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Circulating tumor DNA (ctDNA) has shown great potential in targeted therapy efficacy prediction, monitoring, high-risk population screening, differential diagnosis, minimal residual disease (MRD) monitoring, and prognosis prediction. The detection of specific gene mutations in ctDNA had been included in clinical practice guidelines for certain tumors to predict the drug efficacy and monitor resistance. A small number of approved companion diagnostic reagents have been used in clinical setting. However, the clinical validity of most ctDNA-related biomarkers it still in the research stage. Besides, the establishment and validation of laboratory-developed tests (LDT) are also problems that need to be solved urgently. Therefore, for the moment, the clinical application of ctDNA analysis is like two sides of a coin, with both opportunities and challenges.
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Circulating tumor DNA analysis is the focused issue in clinical research. A few of biomarkers have been used in clinical practice, while some are in the discovery phase. The key challenges for clinical laboratories on the way from discovery to clinical practice of the circulating tumor DNA analysis, including choosing the intended use based on evidence for clinical validity and utility, quality assurance for the testing process, reporting and interpretation for the results will be discussed.
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Assays of specific immunoglobulin M (IgM) and immunoglobulin G (IgG) have been supplemented in 'diagnosis and treatment guidelines of Novel Coronavirus pneumonia' (7th edition) issued by National Health Commission of the People’s Republic of China as an auxiliary evidence to diagnose Novel Coronavirus pneumonia. However, the false positive results is a major problem in the application of antibody assays. The factors causing the false positive results were analyzed and the ways were discussed to reduce the false positive results. The false positive results of antibody assays can be reduced, but they cannot be fully resolved. Antibody assays are valuable criteria for the diagnosis of suspected cases with negative nucleic acid results only if at least two dynamic tests are used.
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Assays of specific immunoglobulin M (IgM) and immunoglobulin G (IgG) have been supplemented in "diagnosis and treatment guidelines of COVID-19" (7th edition) issued by National Health Commission of the People′s Republic of China as an auxiliary evidence to diagnose COVID-19. However, the false positive results is a major problem in the application of antibody assays. The factors causing the false positive results were analyzed and the ways were discussed to reduce the false positive results. The false positive results of antibody assays can be reduced, but they cannot be fully resolved. Antibody assays are valuable criteria for the diagnosis of suspected cases with negative nucleic acid results only if at least two dynamic tests are used.
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Circulating tumor DNA analysis is the focused issue in clinical research. A few of biomarkers have been used in clinical practice, while some are in the discovery phase. The key challenges for clinical laboratories on the way from discovery to clinical practice of the circulating tumor DNA analysis, including choosing the intended use based on evidence for clinical validity and utility, quality assurance for the testing process, reporting and interpretation for the results will be discussed.
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Autoantibodies are useful in diagnosis , monitoring treatment and prognosis for patients with autoimmune disease.Recently, some laboratories expanded the use of autoantibodies to the screening of autoimmune diseases for all population , as well as prediction of onsets of diseases .We will emphasize on the correct use of autoantibodies and discuss the problems to screen autoimmune diseases for all population and predict autoimmune diseases .The correct intended use for a test is the first step of quality assurance and the premise to ensure the clinical validity.Otherwise, the other actions for quality control will be in a way that defeats one′s purpose , that is "go south by driving the chariot north".
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Diverse technological advances in laboratory testing like DNA sequencing,have played important roles at the beginning of precision medicine.And the development of precision medicine will also require the advances of laboratory testing.However,with more new methods and biomarkers applied in clinical practice,the standardization of clinical laboratories testing is confronting great challenges.We will discuss the key challenges related to standardization of commercial reagents or systems and clinical tests,such as the choice of biomarkers,laboratory-developed tests and interpretation and reporting of the results.
