Biomedical subjects

Yingye Zheng

Publications and source records attributed to Yingye Zheng.

17 recordsLinked to original sources

PubMed2026

Clinical Validation of a Multiplex Urine Biomarker Assay for Surveillance of Recurrent Bladder Cancer.

PURPOSE: More than 50% of patients with non-muscle-invasive bladder cancer experience recurrence, requiring lifelong surveillance with repeated cystoscopy. Given the invasive nature and cost of cystoscopy, accurate noninvasive tools are needed to support risk-adapted monitoring. We evaluated the ability of Oncuria-Monitor, a multiplex urine biomarker assay, to detect recurrent bladder cancer during surveillance. PATIENTS AND METHODS: Between February 2017 and August 2020, six medical centers in the United States and Japan prospectively enrolled 300 patients with a history of bladder cancer, generating 1,248 serial urine samples. Participants were divided into training and validation cohorts. At each surveillance visit over 2 years, urine samples were analyzed in a blinded manner using Oncuria-Monitor and BladderChek, alongside urine cytology. Test performance was compared with cystoscopy and histopathology-confirmed recurrence. RESULTS: Recurrent bladder cancer was identified in 31% (93/300) of participants, with 143 total recurrences during follow-up, including 90 tumors in the validation cohort. In the validation cohort, Oncuria-Monitor achieved a sensitivity of 85.6% [95% confidence interval (CI), 78.1%-92.2%] and a negative predictive value (NPV) of 93% (95% CI, 89.2%-96.4%). In comparison, BladderChek demonstrated a sensitivity of 20.0% and an NPV of 88%, whereas urine cytology showed a sensitivity of 36.9% and an NPV of 91.6%. The number needed to evaluate to detect one recurrence was 3 for both cystoscopy and Oncuria-Monitor, compared with 15 for BladderChek and 8 for cytology. CONCLUSIONS: In this large prospective longitudinal study, Oncuria-Monitor demonstrated clinically actionable performance, enabling a rule-out strategy that could safely reduce cystoscopy in approximately 25% of surveillance visits. These findings support a paradigm shift toward biomarker-guided, risk-adapted surveillance in bladder cancer that reduces unnecessary invasive procedures while maintaining oncologic safety.

Humans↗

PubMed2007

Changes in cancer worry associated with participation in ovarian cancer screening.

While ovarian cancer is rare and screening is not recommended for most women, it is being studied as a way to reduce ovarian cancer mortality. As effective strategies for screening emerge it will be important to understand the quality of life (QOL) effects of participation in ovarian cancer screening. In this study, we examined the effects of participation in an ovarian cancer screening program on worry about cancer risk and QOL. A randomized controlled clinical trial (n = 592) was conducted. Women without a family history suggestive of a BRCA1/2 mutation were randomly assigned to screening and risk counseling, separately and in combination. Results were compared to women randomized to usual care alone. Levels of cancer worry fell for all study groups and QOL was unaffected; no statistically significant differences were found between groups. Increased levels of worry about ovarian cancer at 2-year follow-up were found among participants in screening receiving abnormal test results. For those who receive abnormal results, screening may have long-term effects and increase worry about cancer risk. Further research will be required to examine the possibility that screening reduces worry when women receive only normal, presumably reassuring, results.

Adult↗

PubMed2006

Application of a methylation gene panel by quantitative PCR for lung cancers.

Detection of lung cancer at early stages could potentially increase survival rates. One promising approach is the application of suitable lung cancer-specific biomarkers to specimens obtained by non-invasive methods. Thus far, clinically useful biomarkers that have high sensitivity have proven elusive. Certain genes, which are involved in cellular pathways such as signal transduction, apoptosis, cell to cell communication, cell cycles and cytokine signaling are down-regulated in cancers and may be considered as potential tumor suppressor genes. Aberrant promoter hypermethylation is a major mechanism for silencing tumor suppressor genes in many kinds of human cancers. Using quantitative real time PCR, we tested 11 genes (3-OST-2, RASSF1A, DcR1, DcR2, P16, DAPK, APC, ECAD, HCAD, SOCS1, SOCS3) for levels of methylation within their promoter sequences in non-small cell lung cancers (NSCLC), adjacent non-malignant lung tissues, in peripheral blood mononuclear cells (PBMC) from cancer free patients, in sputum of cancer patients and controls. Of all the 11 genes tested 3-OST-2 showed the highest levels of promoter methylation in tumors combined with lowest levels of promoter methylation in control tissues. 3-OST-2 followed by, RASSF1A showed increased levels of methylation with advanced tumor stage (P<0.05). Thus, quantitative analysis of 3-OST-2 and RASSF1A methylation appears to be a promising biomarker assay for NSCLC and should be further explored in a clinical study. Our preliminary data on the analysis of sputum DNA specimens from cancer patients further support these observations.

