Detection and treatment of colorectal cancer(CRC)at an early stage is vital for long-term survival.Liquid biopsy has emerged as a promising new avenue for non-invasive screening of CRC as well as prognostication and s...Detection and treatment of colorectal cancer(CRC)at an early stage is vital for long-term survival.Liquid biopsy has emerged as a promising new avenue for non-invasive screening of CRC as well as prognostication and surveillance of minimal residual disease.Cell free DNA(cfDNA)is a promising liquid biopsy analyte and has been approved for use in clinical practice.Here,we explore the current challenges of utilizing cfDNA in the screening and prognostication of CRC but also for detecting driver mutations in healthy,presymptomatic patients with normal colonic crypts.CfDNA for the detection of cancerous or premalignant colonic lesions has already been extensively explored,however few have considered utilizing cfDNA in the detection of driver mutations in healthy patients.Theoretically,this would allow us to detect patients who are at a higher risk of tumorigenesis decades in advance of established malignancy and stratify them into higher risk groups for early-intervention screening programs.We also explore the solutions necessary to overcome the challenges that prevent liquid biopsy from entering mainstream clinical use.The potential for liquid biopsy is immense if these challenges are successfully circumvented,and can dramatically reduce CRC rates as well as improve survival in patients.展开更多
We established a quick and reliable method for recovering cell-free seminal DNA （cfsDNA）, by using the binding-washing-elution procedure on the DNA purification column. Low variations （below 15%） among the triplic...We established a quick and reliable method for recovering cell-free seminal DNA （cfsDNA）, by using the binding-washing-elution procedure on the DNA purification column. Low variations （below 15%） among the triplicate values of cfsDNA quantity verified the reproducibility of our cfsDNA recovery method. Similar cfsDNA yield and size distribution between seminal plasma acquired by filtration and centrifugation confirmed the presence of cfsDNA. To investigate the general characterization of cfsDNA, the quantitation and size distribution of cfsDNA from normozoospermic and azoospermic semen were analyzed by real-time PCR and electrophoresis, respectively. CfsDNA concentration in semen with normozoospermia （n = 11） was 1.34 ± 0.65 μg ·mL^-1, whereas a higher cfsDNA concentration was observed in azoospermia （2.56 ± 1.43 μg ·mL^-1, n = 9）. The continuous distribution of DNA fragments ranging from -1 kb to 15 kb and a spectrum of multiples of 180-bp fragments were observed in each normozoospermic and azoospermic sample. Distinct characteristic DNA ladder fragmentations in some azoospermic samples implicated that cfsDNA originate partly from apoptotic cells. CfsDNAs of 36 selected azoospermic patients with known information of Y chromosome microdeletion were subjected to the same microdeletion analysis by multiplex PCR and PCR amplification of sY114 （1 450 bp）. All multiplex PCR reactions with cfsDNA amplified successfully and provided the same result as leukocyte DNA. PCR amplification of sY114 gave a 1 450-bp amplicon as expected. Our data suggested the potential use of cfsDNA in search of biomarker or diagnostic procedures.展开更多
BACKGROUND Mortality due to septic shock is relatively high.The dynamic monitoring of plasma cell-free DNA(cfDNA)can guide the treatment of septic shock.CASE SUMMARY Herein,we present a typical case of septic shock sy...BACKGROUND Mortality due to septic shock is relatively high.The dynamic monitoring of plasma cell-free DNA(cfDNA)can guide the treatment of septic shock.CASE SUMMARY Herein,we present a typical case of septic shock syndrome caused by the bacilli Acinetobacter baumannii and Pantoea.The patient complained of abdominal pain,fever and chills upon admission to the Emergency Department.Marked decreases in white blood cells and procalcitonin(PCT)were observed after the patient received continuous renal replacement and extracorporeal membrane oxygenation.Plasma cfDNA levels were consistently high,peaking at 1366.40 ng/mL,as measured by a duplex real-time PCR assay with an internal control,which was developed as a novel method for the accurate quantification of cfDNA.The patient died of septic shock on HD 8,suggesting that cfDNA could be used to monitor disease progression more effectively than PCT and the other inflammatory factors measured in this case.CONCLUSION CfDNA may be a promising marker that complements other inflammatory factors to monitor disease progression in patients with septic shock.展开更多
