Biomedical subjects

Tomasz Burzykowski

Publications and source records attributed to Tomasz Burzykowski.

At least 19 recordsLinked to original sources

PubMed2006

Prostate-specific antigen (PSA) alone is not an appropriate surrogate marker of long-term therapeutic benefit in prostate cancer trials.

The prostate-specific antigen (PSA) is the most studied marker of prostate cancer. It is used for screening and as indicator of disease evolution for individual patients. PSA being a prognostic factor is however not sufficient to justify using PSA-derived endpoints as surrogate for definitive survival endpoint in phase III trials. First, we clarify the terminology and requirements for a marker to be a valid surrogate endpoint. We then review the published literature pertaining to the validation of PSA endpoints as surrogate in all disease stages. We discuss the limitations of these studies and conclude that so far, PSA is not a validated surrogate endpoint in any of the disease settings and treatment conditions considered. We give some recommendations for the planning of trials that would use PSA endpoints (in hormone refractory disease) and for the early stop of (endocrine treatment) trials on the basis of intermediate results based on PSA.

Antineoplastic Agents, Hormonal↗

PubMed2006

A modeling approach to the analysis of nerve regenerative experiments.

Many experiments aiming at the investigation of nerve repair involve elaborate testing over a certain time period. Data arising from such experiments are often analyzed by time-point. Such a cross-sectional approach is often very inefficient. In this paper, we consider a case study in which repeated measurements of two response variables assumed to be Poisson distributed are obtained. We show how a repeated measures modeling approach, based on generalized linear models, can handle both responses in one model and improve the inference in the nerve repair experiments. The benefits of the model as well as problems that can occur are illustrated and discussed.

Algorithms↗

PubMed2006

The use of background signal in the transformation of cDNA-microarray measurements.

As the application field of microarrays grows, so does the need for appropriate statistical tools to analyse the signal intensity measurements. Normalisation procedures are required to make the signals from different channels and arrays comparable. One objective, which is also the focus of this report, is to remove the curvature seen on plots of the log ratio versus the mean log intensity values of two channels.A number of methods already exist that are based on the assumption of a shift between the measurements of the two channels. In this article, we explore the use of background measurements to estimate and correct for the shift. We compare our proposal with some well known methods by applying them to microarrays from two studies. These two studies investigate the effect of vegetable diets on the gene expression in colon and lung tissue of mice. Graphical illustrations and a robust summary statistic show that all transformations are an improvement to the raw data. Overall, the best results are obtained with our proposed transformation that takes the background measurements into account.

Algorithms↗

PubMed2005

No association of leukemia inhibitory factor (LIF) DNA polymorphisms with multiple sclerosis.

Neuropoietins such as leukemia inhibitory factor (LIF) have been shown to ameliorate experimental autoimmune encephalomyelitis (EAE) and promote oligodendrocyte survival in vivo. We tested whether two previously described LIF polymorphisms are associated with MS by genotyping these single nucleotide polymorphisms (SNPs) in a group of MS patients (n=110), rheumatoid arthritis (RA) patients (n=120) and healthy controls (HC, n=109). Similar allele and genotype frequencies for both SNPs were found for all study groups. Furthermore, no associations with MS type or HLA-DR2 expression could be found. In summary, no association was found between the studied LIF DNA polymorphisms and the prevalence of MS indicating that these polymorphisms are not involved in determining disease susceptibility.

Adult↗

PubMed2005

Is prostate-specific antigen a valid surrogate end point for survival in hormonally treated patients with metastatic prostate cancer? Joint research of the European Organisation for Research and Treatment of Cancer, the Limburgs Universitair Centrum, and AstraZeneca Pharmaceuticals.

PURPOSE: The long duration of phase III clinical trials of overall survival (OS) slows down the treatment-development process. It could be shortened by using surrogate end points. Prostate-specific antigen (PSA) is the most studied biomarker in prostate cancer (PCa). This study attempts to validate PSA end points as surrogates for OS in advanced PCa. PATIENTS AND METHODS: Individual data from 2,161 advanced PCa patients treated in studies comparing bicalutamide to castration were used in a meta-analytic approach to surrogate end-point validation. PSA response, PSA normalization, time to PSA progression, and longitudinal PSA measurements were considered. RESULTS: The known association between PSA and OS at the individual patient level was confirmed. The association between the effect of intervention on any PSA end point and on OS was generally low (determination coefficient, < 0.69). CONCLUSION: It is a common misconception that high correlation between biomarkers and true end point justify the use of the former as surrogates. To statistically validate surrogate end points, a high correlation between the treatment effects on the surrogate and true end point needs to be established across groups of patients treated with two alternative interventions. The levels of association observed in this study indicate that the effect of hormonal treatment on OS cannot be predicted with a high degree of precision from observed treatment effects on PSA end points, and thus statistical validity is unproven. In practice, non-null treatment effects on OS can be predicted only from precisely estimated large effects on time to PSA progression (TTPP; hazard ratio, < 0.50).

