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1.
Lab Med ; 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38619036

ABSTRACT

OBJECTIVE: To assess the appropriateness of laboratory testing intervals and antiphospholipid syndrome (APS) incidence. METHODS: Between January 2010 and August 2022, insurance claims data of patients with disease codes for other thrombophilia (D68.6) and APS (V253) were retrieved in South Korea. Patients who received antiphospholipid antibody tests more than twice were classified as having suspected APS. The interval between the first 2 antiphospholipid antibody tests was evaluated in the patients with suspected APS. Patients with suspected APS who received anticoagulants for >180 days were classified as having APS. RESULTS: Overall, 8656 patients were classified as having suspected APS. The testing interval for the first 2 tests in patients with suspected APS was <6 and <12 weeks in 11.1% and 20.6% of cases, respectively, in 2010, gradually increasing to 21.0% and 35.4%, respectively, in 2021. Subsequently, 4344 patients were classified as having APS, with 65.0% being female. Only 330 patients were diagnosed with APS in 2021, down from 436 in 2020. CONCLUSION: This study showed a gradual increase in patients receiving antiphospholipid antibody testing with an inappropriate short-term interval, underscoring the need for laboratory stewardship to ensure an appropriate interval for APS testing.

2.
Ann Lab Med ; 44(3): 195-209, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38221747

ABSTRACT

Circulating tumor DNA (ctDNA) has emerged as a promising tool for various clinical applications, including early diagnosis, therapeutic target identification, treatment response monitoring, prognosis evaluation, and minimal residual disease detection. Consequently, ctDNA assays have been incorporated into clinical practice. In this review, we offer an in-depth exploration of the clinical implementation of ctDNA assays. Notably, we examined existing evidence related to pre-analytical procedures, analytical components in current technologies, and result interpretation and reporting processes. The primary objective of this guidelines is to provide recommendations for the clinical utilization of ctDNA assays.


Subject(s)
Circulating Tumor DNA , Humans , Circulating Tumor DNA/genetics , Biomarkers, Tumor/genetics , Prognosis , Neoplasm, Residual/genetics , Mutation , High-Throughput Nucleotide Sequencing
3.
Med Phys ; 51(3): 2230-2238, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37956307

ABSTRACT

BACKGROUND: Despite extensive efforts to obtain accurate segmentation of magnetic resonance imaging (MRI) scans of a head, it remains challenging primarily due to variations in intensity distribution, which depend on the equipment and parameters used. PURPOSE: The goal of this study is to evaluate the effectiveness of an automatic segmentation method for head MRI scans using a multistep Dense U-Net (MDU-Net) architecture. METHODS: The MDU-Net-based method comprises two steps. The first step is to segment the scalp, skull, and whole brain from head MRI scans using a convolutional neural network (CNN). In the first step, a hybrid network is used to combine 2.5D Dense U-Net and 3D Dense U-Net structure. This hybrid network acquires logits in three orthogonal planes (axial, coronal, and sagittal) using 2.5D Dense U-Nets and fuses them by averaging. The resultant fused probability map with head MRI scans then serves as the input to a 3D Dense U-Net. In this process, different ratios of active contour loss and focal loss are applied. The second step is to segment the cerebrospinal fluid (CSF), white matter, and gray matter from extracted brain MRI scans using CNNs. In the second step, the histogram of the extracted brain MRI scans is standardized and then a 2.5D Dense U-Net is used to further segment the brain's specific tissues using the focal loss. A dataset of 100 head MRI scans from an OASIS-3 dataset was used for training, internal validation, and testing, with ratios of 80%, 10%, and 10%, respectively. Using the proposed approach, we segmented the head MRI scans into five areas (scalp, skull, CSF, white matter, and gray matter) and evaluated the segmentation results using the Dice similarity coefficient (DSC) score, Hausdorff distance (HD), and the average symmetric surface distance (ASSD) as evaluation metrics. We compared these results with those obtained using the Res-U-Net, Dense U-Net, U-Net++, Swin-Unet, and H-Dense U-Net models. RESULTS: The MDU-Net model showed DSC values of 0.933, 0.830, 0.833, 0.953, and 0.917 in the scalp, skull, CSF, white matter, and gray matter, respectively. The corresponding HD values were 2.37, 2.89, 2.13, 1.52, and 1.53 mm, respectively. The ASSD values were 0.50, 1.63, 1.28, 0.26, and 0.27 mm, respectively. Comparing these results with other models revealed that the MDU-Net model demonstrated the best performance in terms of the DSC values for the scalp, CSF, white matter, and gray matter. When compared with the H-Dense U-Net model, which showed the highest performance among the other models, the MDU-Net model showed substantial improvements in the HD view, particularly in the gray matter region, with a difference of approximately 9%. In addition, in terms of the ASSD, the MDU-Net model outperformed the H-Dense U-Net model, showing an approximately 7% improvements in the white matter and approximately 9% improvements in the gray matter. CONCLUSION: Compared with existing models in terms of DSC, HD, and ASSD, the proposed MDU-Net model demonstrated the best performance on average and showed its potential to enhance the accuracy of automatic segmentation for head MRI scans.