Analysis of patient＇s materials like cells or nucleic acids obtained in a minimally invasive or noninvasive manner through the sampling of blood or other body fluids serves as liquid biopsies, which has huge potentia...Analysis of patient＇s materials like cells or nucleic acids obtained in a minimally invasive or noninvasive manner through the sampling of blood or other body fluids serves as liquid biopsies, which has huge potential for numerous diagnostic applications. Circulating cell-free DNA（cfDNA） is explored as a prognostic or predictive marker of liquid biopsies with the improvements in genomic and molecular methods. DNA methylation is an important epigenetic marker known to affect gene expression. cfDNA methylation detection is a very promising approach as abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. This re？view summarizes the various investigational applications of cfDNA methylation and its oxidized de？rivatives as biomarkers for cancer diagnosis, prenatal diagnosis and organ transplantation monitoring.The review also provides a brief overview of the technologies for cfDNA methylation analysis based on next generation sequencing.展开更多
BACKGROUND Minimally invasive or noninvasive,sensitive and accurate detection of colorectal cancer(CRC)is urgently needed in clinical practice.AIM To identify a noninvasive,sensitive and accurate circular free DNA mar...BACKGROUND Minimally invasive or noninvasive,sensitive and accurate detection of colorectal cancer(CRC)is urgently needed in clinical practice.AIM To identify a noninvasive,sensitive and accurate circular free DNA marker detected by digital polymerase chain reaction(dPCR)for the early diagnosis of clinical CRC.METHODS A total of 195 healthy control(HC)individuals and 101 CRC patients(38 in the early CRC group and 63 in the advanced CRC group)were enrolled to establish the diagnostic model.In addition,100 HC individuals and 62 patients with CRC(30 early CRC and 32 advanced CRC groups)were included separately to validate the model.CAMK1D was dPCR.Binary logistic regression analysis was used to establish a diagnostic model including CAMK1D and CEA.RESULTS To differentiate between the 195 HCs and 101 CRC patients(38 early CRC and 63 advanced CRC patients),the common biomarkers CEA and CAMK1D were used alone or in combination to evaluate their diagnostic value.The area under the curves(AUCs)of CEA and CAMK1D were 0.773(0.711,0.834)and 0.935(0.907,0.964),respectively.When CEA and CAMK1D were analyzed together,the AUC was 0.964(0.945,0.982).In differentiating between the HC and early CRC groups,the AUC was 0.978(0.960,0.995),and the sensitivity and specificity were 88.90%and 90.80%,respectively.In differentiating between the HC and advanced CRC groups,the AUC was 0.956(0.930,0.981),and the sensitivity and specificity were 81.30%and 95.90%,respectively.After building the diagnostic model containing CEA and CAMK1D,the AUC of the CEA and CAMK1D joint model was 0.906(0.858,0.954)for the validation group.In differentiating between the HC and early CRC groups,the AUC was 0.909(0.844,0.973),and the sensitivity and specificity were 93.00%and 83.30%,respectively.In differentiating between the HC and advanced CRC groups,the AUC was 0.904(0.849,0.959),and the sensitivity and specificity were 93.00%and 75.00%,respectively.CONCLUSION We built a diagnostic model including CEA and CAMK1D for differentiating between HC individuals and CRC patients.Compared with the common biomarker CEA alone,the diagnostic model exhibited significant improvement.展开更多
Epigenetic changes of DNA, including methylation, have long been recognized as key indicators of various diseases, including aging, cancer, and neurological disorders. Biomarker discoveries based on distinct methylati...Epigenetic changes of DNA, including methylation, have long been recognized as key indicators of various diseases, including aging, cancer, and neurological disorders. Biomarker discoveries based on distinct methylation patterns for both hypermethylation and hypomethylation lead the way in discovery of novel diagnosis and treatment targets. Many different approaches are present to detect the level of methylation in whole genome (whole genome bisulfite sequencing, microarray) as well as at specific loci (methylation specific PCR). Cell-free DNA (cf-DNA) found in body fluids like blood provides information about DNA methylation and serves as a less invasive approach for genetic screening. Cell-free DNA and methylation screening technologies, when combined, have the potential to transform the way we approach genetic screening and personalized therapy. These technologies can help enhance disease diagnostic accuracy and inform the development of targeted therapeutics by providing a non-invasive way for acquiring genomic information and identifying disease-associated methylation patterns. We highlight the clinical benefits of using cell-free DNA (cf-DNA) liquid biopsy analysis and available methylation screening technologies that have been crucial in identifying biomarkers for disease from patients using a non-invasive way. Powering such biomarker discoveries are various methods of cf-DNA methylation analysis such as Bisulfite Sequencing and most recently, Methylation-Specific Restriction Enzyme (MSRE-seq) Analysis, paving the way for novel epigenetic biomarker discoveries for more robust diagnosis such as early disease detection, prognosis, monitoring of disease progression and treatment response as well as discovery of novel drug targets.展开更多