Adenocarcinoma↗

PubMed2006

Aberrant promoter methylation of multiple genes during multistep pathogenesis of colorectal cancers.

Aberrant methylation of 5'gene promoter regions associated with gene silencing is an epigenetic phenomenon responsible for silencing of tumor suppressor genes in many cancer types. The aims of our study were to study the role of methylation of a large panel of genes during multistage pathogenesis and to correlate our findings with patient age and other clinico-pathological features. We investigated the aberrant promoter methylation profile of 19 genes in 92 colorectal cancers (CRCs) and corresponding nonmalignant epithelia (NME) (n = 57), and selected 15 genes for studying 26 colorectal adenomas (CAs). On the Basis of our results, the genes could be divided into 3 groups. Group 1 consisted of 13 genes whose methylation was tumor-specific. For 8 of these genes, the methylation frequencies in CAs were similar to those of CRCs, but significantly different from the frequencies in NME. Group 2, consisting of 2 genes demonstrating little or no methylation, were present in any sample type. In Group 3, consisting of 4 genes, relatively frequent methylation was present in both CRCs and NME, and the differences between these specimen types were not significant. Methylation of Group 1 genes were tightly correlated with each other, and these genes demonstrated increased methylation frequencies in CRCs with increasing age. Methylation was not correlated with other clinico-pathological features. In general, methylation frequencies of CAs were intermediate between CRCs and NME. Our study constitutes the most comprehensive methylation profile of CRCs, demonstrates that methylation commences early during CRC pathogenesis and is an age-related phenomenon.

Aged↗

PubMed2006

Application of the time-dependent ROC curves for prognostic accuracy with multiple biomarkers.

The rapid advancement in molecule technology has led to the discovery of many markers that have potential applications in disease diagnosis and prognosis. In a prospective cohort study, information on a panel of biomarkers as well as the disease status for a patient are routinely collected over time. Such information is useful to predict patients' prognosis and select patients for targeted therapy. In this article, we develop procedures for constructing a composite test with optimal discrimination power when there are multiple markers available to assist in prediction and characterize the accuracy of the resulting test by extending the time-dependent receiver operating characteristic (ROC) curve methodology. We employ a modified logistic regression model to derive optimal linear composite scores such that their corresponding ROC curves are maximized at every false positive rate. We provide theoretical justification for using such a model for prognostic accuracy. The proposed method allows for time-varying marker effects and accommodates censored failure time outcome. When the effects of markers are approximately constant over time, we propose a more efficient estimating procedure under such models. We conduct numerical studies to evaluate the performance of the proposed procedures. Our results indicate the proposed methods are both flexible and efficient. We contrast these methods with an application concerning the prognostic accuracies of expression levels of six genes.

Biomarkers↗

PubMed2005

The sensitivity and specificity of markers for event times.

The statistical literature on assessing the accuracy of risk factors or disease markers as diagnostic tests deals almost exclusively with settings where the test, Y, is measured concurrently with disease status D. In practice, however, disease status may vary over time and there is often a time lag between when the marker is measured and the occurrence of disease. One example concerns the Framingham risk score (FR-score) as a marker for the future risk of cardiovascular events, events that occur after the score is ascertained. To evaluate such a marker, one needs to take the time lag into account since the predictive accuracy may be higher when the marker is measured closer to the time of disease occurrence. We therefore consider inference for sensitivity and specificity functions that are defined as functions of time. Semiparametric regression models are proposed. Data from a cohort study are used to estimate model parameters. One issue that arises in practice is that event times may be censored. In this research, we extend in several respects the work by Leisenring et al. (1997) that dealt only with parametric models for binary tests and uncensored data. We propose semiparametric models that accommodate continuous tests and censoring. Asymptotic distribution theory for parameter estimates is developed and procedures for making statistical inference are evaluated with simulation studies. We illustrate our methods with data from the Cardiovascular Health Study, relating the FR-score measured at enrollment to subsequent risk of cardiovascular events.