Subject(s)
Image Processing, Computer-Assisted , Neural Networks, Computer , Image Processing, Computer-Assisted/methods , Brain/diagnostic imaging , Magnetic Resonance Imaging/methods , Scalp
4.
Clin Biochem ; 118: 110609, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37414329

ABSTRACT

BACKGROUND: Interstitial lung abnormalities (ILAs) are associated with the risk of progression to interstitial lung diseases (ILDs). Krebs von den Lungen 6 (KL-6) and surfactant protein (SP)-A have been used as biomarkers of ILDs. In this study, we evaluated the levels of these biomarkers and identified their clinical correlations in healthy individuals to assess their usefulness in the diagnosis of ILAs. METHODS: The patient samples were categorized into three groups: healthy, disease, and ILD groups. We used the automated immunoassay HISCL KL-6 and SP-A assay kits. The analytical performance evaluation involved precision, linearity, comparison, establishment of reference intervals, and determination of the cutoff points. We also analyzed the correlations between presence of abnormalities on chest radiography and computed tomography (CT) or pulmonary function test (PFT) and serum levels in the healthy group. RESULTS: KL-6 and SP-A assays showed good analytical performance. The KL-6 and SP-A cutoff values were 304 U/mL and 43.5 ng/mL between the ILD and healthy groups, respectively, which were lower than the values recommended by the manufacturer. In the clinical correlations with radiological findings, SP-A values in subjects with lung abnormalities on CT scans were significantly higher than those in normal scans. There was no significant difference in KL-6 and SP-A levels among PFT patterns; however, both serum levels in the mixed pattern showed higher values than those in the other patterns. CONCLUSIONS: The results revealed a positive association between increased serum levels of SP-A and KL-6 and clinical characteristics as incidental findings on chest imaging and reduced lung function.


Subject(s)
Lung Diseases, Interstitial , Pulmonary Surfactant-Associated Protein A , Humans , Lung Diseases, Interstitial/diagnostic imaging , Lung Diseases, Interstitial/complications , Biomarkers , Tomography, X-Ray Computed/methods , Mucin-1 , Respiratory Function Tests
5.
Clin Lab ; 69(4)2023 Apr 01.
Article in English | MEDLINE | ID: mdl-37057943

ABSTRACT

BACKGROUND: This study investigated the performance evaluation of total prostate specific antigen (tPSA) testing using Cobas Pure integrated solutions system (calibrated against WHO IS 96/670) and the comparison with established measurement systems with different traceability. METHODS: The evaluation was performed in terms of imprecision, linearity, detection limit, and correlation with Alinity i (calibrated against WHO IS 96/670) and Unicel DxI 800 (calibrated against the manufacturer's working calibrators). RESULTS: Within-laboratory reproducibility and repeatability were observed less than 1.2%. Linearity was achieved within the claimed analytical measurement range. The claimed LoB and LoD were experimentally verified. All the correlation coefficients among the assays indicated good correlation, but the significant mean bias with Unicel DxI 800 using a different calibrator were observed. CONCLUSIONS: Since the tPSA calibrators against different traceability is still commercially available, our research could convey the impact of calibration on tPSA results as well as the performance information of a new assay for tPSA.