AIM:To investigate the value of combined detection of circulating cell-free DNA(cfDNA),a-fetal protein(AFP) and a L-fucosidase(AFU) for diagnosis of hepatocellular carcinoma(HCC).METHODS:Serum samples from 39 HCC pati...AIM:To investigate the value of combined detection of circulating cell-free DNA(cfDNA),a-fetal protein(AFP) and a L-fucosidase(AFU) for diagnosis of hepatocellular carcinoma(HCC).METHODS:Serum samples from 39 HCC patients and 45 normal controls were collected.Branched DNA(bDNA) was used to detect the level of cfDNA,and a receiver operating characteristic curve was employed to evaluate the diagnostic sensitivity,specificity,accuracy,positive predictive value,negative predictive value,positive likelihood ratio,negative likelihood ratio and Youden index,and to assess the diagnostic efficiency and their correlations with the clinicopathological features.AFP and AFU were detected by chemiluminescence and colorimetry,respectively.The significance of combined detection of the three biomarkers was discussed.RESULTS:cfDNA level was increased in 22 of the 39 HCC samples and in 2 of the 45 normal controls.cfDNA level in HCC samples was significantly higher than that in normal controls(P < 0.05).There were significant differences in sex and extra-and intrahepatic metastasis(P < 0.05).There was no significant correlation between cfDNA,AFP and AFU in the detection of HCC.The sensitivity of combined detection of cfDNA with one marker(AFP or AFU) and cfDNA with two markers(AFP and AFU) was 71.8%,87.2% and 89.7% vs 56.4%,53.8% and 66.7% for cfDNA,AFP and AFU used alone,respectively,the difference being statistically significant(P < 0.05).CONCLUSION:Quantitative analysis of cfDNA is sensitive and feasible,and the combined detection of cfDNA with AFP or AFU or both could improve the diagnostic sensitivity for HCC.展开更多
Synovial sarcoma(SS) is genetically characterized by chromosomal translocation, which generates SYT-SSX fusion transcripts. Although SS can occur in any body part, primary gastric SS is substantially rare. Here we des...Synovial sarcoma(SS) is genetically characterized by chromosomal translocation, which generates SYT-SSX fusion transcripts. Although SS can occur in any body part, primary gastric SS is substantially rare. Here we describe a detection of the fusion gene sequence of gastric SS in plasma cell-free DNA(cf DNA). A gastric submucosal tumor was detected in the stomach of a 27-year-old woman and diagnosed as SS. Candidate intronic primers were designed to detect the intronic fusion breakpoint and this fusion sequence was confirmed in intron 10 of SYT and intron 5 of SSX2 by genomic polymerase chain reaction(PCR) and direct sequencing. A locked nucleic acid(LNA) probe specificto the fusion sequence was designed for detecting the fusion sequence in plasma and the fusion sequence was detected in preoperative plasma cfD NA, while not detected in postoperative plasma cfD NA. This technique will be useful for monitoring translocation-derived diseases such as SS.展开更多
Objective: To improve the detecting accuracy of chromosomal aneuploidy of fetus by non-invasive prenatal testing (NIPT) using next generation sequencing data of pregnant women’s cell-free DNA. Methods: We proposed th...Objective: To improve the detecting accuracy of chromosomal aneuploidy of fetus by non-invasive prenatal testing (NIPT) using next generation sequencing data of pregnant women’s cell-free DNA. Methods: We proposed the multi-Z method which uses 21 z-scores for each autosomal chromosome to detect aneuploidy of the chromosome, while the conventional NIPT method uses only one z-score. To do this, mapped read numbers of a certain chromosome were normalized by those of the other 21 chromosomes. Average and standard deviation (SD), which are used for calculating z-score of each sample, were obtained with normalized values between all autosomal chromosomes of control samples. In this way, multiple z-scores can be calculated for 21 autosomal chromosomes except oneself. Results: Multi-Z method showed 100% sensitivity and specificity for 187 samples sequenced to 3 M reads while the conventional NIPT method showed 95.1% specificity. Similarly, for 216 samples sequenced to 1 M reads, Multi-Z method showed 100% sensitivity and 95.6% specificity and the conventional NIPT method showed a result of 75.1% specificity. Conclusion: Multi-Z method showed higher accuracy and robust results than the conventional method even at low coverage reads.展开更多