Aged↗

PubMed2005

Differential methylation of genes that regulate cytokine signaling in lymphoid and hematopoietic tumors.

The perturbations of the cytokine signaling pathway play an important role in lymphoid/hematopoietic tumors. Aberrant promoter methylation is the major mechanism of gene silencing in tumors. We examined 150 lymphoid/hematopoietic tumors or potential premalignant specimens, 55 control specimens and 12 EBV-transformed B lymphoblastoid cultures and 10 lymphoma/leukemia (L/L) or multiple myeloma (MM) cell lines for the methylation (and, in cell lines, of the expression status) of three genes involved in the cytokine signaling pathway. The genes were: SHP1, a protein tyrosine phosphatase; SYK, a protein kinase; and SOCS1, a suppressor of cytokine signaling. Our major findings were: (1) one or more of the three genes was frequently methylated in L/L and MM cell lines and there was good concordance (90-100%) between methylation and loss of gene expression; (2) treatment of L/L cell lines with a demethylating agent resulted in re-expression of SHP1 protein and downregulation of phosphorylated STAT3 in L/L cell lines; (3) all 55 control specimens and the lymphoblastoid cultures were negative for methylation of the three genes; (4) non-Hodgkin's lymphomas (100%), and leukemias (94%) had almost universal methylation of SHP1 and relatively less frequent (<30%) methylation of SOCS1 and SYK; (5) MM and monoclonal gammopathy of unknown significance (MGUS) had infrequent methylation of SHP1 (<20%), and occasional methylation of SOCS1 and SYK; and (6) comparable methylation frequencies for SOCS1 were observed in MM and MGUS, suggesting that SOCS1 methylation is an early event in MM pathogenesis. At least one gene was methylated in 119 of 130 (93%) of the malignant and 12 of 20 (60%) of the MGUS samples. Our findings demonstrate that the perturbations of cytokine signaling via silencing of these three genes are almost universal in lymphoid/hematopoietic tumors but the patterns of gene methylated for L/L and plasma cell dyscrasias are different.

Cell Line, Tumor↗

PubMed2005

Survival model predictive accuracy and ROC curves.

The predictive accuracy of a survival model can be summarized using extensions of the proportion of variation explained by the model, or R2, commonly used for continuous response models, or using extensions of sensitivity and specificity, which are commonly used for binary response models. In this article we propose new time-dependent accuracy summaries based on time-specific versions of sensitivity and specificity calculated over risk sets. We connect the accuracy summaries to a previously proposed global concordance measure, which is a variant of Kendall's tau. In addition, we show how standard Cox regression output can be used to obtain estimates of time-dependent sensitivity and specificity, and time-dependent receiver operating characteristic (ROC) curves. Semiparametric estimation methods appropriate for both proportional and nonproportional hazards data are introduced, evaluated in simulations, and illustrated using two familiar survival data sets.

Biometry↗

PubMed2005

Assessing accuracy of mammography in the presence of verification bias and intrareader correlation.

The performance of a medical diagnostic test is often evaluated by comparing the outcome of the test to the patient's true disease state. Receiver operating characteristic analysis may then be used to summarize test accuracy. However, such analysis may encounter several complications in actual practice. One complication is verification bias, i.e., gold standard assessment of disease status may only be partially available and the probability of ascertainment of disease may depend on both the test result and characteristics of the subject. A second issue is that tests interpreted by the same rater may not be independent. Using estimating equations, we generalize previous methods that address these problems. We contrast the performance of alternative estimators of accuracy using robust sandwich variance estimators to permit valid asymptotic inference. We suggest that in the context of an observational cohort study where rich covariate information is available, a weighted estimating equations approach may be preferable for its robustness against model misspecification. We apply the methodology to mammography as performed by community radiologists.

Bias↗

PubMed2005

Partly conditional survival models for longitudinal data.