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Objective To evaluate the performance of KRAS gene mutation detection in 2014 external quality assessment ( EQA ) program and discuss the problems in clinical laboratories .Methods The sample panel of 2014 EQA program contained 5 artificial formalin-fixed, paraffin-embedded ( FFPE) samples.The participating laboratories were asked to report their results before the deadline .The scores of EQA and the rate of overall coincidence , false positive and false negative were calculated .Results The EQA program for KRAS testing was set twice a year .In 2014, 58 and 57 valid lab results were submitted respectively.About 79.31%(46/58)and 94.73%(54/57) of the laboratories were correct for all samples. The coincidence rate of positive samples were 93.53% ( 217/232 ) and 96.49% ( 165/171 ) . The coincidence rate for negative ones were 100%(58/58) and 98.25% (112/114).The false-negative ratio was 1.29%( 3/232 ) and 0%.The false-positive ratio was 4.14% ( 12/290 ) and 3.15% ( 9/285 ) . Conclusions The results of 2014 EQA for KRAS gene mutation testing suggested that the performance of laboratories had been improved significantly , however , the false-negative and false-positive results had always been the major problems affecting the accuracy of KRAS mutations testing .Laboratories needed to standardize the testing process and manufacturers should optimize the reagents and the way of interpretation , to guarantee the performance of KRAS gene mutation detection .
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As a kind of common autoimmune diseases,rheumatoid arthritis (RA) affected the health of human beings seriously.In the past,serological diagnosis of RA solely relied on the detection of rheumatoid factor (RF),but its specificity was not satisfactory.Lately,people found that anti-cyclic citrullinated peptide (CCP) antibody was a serological indicator of RA.Now,there have been a series of kits for the detection of anti-CCP antibodies to diagnose RA.The sensitivity and specificity of anti-CCP antibody detection are better than those of RF detection.This paper reviews the significance and value of anti-CCP antibody detection used for clinical diagnosis in the recent years,while systematically compares the sensitivities and specificities between several common commercial kits and methods of anti-CCP antibodies detection.
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As a result of the molecular diagnosis blossoming , the time of clinical laboratory can be chronologically divided into two periods , the “pre-molecular diagnosis days” and the “post-molecular diagnosis days”.Functional genomics researches in the post-genome era reveal that gene encoding the drug metabolic enzyme influences on drug response.Based on studies of cell signaling pathways in targeted cancer therapy, curative effect is related to the mutations of corresponding target gene involved.Detection of the genotype and the specific mutation encouraged the era of specific diseases care into the era of individualized care, which allows the clinical laboratories working behind-the-scenes come to the fore in disease treatment.Gene amplification technology has been one of backbone technology used in molecular diagnosis.The key of whether the results of molecular diagnosis can be used in the diagnosis and treatment includes the standard laboratory partitions and the strict quality assurance measures during the pre -, during and post-analysis periods.The personnel team in future molecular diagnostic laboratory will consist of clinical laboratory physicians , pathologists , pharmacists and bioinformatics experts , genetic counselors and clinical experts, and so on.
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Objective To investigate the protective effects of Chinese medicine compound ZDS against digestive tact damage caused by oxygen free radical after the burns. Methods 20 SD rats were randomly divided into ZDS (with ZDS treatment,n=10) and Con (control,n=10) groups. The rats were inflicted with 30%TBSA full thickness burn on the back and fed with Chinese medicine compound ZDS or warm water (2 mL/time,2 times a day) . On the 3rd and 9th postburn day, the serum samples were harvested from portal vein and the serum superoxide dismutase (SOD) activity,the levels of malondiadehycle (MDA) were detected. Meanwhile, the bacteria translocation of parenteral organs and the histology of intestine were also observed. Results The SOD activity in ZDS group on day 9 post burn increased significantly than that in Con group( <0.05);but at the same timepoint, compared with Con group, the MDA level in ZDS group was decreased obviously ( <0.05) . Conclusion Chinese medicine compound ZDS can partly protect the digestive tact against damage caused by oxygen free radical after the burns.
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Multiple chromosomal aberrations, nucleotide substitutions, and epigenetic modifications may occur in human cancer cells, which drive malignant transformation. The Cancer Genome Atlas (TCGA) project aims to promote large-scale multi-dimensional analysis of these molecular characteristics in human cancer and rapidly provide data to researchers. In this study, we introduce four flow paths of the production of TCGA data, the collections of various cancer types, the data category and level, and the standardized pipeline of data analysis, as well as several existing data analytical tools. We used ovarian cancer as an example to introduce the application of the TCGA data in the analyses of mutation, copy number, analysis, and expression. We summarized the important findings of glioblasto-ma by TCGA teams.