Background: Cell-free DNA (cfDNA) holds promise as a tumor marker of clinical importance. We aimed to investigate the prognostic value of baseline cfDNA in non small-cell lung cancer (NSCLC). Material and Methods: Dur...Background: Cell-free DNA (cfDNA) holds promise as a tumor marker of clinical importance. We aimed to investigate the prognostic value of baseline cfDNA in non small-cell lung cancer (NSCLC). Material and Methods: During a three-year period, patients with newly diagnosed, previously untreated advanced NSCLC were included in a consecutive, prospective marker-trial. Plasma was isolated from a pre-treatment peripheral blood sample and the level of total cfDNA was measured by an in-house assay qPCR-method. The treatment comprised carboplatin (AUC 5) intravenously day 1), and vinorelbine (30 mg/m2 intravenously day 1 and 60 mg/m2 perorally day 8) q3w for a maximum of six cycles. The primary end-point was overall survival (OS). Secondary end-points were progression free survival (PFS) and overall response rate (ORR). Results: 245 patients were included and received a minimum of 1 cycle of chemotherapy (median 4). The median OS was 8.9 months, the median PFS by intention to treat 5.4 months and the ORR was 25%. The patients were divided into four groups based on quartiles of cfDNA and subsequently dichotomized by the 75th percentile revealing a significantly worse prognosis for patients in the upper 75th percentile (median OS 4.9 months) compared to patients with lower levels (10.0 months) (HR 2.1, 95%CI 1.4 - 3.1, p 0.0001). A multivariate analysis confirmed the independent prognostic value of cfDNA. A subgroup analysis of patients with high cfDNA and poor performance status (PS = 2) identified a group of patients with even worse prognosis (median OS 2.0 versus 9.1 months, HR 3.6, 95%CI 1.4 - 9.2, p 0.0001). Similar and significant results were found when comparing level of cfDNA and PFS. Conclusions: High pre-treatment level of cfDNA seems to have a strong prognostic impact in patients with newly diagnosed advanced NSCLC. Combined with PS it identifies a patient group with minimal or no benefit of chemotherapy.展开更多
Screening for colorectal cancer(CRC)is among the mosteffective approaches to cancer prevention,yet achievinghigh adherence to effective screening offers is challenging[1].Blood-based tests that could be easily impleme...Screening for colorectal cancer(CRC)is among the mosteffective approaches to cancer prevention,yet achievinghigh adherence to effective screening offers is challenging[1].Blood-based tests that could be easily implemented inroutine medical practice might be a promising approachto achieve higher adherence rates than with conven-tional stool-based or endoscopic screening[2,3].However,neoplasm detection rates of previously developed and pro-posed blood-based tests have not been competitive tothose of modern stool-based tests[2],in particular fecalimmunochemical tests(FITs)that are meanwhile widelyused for CRC screening in an increasing number of coun-tries[4].Most recently,performance of a novel cell-freeDNA(cfDNA)blood-based test for detecting colorectalneoplasms was validated in the ECLIPSE study,a largescreening population undergoing screening colonoscopy[5],being the first of its kind to achieve FDA approval asa primary screening option for CRC.展开更多
Pediatric ear,nose,and throat(ENT)infections are common and vary from simple to life-threatening cases,including complicated sinusitis,deep neck space abscesses,and mastoiditis.ENT infections in children are a primary...Pediatric ear,nose,and throat(ENT)infections are common and vary from simple to life-threatening cases,including complicated sinusitis,deep neck space abscesses,and mastoiditis.ENT infections in children are a primary driver of antibiotic prescriptions.1 While invasive surgical cultures often yield successful pathogen identification,they require anesthesia and inpatient care.Patients are prescribed broad-spectrum antibiotics until the culture results become available.展开更多
Cancer treatment has entered the era of precision medicine, where knowledge of a patient's genetic profile is used to facilitate early diagnosis, drug selection, prognosis, prediction of drug responsiveness, the o...Cancer treatment has entered the era of precision medicine, where knowledge of a patient's genetic profile is used to facilitate early diagnosis, drug selection, prognosis, prediction of drug responsiveness, the onset of secondary resistance, and relapse. Circulating free DNA (cfDNA) has emerged as an ideal source of genetic information for cancer patients, and numerous studies have explored its validity in various clinical applications. However, clinical implementation of cfDNA-based tests has been slow. In this review, we addressed some of the pre-and post-analytical issues regarding cfDNA tests. First, we summarized the charac-teristics of cfDNA and reviewed the methods used to identify tumor-derived cfDNA from the pool of total cfDNA. Second, we described the procedures used to extract cfDNA, which have a great impact on representativeness and yield. Finally, we discussed our thoughts on the validation of cfDNA-based tests and the reporting of test results amid drastic limitations.展开更多