It is common in longitudinal studies to collect information on the time until a key clinical event, such as death, and to measure markers of patient health at multiple follow-up times. One approach to the joint analysis of survival and repeated measures data adopts a time-varying covariate regression model for the event time hazard. Using this standard approach, the instantaneous risk of death at time t is specified as a possibly semi-parametric function of covariate information that has accrued through time t. In this manuscript, we decouple the time scale for modeling the hazard from the time scale for accrual of available longitudinal covariate information. Specifically, we propose a class of models that condition on the covariate information through time s and then specifies the conditional hazard for times t, where t > s. Our approach parallels the "partly conditional" models proposed by Pepe and Couper (1997, Journal of the American Statistical Association 92, 991-998) for pure repeated measures applications. Estimation is based on the use of estimating equations applied to clusters of data formed through the creation of derived survival times that measure the time from measurement of covariates to the end of follow-up. Patient follow-up may be terminated either by the occurrence of the event or by censoring. The proposed methods allow a flexible characterization of the association between a longitudinal covariate process and a survival time, and facilitate the direct prediction of survival probabilities in the time-varying covariate setting.

Acquired Immunodeficiency Syndrome↗

PubMed2004

Presence of simian virus 40 DNA sequences in human lymphoid and hematopoietic malignancies and their relationship to aberrant promoter methylation of multiple genes.

The simian polyoma virus SV40 has been detected in specific human tumors including non-Hodgkin's lymphomas, although a causative role for the virus has not been convincingly demonstrated. Aberrant methylation of CpG islands in promoter regions is a frequent method of silencing tumor suppressor genes (TSGs) in cancers and may be induced by oncogenic viruses. We investigated the relationship between the presence of SV40 or EBV DNA sequences and the methylation profiles for 10 TSGs in 90 cases of non-Hodgkin's lymphomas/leukemias and 56 control tissues. SV40 sequences were present in 33/90 (37%) non-Hodgkin's lymphomas/leukemias, and EBV was present in 11/42 (26%) of non-Hodgkin's lymphomas. We found a highly significant correlation between the presence of SV40 and methylation of seven genes (P values, 0.006 to <0.0001). In lymphomas, there was no relationship between EBV and methylation. Oncogenic viruses and methylation were rarely present in control tissues. We investigated methylation of the same 10 TSGs in peripheral blood mononuclear cells (PBMC) from a healthy volunteer infected with EBV or EBV and SV40. Promoter methylation of CDH1 and CDH13 were noted in dual SV40- and EBV-infected PBMC, and these two genes were also highly significantly correlated to the presence of SV40 sequences in tumors. SV40 infection also resulted in appearance of the lymphoma/leukemia-specific marker, methylated SHP1. Methylation was completely absent in uninfected and EBV-infected PBMC. Our results demonstrate that the presence of SV40 in hematological malignancies is associated with promoter methylation of TSGs and that in all probability, the virus plays a role in tumor pathogenesis.

DNA Methylation↗

PubMed2004

DNA methylation profiles of lymphoid and hematopoietic malignancies.

PURPOSE: Aberrant methylation of the 5' gene promoter regions is an epigenetic phenomenon that is the major mechanism for silencing of tumor suppressor genes in many cancer types. The aims of our study were (a) to compare the methylation profiles of the major forms of hematological malignancies and (b) to determine the methylation profile of monoclonal gammopathy of undetermined significance (MGUS) and compare it with that of multiple myeloma (MM). EXPERIMENTAL DESIGN: We compared the aberrant promoter methylation profile of 14 known or suspected tumor suppressor genes in leukemias (n = 48), lymphomas (n = 42), and MMs (n = 40). We also examined the methylation profile of MGUS (n = 20), a premalignant plasma cell dyscrasia. The genes studied represent five of the six "hallmarks of cancer." RESULTS: Peripheral blood lymphocytes (n = 14) from healthy volunteers were negative for methylation of all genes, and methylation percentages in 41 nonmalignant tissues (peripheral blood mononuclear cells, bone marrows, and lymph nodes) from hematological patients were low (0-9%) for all 14 genes, confirming that methylation was tumor specific. Ten of the genes were methylated at frequencies of 29-68% in one or more tumor types, and the methylation indices (an indicator of overall methylation) varied from 0.25 to 0.34. With two exceptions, the methylation patterns of leukemias and lymphomas were similar. However, the pattern of MMs varied from the other tumor types for six genes. In general, the methylation pattern of MGUS was similar to that of MM, although the methylation frequencies were lower (the methylation index of MGUS was 0.15, and that of MM was 0.3). However, the methylation frequencies of six genes were significantly higher in MGUS than in control tissues. The relatively high frequencies of methylation in MGUS are consistent with it being a premalignant condition. CONCLUSIONS: The three major forms of lymphoid/hematopoietic malignancies show overlapping but individual patterns of methylation.