Subject(s)
Prostate-Specific Antigen , Prostatic Neoplasms , Humans , Male , Calibration , Reproducibility of Results , Immunologic Tests , Laboratories , Prostatic Neoplasms/diagnosis
6.
Nutrients ; 15(4)2023 Feb 04.
Article in English | MEDLINE | ID: mdl-36839166

ABSTRACT

Acetaminophen (APAP) overdose-induced hepatotoxicity reduces the activity of sirtuin-1 (Sirt1) along with heme oxygenase 1 (HO-1) and promotes inflammatory responses and oxidative stress. Although the extract of Curcuma aromatica Salisb. (CAS) possesses hepatoprotective properties, scientific evidence on whether CAS prevents hepatotoxicity and the underlying molecular mechanisms are lacking. Here, we hypothesized that CAS ameliorates hepatotoxicity by inhibiting inflammation and oxidative stress via Sirt1/HO-1 signaling. CAS pretreatment at doses of 200 and 400 µg/mL significantly increased cell viability in APAP-treated primary hepatocytes. The expression of inducible nitric oxide synthase (iNOS) substantially increased after APAP treatment; however, this expression significantly decreased in cells pretreated with 100, 200, and 400 µg/mL CAS. CAS increased Sirt1 and HO-1 levels in APAP-treated hepatocytes in a dose-dependent manner. When CAS was orally administered to mice at doses of 20 or 100 mg/kg for 7 days, the APAP-induced increase in serum aspartate aminotransferase and alanine aminotransferase levels was inhibited. Moreover, CAS decreased IL-6, TNF-α, and IL-1ß, increased IL-10, suppressed ROS generation, increased glutathione levels, inhibited iNOS and cyclooxygenase-2, and enhanced Sirt1 and HO-1 in the mouse model of APAP-induced hepatotoxicity. These findings suggest that CAS could be used as a natural hepatoprotective drug to treat APAP-induced injury.


Subject(s)
Acetaminophen , Chemical and Drug Induced Liver Injury , Curcuma , Plant Extracts , Animals , Mice , Acetaminophen/adverse effects , Chemical and Drug Induced Liver Injury/drug therapy , Chemical and Drug Induced Liver Injury/metabolism , Curcuma/chemistry , Heme Oxygenase-1/metabolism , Liver/metabolism , Mice, Inbred C57BL , Oxidative Stress , Signal Transduction , Sirtuin 1/metabolism , Plant Extracts/pharmacology
7.
Ann Lab Med ; 43(1): 29-37, 2023 01 01.
Article in English | MEDLINE | ID: mdl-36045054

ABSTRACT

Background: High LDL-cholesterol (LDL-C) is an established risk factor for cardiovascular disease and is considered an important therapeutic target. It can be measured directly or calculated from the results of other lipid tests. The Friedewald formula is the most widely used formula for calculating LDL-C. We modified the Friedewald formula for a more accurate and practical estimation of LDL-C. Methods: Datasets, including measured triglyceride, total cholesterol, HDL-cholesterol, and LDL-C concentrations were collected and assigned to derivation and validation sets. The datasets were further divided into five groups based on triglyceride concentrations. In the modified formula, LDL-C was defined as total cholesterol - HDL-cholesterol - (triglyceride/adjustment factor). For each group, the adjustment factor that minimized the difference between measured LDL-C and calculated LDL-C using modified formula was obtained. For validation, measured LDL-C and LDL-C calculated using the modified formula (LDL-CM), Friedewald formula (LDL-CF), Martin-Hopkins formula (LDL-CMa), and Sampson formula (LDL-CS) were compared. Results: In the derivation set, the adjustment factors were 4.7, 5.9, 6.3, and 6.4 for the groups with triglyceride concentrations <100, 101-200, 201-300, and >300 mg/dL, respectively. In the validation set, the coefficient of determination (R2) between measured and calculated LDL-C was higher for LDL-CM than for LDL-CF (R2=0.9330 vs. 0.9206). The agreement according to the National Cholesterol Education Program Adult Treatment Panel III classification of LDL-C was 86.36%, 86.08%, 86.82%, and 86.15% for LDL-CM, LDL-CF, LDL-CMa, and LDL-CS, respectively. Conclusions: We proposed a practical, improved LDL-C calculation formula by applying different factors depending on the triglyceride concentration.