Non-small-cell lung cancer （NSCLC）, the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymetbylcy...Non-small-cell lung cancer （NSCLC）, the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymetbylcytosine （ShmC） signatures in circulating cell-free DNA （cfDNA） that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminat- ing tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here, we employed a sensitive and reliable method to map genome-wide 5hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls. Specifically, we identi- fied six potential biomarkers from 66 patients and 67 healthy controls （mean decrease accuracy 〉 3.2, P 〈 3.68E-19） using machine-learning-based tumor classifiers with high accuracy. Thus, the unique signature of 5hmC in tumor patient＇s cfDNA identified in our study may provide valuable information in facilitating the development of new diagnostic and therapeutic modalities for NSCLC.展开更多
文摘Detection and treatment of colorectal cancer(CRC)at an early stage is vital for long-term survival.Liquid biopsy has emerged as a promising new avenue for non-invasive screening of CRC as well as prognostication and surveillance of minimal residual disease.Cell free DNA(cfDNA)is a promising liquid biopsy analyte and has been approved for use in clinical practice.Here,we explore the current challenges of utilizing cfDNA in the screening and prognostication of CRC but also for detecting driver mutations in healthy,presymptomatic patients with normal colonic crypts.CfDNA for the detection of cancerous or premalignant colonic lesions has already been extensively explored,however few have considered utilizing cfDNA in the detection of driver mutations in healthy patients.Theoretically,this would allow us to detect patients who are at a higher risk of tumorigenesis decades in advance of established malignancy and stratify them into higher risk groups for early-intervention screening programs.We also explore the solutions necessary to overcome the challenges that prevent liquid biopsy from entering mainstream clinical use.The potential for liquid biopsy is immense if these challenges are successfully circumvented,and can dramatically reduce CRC rates as well as improve survival in patients.
基金Acknowledgment The investigation was supported by grants from the National Natural Science Foundation of China （No. 30801144）, by the Specialized Research Fund for the Doctoral Program of Higher Education （No. 200804871092） and by the National Key Technology Research and Development Program for the 10th Five- Year Plan, China （No. 2004BA720A33-01）.
文摘We established a quick and reliable method for recovering cell-free seminal DNA （cfsDNA）, by using the binding-washing-elution procedure on the DNA purification column. Low variations （below 15%） among the triplicate values of cfsDNA quantity verified the reproducibility of our cfsDNA recovery method. Similar cfsDNA yield and size distribution between seminal plasma acquired by filtration and centrifugation confirmed the presence of cfsDNA. To investigate the general characterization of cfsDNA, the quantitation and size distribution of cfsDNA from normozoospermic and azoospermic semen were analyzed by real-time PCR and electrophoresis, respectively. CfsDNA concentration in semen with normozoospermia （n = 11） was 1.34 ± 0.65 μg ·mL^-1, whereas a higher cfsDNA concentration was observed in azoospermia （2.56 ± 1.43 μg ·mL^-1, n = 9）. The continuous distribution of DNA fragments ranging from -1 kb to 15 kb and a spectrum of multiples of 180-bp fragments were observed in each normozoospermic and azoospermic sample. Distinct characteristic DNA ladder fragmentations in some azoospermic samples implicated that cfsDNA originate partly from apoptotic cells. CfsDNAs of 36 selected azoospermic patients with known information of Y chromosome microdeletion were subjected to the same microdeletion analysis by multiplex PCR and PCR amplification of sY114 （1 450 bp）. All multiplex PCR reactions with cfsDNA amplified successfully and provided the same result as leukocyte DNA. PCR amplification of sY114 gave a 1 450-bp amplicon as expected. Our data suggested the potential use of cfsDNA in search of biomarker or diagnostic procedures.
基金Supported by National Natural Science Foundation of China,No.81672100 and No.81671836the Key Laboratory for Laboratory Medicine of Jiangsu Province of China,No.ZDXKB2016005
文摘BACKGROUND Mortality due to septic shock is relatively high.The dynamic monitoring of plasma cell-free DNA(cfDNA)can guide the treatment of septic shock.CASE SUMMARY Herein,we present a typical case of septic shock syndrome caused by the bacilli Acinetobacter baumannii and Pantoea.The patient complained of abdominal pain,fever and chills upon admission to the Emergency Department.Marked decreases in white blood cells and procalcitonin(PCT)were observed after the patient received continuous renal replacement and extracorporeal membrane oxygenation.Plasma cfDNA levels were consistently high,peaking at 1366.40 ng/mL,as measured by a duplex real-time PCR assay with an internal control,which was developed as a novel method for the accurate quantification of cfDNA.The patient died of septic shock on HD 8,suggesting that cfDNA could be used to monitor disease progression more effectively than PCT and the other inflammatory factors measured in this case.CONCLUSION CfDNA may be a promising marker that complements other inflammatory factors to monitor disease progression in patients with septic shock.