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Purpose To explore the relationship between the change of space anterior to right portal vein and the pathological staging in liver ifbrosis/cirrhosis. Materials and Methods Plain and contrast enhanced CT scan were performed in patients with biopsy proven liver ifbrosis/cirrhosis including S1 in 17 patients, S2 in 13 patients, S3 in 15 patients, S4 in 21 patients and cirrhosis in 22 patients. Twenty subjects were included as control group. The width of anterior space of right portal vein was measured on contrast enhanced CT and correlated with ifbrosis staging. The receiver operating characteristic curve was created for cirrhosis diagnosis. Results The width of anterior space of right portal vein enlarged in patients with S3 ifbrosis to cirrhosis (P<0.05 or P<0.01). It was signiifcantly bigger in group S4 compared to other groups (P<0.01). Spearman rank correlation analysis showed significant positive correlation between the width of anterior space and liver fibrosis staging (r=0.704, P<0.01). ROC curve analysis showed the area under curve (AUC) of 0.897 with the optimum width of ≥10 mm. Conclusion The change in the space anterior to the right portal vein is positively correlated with live ifbrosis staging. CT measurement helps early diagnose and assess the severity of liver ifbrosis and cirrhosis.
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BACKGROUND: The participation of laboratories in external quality assessment (EQA) programs is required for the quality assurance of nucleic acid amplification of Chlamydia trachomatis. This study aimed to construct a new quality control (QC) material applicated in EQA of C. trachomatis PCR. METHODS: A QC material-HTB-SiHa cells transfected with a recombinant plasmid containing the cryptic plasmid sequence-was constructed for C. trachomatis PCR detection, and four different panels, each consisting of 4 positive samples with serial dilution of the constructed QC material and 1 negative sample, were distributed by the National Center for Clinical Laboratories among four groups of 275, 268, 317, and 304 participants across China from 2011 through 2012. A total of eight commercial kits were used for C. trachomatis PCR detection in participants. RESULTS: Nine laboratories reported false-positive results (0.9%). As the series dilution increased, the correct reporting of the data sets decreased; the lowest correct rate was 96.3% in the weakest positive samples (104 copies/mL). Eight laboratories reported false-positive results, and 42 laboratories reported false-negative results in the EQA detection of C. trachomatis. No significant differences were observed in the detection of the constructed C. trachomatis positive samples (97.9%, 98.5%, 100%, 98.5%; P=0.36) and negative samples (100%, 99.0%, 100%, 99.0%; P=0.764) using four commercial kits commonly used in China. CONCLUSIONS: The results of the EQA study indicated that the constructed material provides a noninfectious, stable control material with sufficient volume for PCR detection of C. trachomatis.
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Humans , Cell Line , Chlamydia Infections/diagnosis , Chlamydia trachomatis/genetics , DNA, Bacterial/analysis , False Negative Reactions , Laboratories/standards , Plasmids/genetics , Polymerase Chain Reaction/standards , Quality Control , Reagent Kits, DiagnosticABSTRACT
<p><b>OBJECTIVE</b>To explore the pathogenesis of ovarian cancer from the perspective of molecular genetic variation and changes in mRNA expression profiles.</p><p><b>METHOD</b>The data of DNA copy number and mRNA expression profiles of high-grade serious ovarian cancer were obtained from TCGA. The significant copy number variation regions were identified using the bioinformatics tool GISTIC, and the differentially expressed genes in these regions were identified using the samr package of SAM. The selected genes were subjected to bioinformatics analysis using GSEA tools.</p><p><b>RESULTS</b>GISTIC analysis identified 45 significant copy number amplification regions in ovarian cancer, and SAM and Fisher's exact test found that 40 of these genes showed altered expression levels. GSEA enrichment analysis revealed that most of these genes were reported in several published studies describing genetic study of tumorigenesis.</p><p><b>CONCLUSION</b>An integrative bioinformatics study of DNA copy number variation data and microarray data can identify genes involved in tumor pathogenesis. and offer new clues for studying early diagnosis and therapeutic target of ovarian cancer.</p>