Subject(s)
Cardiovascular Diseases , Hypercholesterolemia , Hyperlipidemias , Adult , Cholesterol, HDL , Cholesterol, LDL , Humans , Triglycerides
8.
J Clin Lab Anal ; 37(1): e24807, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36525335

ABSTRACT

BACKGROUND: Small dense low-density lipoprotein (sdLDL) possesses atherogenic potential and is predicted to be susceptible to atherogenic modifications, which further increases its atherogenicity. However, studies on the association between measured or estimated sdLDL cholesterol (sdLDL-C) levels and atherogenic modification in diverse population groups are lacking. METHODS: Surplus serum samples were collected from male subjects with type 2 diabetes mellitus (DM) under treatment (n = 300) and without DM (non-DM; n = 150). sdLDL and oxidized LDL (oxLDL) levels were measured using the Lipoprint LDL subfractions kit (Quantimetrix Corporation) and the Mercodia oxidized LDL competitive enzyme-linked immunosorbent assay kit (Mercodia), respectively. The estimated sdLDL-Cs were calculated from two relevant equations. The effects of sdLDL-C on oxLDL were assessed using multiple linear regression (MLR) models. RESULTS: The mean (±SD) of measured sdLDL-C and oxLDL concentrations were 11.8 ± 10.0 mg/dl and 53.4 ± 14.2 U/L in the non-DM group and 0.20 ± 0.81 mg/dl and 46.0 ± 15.3 U/L in the DM group, respectively. The effects of measured sdLDL-Cs were significant (p = 0.031), whereas those of estimated sdLDL-Cs were not (p = 0.060, p = 0.116) in the non-DM group in the MLR models. The effects of sdLDL-Cs in the DM group were not significant. CONCLUSION: In the general population, high level of sdLDL-C appeared to be associated with high level of oxLDL. The equation for estimating sdLDL-C developed from a general population should be applied with caution to a special population, such as patients with DM on treatment.


Subject(s)
Atherosclerosis , Diabetes Mellitus, Type 2 , Humans , Male , Cholesterol, LDL , Biomarkers , Risk Factors
9.
Ann Lab Med ; 43(3): 244-252, 2023 May 01.
Article in English | MEDLINE | ID: mdl-36544336

ABSTRACT

Background: New creatinine-based estimated glomerular filtration rate (eGFR) equations, including the 2021 Chronic Kidney Disease Epidemiology Collaboration (2021 CKD-EPI) and European Kidney Function Consortium (EKFC) equations, have been introduced recently. We assessed the performance of the 2021 CKD-EPI and EKFC equations in the Korean population. Methods: We analyzed 1,654 Korean patients aged ≥18 years who underwent chromium-51-ethylenediamine tetraacetic acid GFR measurements (mGFR). Bias (eGFR-mGFR), root mean square error (RMSE), and proportion of eGFR within 30% of mGFR (P30) of the 2009 CKD-EPI, 2021 CKD-EPI, and EFKC equations were compared. The concordance rate between eGFR and mGFR categories was evaluated. Both eGFR and mGFR categories were classified into six groups: ≥90, 89-60, 59-45, 44-30, 29-15, and <15 mL/min/1.73 m2. Results: The median bias (mL/min/1.73 m2) was 1.8 for the 2009 CKD-EPI equation, 4.8 for the 2021 CKD-EPI equation, and -0.3 for the EKFC equation. The P30 and RMSE were 78.2% and 17.0 for the 2009 CKD-EPI equation, 75.6% and 17.4 for the 2021 CKD-EPI equation, and 80.0% and 16.7 for the EKFC equation, respectively. The overall GFR category concordance rate between eGFR and mGFR was 63.4% for the 2009 CKD-EPI equation, 60.5% for the 2021 CKD-EPI equation, and 61.0% for the EKFC equation. Conclusions: Among the three eGFR equations, the EKFC equation had the smallest bias and highest P30 in Koreans. The 2009 CKD-EPI equation had a lower bias than the 2021 CKD-EPI equation.


Subject(s)
East Asian People , Renal Insufficiency, Chronic , Humans , Adolescent , Adult , Glomerular Filtration Rate , Creatinine , Renal Insufficiency, Chronic/diagnosis
10.
Sensors (Basel) ; 22(19)2022 Sep 30.
Article in English | MEDLINE | ID: mdl-36236548

ABSTRACT

Soil moisture has been considered a key variable in governing the terrestrial ecosystem. However, it is challenging to preserve indigenous soil characteristics using conventional soil moisture monitoring methods that require maximum soil contacts. To overcome this issue, we developed a non-destructive method of evaluating soil moisture using a contactless ultrasonic system. This system was designed to measure leaky Rayleigh waves at the air-soil joint-half space. The influences of soil moisture on leaky Rayleigh waves were explored under sand, silt, and clay in a controlled experimental design. Our results showed that there were strong relationships between the energy and amplitude of leaky Rayleigh waves and soil moisture for all three soil cases. These results can be explained by reduced soil strengths during evaporation processes for coarse soil particles as opposed to fine soil particles. To evaluate soil moisture based on the dynamic parameters and wave properties obtained from the observed leaky Rayleigh waves, we used the random forest model. The accuracy of predicted soil moisture was exceptional for test data sets under all soil types (R2 ≥ 0.98, RMSE ≤ 0.0089 m3 m-3). That is, our study demonstrated that the leaky Rayleigh waves had great potential to continuously assess soil moisture variations without soil disturbances.