基金supported by grants from the National Basic Research Program of China(MOST2016YFC0900301 and 2014CB964900)the National Natural Science Foundation of China(No. 91519325)the Beijing Natural Science Foundation (No. 5162012)
文摘Analysis of patient＇s materials like cells or nucleic acids obtained in a minimally invasive or noninvasive manner through the sampling of blood or other body fluids serves as liquid biopsies, which has huge potential for numerous diagnostic applications. Circulating cell-free DNA（cfDNA） is explored as a prognostic or predictive marker of liquid biopsies with the improvements in genomic and molecular methods. DNA methylation is an important epigenetic marker known to affect gene expression. cfDNA methylation detection is a very promising approach as abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. This re？view summarizes the various investigational applications of cfDNA methylation and its oxidized de？rivatives as biomarkers for cancer diagnosis, prenatal diagnosis and organ transplantation monitoring.The review also provides a brief overview of the technologies for cfDNA methylation analysis based on next generation sequencing.
基金Supported by the Henan Medical Science and Technology Research Program,No.LHGJ20210045.
文摘BACKGROUND Minimally invasive or noninvasive,sensitive and accurate detection of colorectal cancer(CRC)is urgently needed in clinical practice.AIM To identify a noninvasive,sensitive and accurate circular free DNA marker detected by digital polymerase chain reaction(dPCR)for the early diagnosis of clinical CRC.METHODS A total of 195 healthy control(HC)individuals and 101 CRC patients(38 in the early CRC group and 63 in the advanced CRC group)were enrolled to establish the diagnostic model.In addition,100 HC individuals and 62 patients with CRC(30 early CRC and 32 advanced CRC groups)were included separately to validate the model.CAMK1D was dPCR.Binary logistic regression analysis was used to establish a diagnostic model including CAMK1D and CEA.RESULTS To differentiate between the 195 HCs and 101 CRC patients(38 early CRC and 63 advanced CRC patients),the common biomarkers CEA and CAMK1D were used alone or in combination to evaluate their diagnostic value.The area under the curves(AUCs)of CEA and CAMK1D were 0.773(0.711,0.834)and 0.935(0.907,0.964),respectively.When CEA and CAMK1D were analyzed together,the AUC was 0.964(0.945,0.982).In differentiating between the HC and early CRC groups,the AUC was 0.978(0.960,0.995),and the sensitivity and specificity were 88.90%and 90.80%,respectively.In differentiating between the HC and advanced CRC groups,the AUC was 0.956(0.930,0.981),and the sensitivity and specificity were 81.30%and 95.90%,respectively.After building the diagnostic model containing CEA and CAMK1D,the AUC of the CEA and CAMK1D joint model was 0.906(0.858,0.954)for the validation group.In differentiating between the HC and early CRC groups,the AUC was 0.909(0.844,0.973),and the sensitivity and specificity were 93.00%and 83.30%,respectively.In differentiating between the HC and advanced CRC groups,the AUC was 0.904(0.849,0.959),and the sensitivity and specificity were 93.00%and 75.00%,respectively.CONCLUSION We built a diagnostic model including CEA and CAMK1D for differentiating between HC individuals and CRC patients.Compared with the common biomarker CEA alone,the diagnostic model exhibited significant improvement.
文摘Epigenetic changes of DNA, including methylation, have long been recognized as key indicators of various diseases, including aging, cancer, and neurological disorders. Biomarker discoveries based on distinct methylation patterns for both hypermethylation and hypomethylation lead the way in discovery of novel diagnosis and treatment targets. Many different approaches are present to detect the level of methylation in whole genome (whole genome bisulfite sequencing, microarray) as well as at specific loci (methylation specific PCR). Cell-free DNA (cf-DNA) found in body fluids like blood provides information about DNA methylation and serves as a less invasive approach for genetic screening. Cell-free DNA and methylation screening technologies, when combined, have the potential to transform the way we approach genetic screening and personalized therapy. These technologies can help enhance disease diagnostic accuracy and inform the development of targeted therapeutics by providing a non-invasive way for acquiring genomic information and identifying disease-associated methylation patterns. We highlight the clinical benefits of using cell-free DNA (cf-DNA) liquid biopsy analysis and available methylation screening technologies that have been crucial in identifying biomarkers for disease from patients using a non-invasive way. Powering such biomarker discoveries are various methods of cf-DNA methylation analysis such as Bisulfite Sequencing and most recently, Methylation-Specific Restriction Enzyme (MSRE-seq) Analysis, paving the way for novel epigenetic biomarker discoveries for more robust diagnosis such as early disease detection, prognosis, monitoring of disease progression and treatment response as well as discovery of novel drug targets.