Subject(s)
Female , Humans , Computational Biology , DNA Copy Number Variations , Gene Expression Regulation, Neoplastic , Ovarian Neoplasms , GeneticsABSTRACT
<p><b>BACKGROUND</b>Alcohol dependence (AD) is a serious and common public health problem. The identification of genes that contribute to the AD variation will improve our understanding of the genetic mechanism underlying this complex disease. Previous genome-wide association studies (GWAS) and candidate gene genetic association studies identified individual genes as candidates for alcohol phenotypes, but efforts to generate an integrated view of accumulative genetic variants and pathways under alcohol drinking are lacking.</p><p><b>METHODS</b>We applied enrichment gene set analysis to existing genetic association results to identify pertinent pathways to AD in this study. A total of 1 438 SNPs (P < 1.0 × 10(-3)) associated to alcohol drinking related traits have been collected from 31 studies (10 candidate gene association studies, 19 GWAS of SNPs, and 2 GWAS of copy number variants).</p><p><b>RESULTS</b>Among all of the KEGG pathways, the calcium signaling pathway (hsa04020) showed the most significant enrichment of associations (21 genes) to alcohol consumption phenotypes (P = 5.4 × 10(-5)). Furthermore, the calcium signaling pathway is the only pathway that turned out to be significant after multiple test adjustments, achieving Bonferroni P value of 0.8 × 10(-3) and FDR value of 0.6 × 10(-2), respectively. Interestingly, the calcium signaling pathway was previously found to be essential to regulate brain function, and genes in this pathway link to a depressive effect of alcohol consumption on the body.</p><p><b>CONCLUSIONS</b>Our findings, together with previous biological evidence, suggest the importance of gene polymorphisms of calcium signaling pathway to AD susceptibility. Still, further investigations are warranted to uncover the role of this pathway in AD and related traits.</p>
Subject(s)
Humans , Alcoholism , Genetics , Calcium Signaling , Genetics , Physiology , Genetic Predisposition to Disease , Genetics , Genome-Wide Association Study , Methods , Polymorphism, Single Nucleotide , GeneticsABSTRACT
Objective To evaluate the agreement of antinuclear antibody (ANA) titer reported in clinical laboratories and analyze possible problems in clinical laboratories.Methods Experiment survey.The panel consisting of 5 samples was distributed to 533 laboratories.Each panel contains one negative sample and 4 positive samples,which were from individuals of autoimmune disease.ANA titer system was divided into traditional titer system with two-fold dilution and titer system with 3.2 times dilution.Clinical laboratories were required to report the ANA titers and initial screening dilution according to the standard used in routine work.Results were expressed as median titers and range for acceptable performance.As to titer system with two-fold dilution,acceptable performance on proficiency testing was defined by a result equal to median titer ± two two-fold dilutions.While as to titer system with 3.2 times dilution,acceptable performance on proficiency testing was defined by a result equal to median titer ± 3.2 times dilutions.The laboratories percentages with acceptable performance were calculated to evaluate their agreements.Results 412 laboratories reported ANA titer results,of which 11.9％ (49/412)reported results with two-fold dilution titer system,88.1％ (363/412)reported results with 3.2 times dilution titer system.The median titers of sample 1211,1212,1213 and 1215 reported with two-fold titer system were 1 ∶ 640,1∶ 320,＞ 1 ∶ 1280 and1∶ 160,respectively.The agreement within the median ANA titer reported with two-fold dilution titer system ranged from 24.5％ (12/49) to 57.1％ (28/49) and the lowest percentage of the results within the acceptable limits was 87.8％ (43/49).The median titers of sample 1211,1212,1213 and 1215 reported with 3.2 times dilution titer system were 1 ∶ 1000,1∶ 1000,＞ 1 ∶ 3200 and 1 ∶ 320,respectively.The agreement within the median ANA titer reported with 3.2 times dilution titer system ranged from 63.3％ (31/49)to 83.7％ (41/49).The lowest percentage of the results within the acceptable limits was 98.0％ (48/49).Conclusions The results of ANA titer reported are unsatisfactory.Standardization for reagent,microscopy,procedure and result interpretation is necessary to improve the agreement of ANA titer report in different laboratories.