Subject(s)
Ecosystem , Soil , Clay , Sand , Ultrasonics
11.
Sensors (Basel) ; 22(18)2022 Sep 16.
Article in English | MEDLINE | ID: mdl-36146379

ABSTRACT

A recently developed contactless ultrasonic testing scheme is applied to define the optimal saw-cutting time for concrete pavement. The ultrasonic system is improved using wireless data transfer for field applications, and the signal processing and data analysis are proposed to evaluate the modulus of elasticity of early-age concrete. Numerical simulation of leaky Rayleigh wave in joint-half space including air and concrete is performed to demonstrate the proposed data analysis procedure. The hardware and algorithms developed for the ultrasonic system are experimentally validated with a comparison of saw-cutting procedures. In addition, conventional methods for the characterization of early-age concrete, including pin penetration and maturity methods, are applied. The results demonstrated that the developed wireless system presents identical results to the wired system, and the initiation time of leaky Rayleigh wave possibly represents 5% of raveling damage compared to the optimal saw cutting. Further data analysis implies that saw-cutting would be optimally performed at approximately 11.5 GPa elastic modulus of concrete obtained by the wireless and contactless ultrasonic system.


Subject(s)
Algorithms , Ultrasonics , Computer Simulation , Elastic Modulus , Elasticity
12.
Ann Lab Med ; 42(6): 630-637, 2022 Nov 01.
Article in English | MEDLINE | ID: mdl-35765871

ABSTRACT

Background: The top-down (TD) approach using internal quality control (IQC) data is regarded a practical method for estimating measurement uncertainty (MU) in clinical laboratories. We estimated the MU of 14 clinical chemistry analytes using the TD approach and evaluated the effect of lot changes on the MU. Methods: MU values were estimated using subgrouping by reagent lot changes or using the data as a whole, and both methods were compared. Reagent lot change was simulated using randomly generated data, and the mean values and MU for two IQC datasets (different QC material lots) were compared using statistical methods. Results: All MU values calculated using subgrouping were lower than the total values; however, the average differences were minimal. The simulation showed that the greater the increase in the extent of the average shift, the larger the difference in MU. In IQC data comparison, the mean values and MU exhibited statistically significant differences for most analytes. The MU calculation methods gave rise to minimal differences, suggesting that IQC data in clinical laboratories show no significant shift. However, the simulation results demonstrated that notable differences in the MU can arise from significant variations in IQC results before and after a reagent lot change. Additionally, IQC material lots should be treated separately when IQC data are collected for MU estimation. Conclusions: Lot changes in IQC data are a key factor affecting MU estimation and should not be overlooked during MU estimation.


Subject(s)
Chemistry, Clinical , Clinical Laboratory Services , Humans , Laboratories, Clinical , Quality Control , Uncertainty
13.
Surg Endosc ; 36(2): 1310-1319, 2022 02.
Article in English | MEDLINE | ID: mdl-33709227

ABSTRACT

BACKGROUND: Although upper gastrointestinal (GI) neoplasms are not rare in patients with familial adenomatous polyposis (FAP), few studies have focused on them and the long-term outcomes of their treatment by endoscopy. Therefore, we aimed to investigate the prevalence and endoscopic treatment outcomes of upper GI neoplasms in patients with FAP. METHODS: Among 215 patients diagnosed with FAP between January 1991 and December 2019, 208 who underwent esophagogastroduodenoscopy were eligible. The clinical features and endoscopic treatment outcomes of upper GI neoplasms were retrospectively investigated and analyzed. RESULTS: Among the enrolled patients, 113 (54.3%) had one or more upper GI neoplasms: gastric adenoma (n = 34), gastric cancer (n = 7), nonampullary duodenal adenoma (n = 86), and ampullary adenoma (n = 53). Among patients with gastric neoplasms (n = 37), 24 (64.9%) underwent treatment (endoscopic treatment: 22, surgery: 2). No tumor-related mortality occurred during median follow-up of 106 months (interquartile range [IQR] 63-174). Endoscopic treatment was performed in 47 (54.7%) of 86 patients with nonampullary duodenal adenoma and in 32 (60.4%) of 53 patients with ampullary adenoma. No patient underwent surgery for duodenal neoplasms, and no tumor-related mortality occurred during median follow-up of 88 months (IQR 42-145). The proportion of patients with increased Spigelman stage at 2 years after the initial diagnosis or treatment was significantly higher in untreated group than in the group treated for duodenal neoplasms (27.3% vs. 0.0%, p = 0.001). CONCLUSION: Endoscopic surveillance in FAP patients is important for the detection and treatment of upper GI neoplasms in early stage. In particular, endoscopic therapy for duodenal neoplasms can reduce the severity of duodenal polyposis.