Age Factors↗

PubMed2004

Semiparametric estimation of time-dependent ROC curves for longitudinal marker data.

One approach to evaluating the strength of association between a longitudinal marker process and a key clinical event time is through predictive regression methods such as a time-dependent covariate hazard model. For example, a Cox model with time-varying covariates specifies the instantaneous risk of the event as a function of the time-varying marker and additional covariates. In this manuscript we explore a second complementary approach which characterizes the distribution of the marker as a function of both the measurement time and the ultimate event time. Our goal is to extend the standard diagnostic accuracy concepts of sensitivity and specificity so as to recognize explicitly both the timing of the marker measurement and the timing of disease. The accuracy of a longitudinal marker can be fully characterized using time-dependent receiver operating characteristic (ROC) curves. We detail a semiparametric estimation method for time-dependent ROC curves that adopts a regression quantile approach for longitudinal data introduced by Heagerty and Pepe (1999, Applied Statistics, 48, 533-551). We extend the work of Heagerty and Pepe (1999, Applied Statistics, 48, 533-551) by developing asymptotic distribution theory for the ROC estimators where the distributional shape for the marker is allowed to depend on covariates. To illustrate our method, we analyze pulmonary function measurements among cystic fibrosis subjects and estimate ROC curves that assess how well the pulmonary function measurement can distinguish subjects that progress to death from subjects that remain alive. Comparing the results from our semiparametric analysis to a fully parametric method discussed by Etzioni et al. (1999, Medical Decision Making, 19, 242-251) suggests that the ability to relax distributional assumptions may be important in practice.

Adolescent↗

PubMed2003

The difference engine: a model of diversity in speeded cognition.

A theory of diversity in speeded cognition, the difference engine, is proposed, in which information processing is represented as a series of generic computational steps. Some individuals tend to perform all of these computations relatively quickly and other individuals tend to perform them all relatively slowly, reflecting the existence of a general cognitive speed factor, but the time required for response selection and execution is assumed to be independent of cognitive speed. The difference engine correctly predicts the positively accelerated form of the relation between diversity of performance, as measured by the standard deviation for the group, and task difficulty, as indexed by the mean response time (RT) for the group. In addition, the difference engine correctly predicts approximately linear relations between the RTs of any individual and average performance for the group, with the regression lines for fast individuals having slopes less than 1.0 (and positive intercepts) and the regression lines for slow individuals having slopes greater than 1.0 (and negative intercepts). Similar predictions are made for comparisons of slow, average, and fast subgroups, regardless of whether those subgroups are formed on the basis of differences in ability, age, or health status. These predictions are consistent with evidence from studies of healthy young and older adults as well as from studies of depressed and age-matched control groups.

Cognition↗

PubMed2002

Detection of ductal carcinoma in situ in women undergoing screening mammography.

BACKGROUND: With the large number of women having mammography-an estimated 28.4 million U.S. women aged 40 years and older in 1998-the percentage of cancers detected as ductal carcinoma in situ (DCIS), which has an uncertain prognosis, has increased. We pooled data from seven regional mammography registries to determine the percentage of mammographically detected cancers that are DCIS and the rate of DCIS per 1000 mammograms. METHODS: We analyzed data on 653 833 mammograms from 540 738 women between 40 and 84 years of age who underwent screening mammography at facilities participating in the National Cancer Institute's Breast Cancer Surveillance Consortium (BCSC) throughout 1996 and 1997. Mammography results were linked to population-based cancer and pathology registries. We calculated the percentage of screen-detected breast cancers that were DCIS, the rate of screen-detected DCIS per 1000 mammograms by age and by previous mammography status, and the sensitivity of screening mammography. Statistical tests were two-sided. RESULTS: A total of 3266 cases of breast cancer were identified, 591 DCIS and 2675 invasive breast cancer. The percentage of screen-detected breast cancers that were DCIS decreased with age (from 28.2% [95% confidence interval (CI) = 23.9% to 32.5%] for women aged 40-49 years to 16.0% [95% CI = 13.3% to 18.7%] for women aged 70-84 years). However, the rate of screen-detected DCIS cases per 1000 mammograms increased with age (from 0.56 [95% CI = 0.41 to 0.70] for women aged 40-49 years to 1.07 [95% CI = 0.87 to 1.27] for women aged 70-84 years). Sensitivity of screening mammography in all age groups combined was higher for detecting DCIS (86.0% [95% CI = 83.2% to 88.8%]) than it was for detecting invasive breast cancer (75.1% [95% CI = 73.5% to 76.8%]). CONCLUSIONS: Overall, approximately 1 in every 1300 screening mammography examinations leads to a diagnosis of DCIS. Given uncertainty about the natural history of DCIS, the clinical significance of screen-detected DCIS needs further investigation.