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<p><b>OBJECTIVE</b>To propose a new method for acquiring pulmonary function parameters based on measurement of volume changes of thoracic impedance.</p><p><b>METHODS</b>We studied the relationship between the volume changes of thoracic impedance and pulmonary function parameters during forced breathing based on bioimpedance measurement, and developed an instrument for measuring thoracic impedance. Using this instrument and a MRI spirolab III lung function test instrument, both based on flowmeter measurement, we measured such pulmonary function parameters including forced vital capacity (FVC), forced expiratory volume in one second/FVC (FEV1/FVC), and peak expiratory flow in 10 healthy volunteers and compared the measurement results.</p><p><b>RESULTS</b>The differences in the parameters measured using the two instruments were all within two folds of the positive and negative standard deviations of the average values, demonstrating good consistency in the measurement between the two methods.</p><p><b>CONCLUSIONS</b>The measurement results of the bioimpedance-based instrument we developed show good consistency with those by the commercially available pulmonary function test instrument.</p>
Subject(s)
Adult , Humans , Young Adult , Electric Impedance , Forced Expiratory Volume , Peak Expiratory Flow Rate , Respiratory Function Tests , Methods , Thorax , Physiology , Vital CapacityABSTRACT
Objective To evaluate the performance of HCV RNA detection in the first EQA program in 2012 and analyze possible problems in clinical laboratories.Methods The panel consisting of 5 samples was distributed to 927 laboratories.Each panel contains one negative sample and 4 positive samples,which were virus-like particles calibrated by international standard.The pere ent agreements of all the laboratories for qualitative and quantitative results were calculated.Genomic means (GM) and standard deviations (s) of all laboratories and each reagent were calculated.The overall GM and the GM of each reagent were compared with expected results and correlation curves were calculated.Results The percent agreements of sample 1211,1212,1213,1214 for qualitative results wcrc 99.5％ (403/405),98.5％ (400/406),100.0％ (405/405),100.0％ (406/406),respectively.The percent agreement of the negative sample was 99％ (401/405).The percent agreements of sample 1211,1212 and 1213 for quantitive results were similar,which were 93.8％ (549/585),92.3 ％ (541/586) and 94.5％ (554/586).However,the agreement of sample 1214 was only 87.7％ (514/586)and the agreement of sample 1214 for reagent A was 67.2％ (92/137).The overall GM agreed with expected results,while GMs of reagent C,E and G deviated from expected results.GMs of sample 1211,1212,1213 and 1214 reported by labs using reagent C were 4.22,3.56,5.16 and 5.90,respectively.GMs of sample 1211,1212,1213 and 1214 reported by labs using reagent E were 4.52,3.78,5.55 and 6.29,respectively.GMs of sample 1211,1212,1213 and 1214 reported by labs using reagent G were 4.83,4.36,5.72 and 6.56,respectively.Conclusions The overall results of HCV RNA qualitative and quantitative detection are satisfactory.However,some problems still exist,such as deviation of GM of some reagents,the interassay variability,systematic deviation and accidental deviation,which show that the quality of reagents should be improved.
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Objective To investigate the potential role of human cytomegalovirus lower matrix phosphoprotein 65 (HCMV pp65) in murine systemic lupus erythematosus (SLE).Methods The prokaryotic vector pET-28b and eukaryotic vector pcDNA 3.0 were constructed to express the HCMV pp65 protein.All the C57BL/6 mice were inoculated with pp65 eukaryotic vector intramuscularly five times at 2-week intervals and then were bled via the retro-orbital vein.Subsequently,indirect ELISA was used to evaluate the concentration of anti-pp65 IgG,anti-dsDNA and ANA.At the same time,IL-1 b,IL-6,and TNF-α were determined by competitive ELISA.Results The early onset of autoantibodies and an overexpression of IL-6 were observed in immunized male C57BL/6 mice.Conclusion HCMV pp65 triggers the deregulation of humoral immunity in C57BL/6 mice,which indicates that the immune responses induced by HCMV pp65 may be involved in the development of SLE.