Subject(s)
Adenomatous Polyposis Coli , Adenomatous Polyposis Coli/epidemiology , Adenomatous Polyposis Coli/surgery , Endoscopy, Gastrointestinal , Humans , Prevalence , Retrospective Studies , Treatment Outcome
16.
Nutrients ; 13(12)2021 Nov 27.
Article in English | MEDLINE | ID: mdl-34959841

ABSTRACT

Gongjin-dan (GJD) is a multiherbal formula produced from 10 medicinal herbs and has been traditonally used as an oriental medicine to treat cardiovascular diseases, alcoholic hepatitis, mild dementia, and anemia. Additionally, increasing evidence suggests that GJD exerts neuroprotective effects by suppressing inflammation and oxidative stress-induced events to prevent neurological diseases. However, the mechanism by which GJD prevents oxidative stress-induced neuronal injury in a mature neuron remains unknown. Here, we examined the preventive effect and mechanism of GJD on primary cortical neurons exposed to hydrogen peroxide (H2O2). In the neuroprotection signaling pathway, Sirtuin1 is involved in neuroprotective action as a therapeutic target for neurological diseases. After pre-treatment with GJD at three concentrations (10, 25, and 50 µg/mL) and stimulation by H2O2 (30 µM) for 24 h, the influence of GJD on Sirtuin1 activation was assessed using immunocytochemistry, real-time PCR, western blotting, and flow cytometry. GJD effectively ameliorated H2O2-induced neuronal death against oxidative damage through Sirtuin1 activation. In addition, GJD-induced Sirtuin1 activation accelerated elongation of new axons and formation of synapses via increased expression of nerve growth factor and brain-derived neurotrophic factor, as well as regeneration-related genes. Thus, GJD shows potential for preventing neurological diseases via Sirtuin1 activation.


Subject(s)
Neuronal Outgrowth/drug effects , Oxidative Stress/drug effects , Plant Extracts/pharmacology , Signal Transduction/drug effects , Sirtuin 1/metabolism , Animals , Cerebral Cortex/growth & development , Hydrogen Peroxide/adverse effects , Neurons/drug effects , Neuroprotective Agents/pharmacology , Rats , Rats, Sprague-Dawley
17.
Genes (Basel) ; 12(6)2021 05 26.
Article in English | MEDLINE | ID: mdl-34073420

ABSTRACT

Grading the pathogenicity of BRCA1/2 variants has great clinical importance in patient treatment as well as in the prevention and screening of hereditary breast and ovarian cancer (HBOC). For accurate evaluation, confirming the splicing effect of a possible splice site variant is crucial. We report a significant splicing variant (c.5074+3A>C) in BRCA1 in a patient with recurrent ovarian cancer. Next-generation sequencing (NGS) of BRCA1/2 from patient's peripheral blood identified the variant, which was strongly suspected of being a splicing mutation based on in silico predictions. Direct RNA analysis yielded multiple transcripts, and TOPO cloning of the complementary DNA (cDNA) and Sanger sequencing revealed an aberrant transcript with an insertion of the first 153 bp of intron 17, and another transcript with the 153 bp insertion along with an exon 18 deletion. A premature termination codon was presumed to be formed by the 153 bp partial intron retention common to the two transcripts. Therefore, BRCA1 c.5074+3A>C was classified as a likely pathogenic variant. Our findings show that active use of functional studies of variants suspected of altered splicing are of great help in classifying them.