文摘AIM:To investigate the value of combined detection of circulating cell-free DNA(cfDNA),a-fetal protein(AFP) and a L-fucosidase(AFU) for diagnosis of hepatocellular carcinoma(HCC).METHODS:Serum samples from 39 HCC patients and 45 normal controls were collected.Branched DNA(bDNA) was used to detect the level of cfDNA,and a receiver operating characteristic curve was employed to evaluate the diagnostic sensitivity,specificity,accuracy,positive predictive value,negative predictive value,positive likelihood ratio,negative likelihood ratio and Youden index,and to assess the diagnostic efficiency and their correlations with the clinicopathological features.AFP and AFU were detected by chemiluminescence and colorimetry,respectively.The significance of combined detection of the three biomarkers was discussed.RESULTS:cfDNA level was increased in 22 of the 39 HCC samples and in 2 of the 45 normal controls.cfDNA level in HCC samples was significantly higher than that in normal controls(P < 0.05).There were significant differences in sex and extra-and intrahepatic metastasis(P < 0.05).There was no significant correlation between cfDNA,AFP and AFU in the detection of HCC.The sensitivity of combined detection of cfDNA with one marker(AFP or AFU) and cfDNA with two markers(AFP and AFU) was 71.8%,87.2% and 89.7% vs 56.4%,53.8% and 66.7% for cfDNA,AFP and AFU used alone,respectively,the difference being statistically significant(P < 0.05).CONCLUSION:Quantitative analysis of cfDNA is sensitive and feasible,and the combined detection of cfDNA with AFP or AFU or both could improve the diagnostic sensitivity for HCC.
文摘Synovial sarcoma(SS) is genetically characterized by chromosomal translocation, which generates SYT-SSX fusion transcripts. Although SS can occur in any body part, primary gastric SS is substantially rare. Here we describe a detection of the fusion gene sequence of gastric SS in plasma cell-free DNA(cf DNA). A gastric submucosal tumor was detected in the stomach of a 27-year-old woman and diagnosed as SS. Candidate intronic primers were designed to detect the intronic fusion breakpoint and this fusion sequence was confirmed in intron 10 of SYT and intron 5 of SSX2 by genomic polymerase chain reaction(PCR) and direct sequencing. A locked nucleic acid(LNA) probe specificto the fusion sequence was designed for detecting the fusion sequence in plasma and the fusion sequence was detected in preoperative plasma cfD NA, while not detected in postoperative plasma cfD NA. This technique will be useful for monitoring translocation-derived diseases such as SS.
文摘Objective: To improve the detecting accuracy of chromosomal aneuploidy of fetus by non-invasive prenatal testing (NIPT) using next generation sequencing data of pregnant women’s cell-free DNA. Methods: We proposed the multi-Z method which uses 21 z-scores for each autosomal chromosome to detect aneuploidy of the chromosome, while the conventional NIPT method uses only one z-score. To do this, mapped read numbers of a certain chromosome were normalized by those of the other 21 chromosomes. Average and standard deviation (SD), which are used for calculating z-score of each sample, were obtained with normalized values between all autosomal chromosomes of control samples. In this way, multiple z-scores can be calculated for 21 autosomal chromosomes except oneself. Results: Multi-Z method showed 100% sensitivity and specificity for 187 samples sequenced to 3 M reads while the conventional NIPT method showed 95.1% specificity. Similarly, for 216 samples sequenced to 1 M reads, Multi-Z method showed 100% sensitivity and 95.6% specificity and the conventional NIPT method showed a result of 75.1% specificity. Conclusion: Multi-Z method showed higher accuracy and robust results than the conventional method even at low coverage reads.