Adult↗

PubMed2002

Performance of diagnostic mammography for women with signs or symptoms of breast cancer.

BACKGROUND: The performance of diagnostic mammography for women with signs or symptoms of breast cancer has not been well studied. We evaluated whether age, breast density, self-reported breast lump, and previous mammography influence the performance of diagnostic mammography. METHODS: From January 1996 through March 1998, prospective diagnostic mammography data from women aged 25-89 years with no previous breast cancer were linked to cancer outcomes data in six mammography registries participating in the Breast Cancer Surveillance Consortium. We used the final mammographic assessment at the end of the imaging work-up to determine abnormal mammographic examination rate, positive predictive value (PPV), sensitivity, specificity, and area under the receiver operating characteristic (ROC) curve. We used age, breast density, prior mammogram, and self-reported breast lump jointly as predictors of performance. All statistical tests were two-sided. RESULTS: Of 41 427 diagnostic mammograms, 6279 (15.2%) were judged abnormal. The overall PPV was 21.8%, sensitivity was 85.8%, and specificity was 87.7%. Multivariate analysis showed that sensitivity and specificity generally declined as breast density increased (P =.007 and P<.001, respectively), that previous mammography decreased sensitivity (odds ratio [OR] = 0.52, 95% confidence interval [CI] = 0.36 to 0.74; P<.001) but increased specificity (OR = 1.43, 95% CI = 1.31 to 1.57; P<.001), and that a self-reported breast lump increased sensitivity (OR = 1.64, 95% CI = 1.13 to 2.38; P =.013) but decreased specificity (OR = 0.54, 95% CI = 0.49 to 0.59; P<.001). ROC analysis showed that higher breast density and previous mammography were negatively related to accuracy (P<.001 for both). CONCLUSIONS: Diagnostic mammography in women with signs or symptoms of breast cancer shows higher sensitivity and lower specificity than screening mammography does. Higher breast density and previous mammographic examination appear to impair performance.

Adult↗

PubMed2002

Use of the American College of Radiology BI-RADS to report on the mammographic evaluation of women with signs and symptoms of breast disease.

PURPOSE: To examine whether mammographic assessments and recommendations are linked as expected, based on the Breast Imaging Reporting and Data System (BI-RADS), for the evaluation of women with signs and symptoms of breast disease. MATERIALS AND METHODS: Eight mammography registries from the Breast Cancer Surveillance Consortium contributed mammographic data from 1996 through 1997 for women 25 years of age or older, with signs or symptoms of breast cancer. The association of assessments and recommendations and the relationship of self-reported symptoms to assessments are described. RESULTS: A total of 51,673 diagnostic mammograms were included in the analyses and the expected management recommendation was provided 85%-90% of the time for mammograms classified as assessment categories 1, 2, 4, or 5. Category 3 ("probably benign finding") had the most variability in associated management recommendations, with only 40% (2,998 of 7,423) of cases associated with the recommendation for short interval follow-up. Of the 1,648 category 0 mammograms ("needs additional imaging") that did not have a final assessment, 64% were recommended for additional imaging, while another 20% of the cases were recommended for either a consultation or biopsy. The number of women who reported a lump as a symptom decreased with age but was associated with higher BI-RADS assessments. CONCLUSION: BI-RADS assessment categories were generally used as intended for all categories but 0 and 3. Additional education about the use of these categories may be warranted. The inconsistencies between assessment category and management recommendations may present difficulties in conducting outcome audits.

Adult↗