in their efficacy. This study aims to harness the potential of microRNAs (miRNAs) as novel, noninvasive diagnostic biomarkers for EC. Our objective was to determine the diagnostic accuracy of miRNAs, particularly in distinguishing miRNAs associated with EC from control miRNAs.
Methods: We applied machine learning (ML) techniques in WEKA (Waikato Environment for Knowledge Analysis) and TensorFlow Keras to a dataset of miRNA sequences and gene targets, assessing the predictive power of several classifiers: naïve Bayes, multilayer perceptron, Hoeffding tree, random forest, and random tree. The data were further subjected to InfoGain feature selection to identify the most informative miRNA sequence and gene target descriptors. The ML models' abilities to distinguish between miRNA implicated in EC and control group miRNA was then tested.
Results: Of the tested WEKA classifiers, the top 3 performing ones were random forest, Hoeffding tree, and naïve Bayes. The TensorFlow Keras neural network model was subsequently trained and tested, the model's predictive power was further validated using an independent dataset. The TensorFlow Keras gave an accuracy 0.91. The WEKA best algorithm (naïve Bayes) model yielded an accuracy of 0.94.
Conclusions: The results demonstrate the potential of ML-based miRNA classifiers in diagnosing EC. However, further studies are necessary to validate these findings and explore the full clinical potential of this approach.
背景:食管癌(EC)仍是一项全球性的健康挑战,通常在晚期才被诊断出来,死亡率很高。目前的食管癌诊断工具疗效有限。本研究旨在利用微RNA(miRNA)作为食管癌新型非侵入性诊断生物标志物的潜力。我们的目标是确定 miRNAs 的诊断准确性,尤其是在区分与心血管疾病相关的 miRNAs 和对照 miRNAs 方面:我们将WEKA(Waikato Environment for Knowledge Analysis)和TensorFlow Keras中的机器学习(ML)技术应用于miRNA序列和基因靶标数据集,评估了几种分类器的预测能力:天真贝叶斯、多层感知器、Hoeffding树、随机森林和随机树。数据进一步经过 InfoGain 特征选择,以确定信息量最大的 miRNA 序列和基因靶标描述符。然后测试了 ML 模型区分与 EC 有关的 miRNA 和对照组 miRNA 的能力:结果:在测试的 WEKA 分类器中,表现最好的 3 个分类器分别是随机森林、Hoeffding 树和天真贝叶斯。随后对 TensorFlow Keras 神经网络模型进行了训练和测试,并使用独立数据集进一步验证了该模型的预测能力。TensorFlow Keras 的准确率为 0.91。WEKA 最佳算法(天真贝叶斯)模型的准确率为 0.94:研究结果证明了基于 ML 的 miRNA 分类器在诊断心血管疾病方面的潜力。不过,还需要进一步研究来验证这些发现,并探索这种方法的全部临床潜力。
{"title":"Using Machine Learning and miRNA for the Diagnosis of Esophageal Cancer.","authors":"Vishnu A Aravind, Valentina L Kouznetsova, Santosh Kesari, Igor F Tsigelny","doi":"10.1093/jalm/jfae037","DOIUrl":"10.1093/jalm/jfae037","url":null,"abstract":"<p><strong>Background: </strong>Esophageal cancer (EC) remains a global health challenge, often diagnosed at advanced stages, leading to high mortality rates. Current diagnostic tools for EC are limited in their efficacy. This study aims to harness the potential of microRNAs (miRNAs) as novel, noninvasive diagnostic biomarkers for EC. Our objective was to determine the diagnostic accuracy of miRNAs, particularly in distinguishing miRNAs associated with EC from control miRNAs.</p><p><strong>Methods: </strong>We applied machine learning (ML) techniques in WEKA (Waikato Environment for Knowledge Analysis) and TensorFlow Keras to a dataset of miRNA sequences and gene targets, assessing the predictive power of several classifiers: naïve Bayes, multilayer perceptron, Hoeffding tree, random forest, and random tree. The data were further subjected to InfoGain feature selection to identify the most informative miRNA sequence and gene target descriptors. The ML models' abilities to distinguish between miRNA implicated in EC and control group miRNA was then tested.</p><p><strong>Results: </strong>Of the tested WEKA classifiers, the top 3 performing ones were random forest, Hoeffding tree, and naïve Bayes. The TensorFlow Keras neural network model was subsequently trained and tested, the model's predictive power was further validated using an independent dataset. The TensorFlow Keras gave an accuracy 0.91. The WEKA best algorithm (naïve Bayes) model yielded an accuracy of 0.94.</p><p><strong>Conclusions: </strong>The results demonstrate the potential of ML-based miRNA classifiers in diagnosing EC. However, further studies are necessary to validate these findings and explore the full clinical potential of this approach.</p>","PeriodicalId":46361,"journal":{"name":"Journal of Applied Laboratory Medicine","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140899774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}