文摘Background: Cell-free DNA (cfDNA) holds promise as a tumor marker of clinical importance. We aimed to investigate the prognostic value of baseline cfDNA in non small-cell lung cancer (NSCLC). Material and Methods: During a three-year period, patients with newly diagnosed, previously untreated advanced NSCLC were included in a consecutive, prospective marker-trial. Plasma was isolated from a pre-treatment peripheral blood sample and the level of total cfDNA was measured by an in-house assay qPCR-method. The treatment comprised carboplatin (AUC 5) intravenously day 1), and vinorelbine (30 mg/m2 intravenously day 1 and 60 mg/m2 perorally day 8) q3w for a maximum of six cycles. The primary end-point was overall survival (OS). Secondary end-points were progression free survival (PFS) and overall response rate (ORR). Results: 245 patients were included and received a minimum of 1 cycle of chemotherapy (median 4). The median OS was 8.9 months, the median PFS by intention to treat 5.4 months and the ORR was 25%. The patients were divided into four groups based on quartiles of cfDNA and subsequently dichotomized by the 75th percentile revealing a significantly worse prognosis for patients in the upper 75th percentile (median OS 4.9 months) compared to patients with lower levels (10.0 months) (HR 2.1, 95%CI 1.4 - 3.1, p 0.0001). A multivariate analysis confirmed the independent prognostic value of cfDNA. A subgroup analysis of patients with high cfDNA and poor performance status (PS = 2) identified a group of patients with even worse prognosis (median OS 2.0 versus 9.1 months, HR 3.6, 95%CI 1.4 - 9.2, p 0.0001). Similar and significant results were found when comparing level of cfDNA and PFS. Conclusions: High pre-treatment level of cfDNA seems to have a strong prognostic impact in patients with newly diagnosed advanced NSCLC. Combined with PS it identifies a patient group with minimal or no benefit of chemotherapy.
基金funded by grants from the GermanResearch Council(DFG,grant No.BR1704/16-1)the Fed-eral Ministry of Education and Research(BMBF,grantno.01GL1712 and 01KD2104A)the German CancerAid(No.70113330).
文摘Screening for colorectal cancer(CRC)is among the mosteffective approaches to cancer prevention,yet achievinghigh adherence to effective screening offers is challenging[1].Blood-based tests that could be easily implemented inroutine medical practice might be a promising approachto achieve higher adherence rates than with conven-tional stool-based or endoscopic screening[2,3].However,neoplasm detection rates of previously developed and pro-posed blood-based tests have not been competitive tothose of modern stool-based tests[2],in particular fecalimmunochemical tests(FITs)that are meanwhile widelyused for CRC screening in an increasing number of coun-tries[4].Most recently,performance of a novel cell-freeDNA(cfDNA)blood-based test for detecting colorectalneoplasms was validated in the ECLIPSE study,a largescreening population undergoing screening colonoscopy[5],being the first of its kind to achieve FDA approval asa primary screening option for CRC.
文摘Pediatric ear,nose,and throat(ENT)infections are common and vary from simple to life-threatening cases,including complicated sinusitis,deep neck space abscesses,and mastoiditis.ENT infections in children are a primary driver of antibiotic prescriptions.1 While invasive surgical cultures often yield successful pathogen identification,they require anesthesia and inpatient care.Patients are prescribed broad-spectrum antibiotics until the culture results become available.
文摘Cancer treatment has entered the era of precision medicine, where knowledge of a patient's genetic profile is used to facilitate early diagnosis, drug selection, prognosis, prediction of drug responsiveness, the onset of secondary resistance, and relapse. Circulating free DNA (cfDNA) has emerged as an ideal source of genetic information for cancer patients, and numerous studies have explored its validity in various clinical applications. However, clinical implementation of cfDNA-based tests has been slow. In this review, we addressed some of the pre-and post-analytical issues regarding cfDNA tests. First, we summarized the charac-teristics of cfDNA and reviewed the methods used to identify tumor-derived cfDNA from the pool of total cfDNA. Second, we described the procedures used to extract cfDNA, which have a great impact on representativeness and yield. Finally, we discussed our thoughts on the validation of cfDNA-based tests and the reporting of test results amid drastic limitations.
基金supported by grants from the Ministry of Science and Technology of China (Grant No. 2016YFC0900300)National Natural Science Foundation of China (Grant Nos. 31670895, U1504831, 31430022, 31670824, 31400672, and 81703598)+3 种基金Major Science and Technology Project of Henan Province (Grant No. 161100310100)Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDB14030300)Foundation for University Young Key Teacher of Henan Province (Grant No. 2015GGJS-162)Science and Technology Project of Henan Province (Grant No.162102310199), China
文摘Non-small-cell lung cancer （NSCLC）, the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymetbylcytosine （ShmC） signatures in circulating cell-free DNA （cfDNA） that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminat- ing tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here, we employed a sensitive and reliable method to map genome-wide 5hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls. Specifically, we identi- fied six potential biomarkers from 66 patients and 67 healthy controls （mean decrease accuracy 〉 3.2, P 〈 3.68E-19） using machine-learning-based tumor classifiers with high accuracy. Thus, the unique signature of 5hmC in tumor patient＇s cfDNA identified in our study may provide valuable information in facilitating the development of new diagnostic and therapeutic modalities for NSCLC.