Subject(s)
BRCA1 Protein/genetics , Hereditary Breast and Ovarian Cancer Syndrome/genetics , RNA Splicing , Female , Hereditary Breast and Ovarian Cancer Syndrome/pathology , Humans , Middle Aged , Mutation , RNA-Seq
18.
Sensors (Basel) ; 21(10)2021 May 14.
Article in English | MEDLINE | ID: mdl-34069052

ABSTRACT

We propose a novel contactless ultrasonic method for monitoring the hardening behavior of cementitious materials. The goal of this method is to obtain high-quality data to compare the unique hardening process between rapid setting cement (RSC) and ordinary Portland cement (OPC) mortars without physical coupling to the surface of the specimens. To monitor the hardening behavior of cementitious materials, conventional approaches use contact or embedded-type sensors, which limit field application. Our solution is to measure leaky Rayleigh waves at the interface between air and cementitious materials, which allows for the estimation of the physical state of the medium in real time. The modulus development was back-calculated based on the increment of wave velocity using the developed sensor array and transform-based signal processing. We experimentally demonstrated that the proposed method possibly exhibits unique hardening information about flash setting, effects of a retarder, and modulus increments from RSC specimens.

19.
J Clin Lab Anal ; 34(12): e23524, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32812259

ABSTRACT

BACKGROUND: As next-generation sequencing (NGS) technology matures, various amplicon-based NGS tests for BRCA1/2 genotyping have been introduced. This study was designed to evaluate an NGS test using a newly released amplicon-based panel, AmpliSeq for Illumina BRCA Panel (AmpliSeq panel), for detection of clinically significant BRCA variants, and to compare it to another amplicon-based NGS test confirmed by Sanger sequencing. METHODS: We reviewed BRCA test results done by NGS using the TruSeq Custom Amplicon kit from patients suspected of hereditary breast/ovarian cancer syndrome (HBOC) in 2018. Of those, 96 residual samples with 100 clinically significant variants were included in this study using predefined criteria: 100 variants were distributed throughout the BRCA1 and BRCA2 genes. All target variants were confirmed by Sanger sequencing. Duplicate NGS testing of these samples was performed using the AmpliSeq panel, and the concordance of results from the two amplicon-based NGS tests was assessed. RESULTS: Ninety-nine of 100 variants were detected in duplicate BRCA1/2 genotyping using the AmpliSeq panel (sensitivity, 99%; specificity, 100%). In the discordant case, one variant (BRCA1 c.3627dupA) was found only in repeat 1, but not in repeat 2. Automated nomenclature of all variants, except for two indel variants, was in consensus with Human Genome Variation Society nomenclature. CONCLUSION: Our findings confirm that the analytic performance of the AmpliSeq panel is satisfactory, with high sensitivity and specificity.


Subject(s)
BRCA1 Protein/genetics , BRCA2 Protein/genetics , High-Throughput Nucleotide Sequencing , Sequence Analysis, DNA , Female , Genetic Variation/genetics , High-Throughput Nucleotide Sequencing/methods , High-Throughput Nucleotide Sequencing/standards , Humans , Sensitivity and Specificity , Sequence Analysis, DNA/methods , Sequence Analysis, DNA/standards
20.
J Clin Lab Anal ; 34(12): e23550, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32862477

ABSTRACT

BACKGROUND: Delta check is a patient-based QC tool for detecting errors by comparing current and previous test results of patient. Reference change value (RCV) is adopted in guidelines as method for delta check, but the performance is not verified. We applied RCV-based delta check method to patients' data and modified for application. MATERIALS AND METHODS: Reference change value were calculated using results of internal QC materials and biological variation data. Test results of 17 analytes in inpatients, outpatients, and health examination recipients were collected. The detection rates of currently used delta check method and those of RCV-based method were compared, and the methods were modified. RESULTS: Reference change value-based method had higher detection rates compared to conventional method. Applied modifications reduced detection rates. Removing the pairs of results within reference interval reduced detection rates (0.42% ~ 10.92%). When RCV was divided by time interval, the detection rates were similar to prior rates in outpatients (0.19% ~ 1.34%). Using RCV multiplied by twice the upper limit of reference value as cutoff reduced the detection rate (0.07% ~ 1.58%). CONCLUSIONS: Reference change value is a robust criterion for delta check and included in clinical laboratory practice guideline. However, RCV-based method generates high detection rates which increase workload. It needs modification for use in clinical laboratories.


Subject(s)
Clinical Chemistry Tests/standards , Quality Improvement , Clinical Chemistry Tests/methods , Humans , Reference Values , Reproducibility of Results
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