Antineoplastic Agents, Hormonal↗

PubMed2005

Design and analysis of drug combination experiments.

In this paper we present and discuss a novel, simple and easy to implement parametric modeling approach to assess synergy. An extended three parameter log-logistic model is used to analyse the data and calculate confidence intervals of the interaction indices. In addition the model corrects for the bias due to plate-location effects. The analysis is performed with PROC NLMIXED and SAS-code is provided. The approach is illustrated using data coming from an oncology study in which the inhibition effect of a combination of two compounds is studied using 96-well plates and a fixed-ratio design.

Algorithms↗

PubMed2005

A version of the EM algorithm for proportional hazard model with random effects.

Proportional hazard models with multivariate random effects (frailties) acting multiplicatively on the baseline hazard have recently become a topic of an intensive research. One of the main practical problems related to the models is the estimation of parameters. To this aim, several approaches based on the EM algorithm have been proposed. The major difference between these approaches is the method of the computation of conditional expectations required at the E-step. In this paper an alternative implementation of the EM algorithm is proposed, in which the expected values are computed with the use of the Laplace approximation. The method is computationally less demanding than the approaches developed previously. Its performance is assessed based on a simulation study and compared to a non-EM based estimation approach proposed by Ripatti and Palmgren (2000).

Algorithms↗

PubMed2005

Vegetables affect the expression of genes involved in carcinogenic and anticarcinogenic processes in the lungs of female C57BL/6 mice.

Worldwide, lung cancer is the most prevalent and lethal malignant disease. In addition to avoidance of the most predominant risk factor, i.e., tobacco use, consumption of high amounts of vegetables and fruits could be an effective means of preventing lung cancer. However, the molecular mechanisms underlying lung cancer risk reduction by vegetables are not clear. In the present study, the effect of vegetables on gene expression changes in the lungs of female C57Bl/6 mice was investigated using cDNA microarray technology. The mice were fed 1 of 8 diets for 2 wk: a control diet containing no vegetables (diet 1); a diet containing a vegetable mixture at 100 (diet 2, 10% dose), 200 (diet 3, 20% dose), or 400 (diet 4, 40% dose) g/kg; or a diet containing cauliflower at 70 (diet 5, 7% dose); carrots at 73 (diet 6, 7.3% dose); peas at 226 (diet 7, 22.6% dose); or onions at 31 (diet 8, 3.1% dose) g/kg. The vegetable mixture consisted of these 4 individual vegetables. After the mice were killed, the lungs were removed and total RNA was isolated from the lungs for expression analysis of 602 genes involved in pathways of (anti)-carcinogenesis. The results of this study suggest that individual vegetables have a higher potential of modulating genes (5 from the 8 modulated genes) in favor of lung cancer risk prevention, in comparison with the vegetable mixture (2 from the 7 modulated genes); the other gene modulations are expected to enhance lung cancer risk. The pathways involved were miscellaneous and included cell growth, apoptosis, biotransformation, and immune response. Furthermore, carrots were able to modulate most gene expressions, and most of these effects occurred in processes that favored lung cancer risk prevention. The current study provides more insight into the genetic mechanisms by which vegetables, in particular carrots, can prevent lung cancer risk.

Animals↗

PubMed2005

Vegetables affect the expression of genes involved in anticarcinogenic processes in the colonic mucosa of C57BL/6 female mice.

There is abundant epidemiological evidence that vegetable consumption decreases colorectal cancer (CRC) risk. However, the molecular targets in the genome are mostly unknown. The present study investigated the effects of vegetable consumption on gene expression in the colon mucosa of female C57Bl/6 mice using cDNA microarray technology. Mice were fed one of 8 diets: a control diet containing no vegetables (diet 1); a diet containing 100 g/kg (diet 2, 10% dose), 200 g/kg (diet 3, 20% dose), or 400 g/kg (diet 4, 40% dose) of a vegetable mixture; or a diet containing 70 g/kg of cauliflower (diet 5, 7% dose), 73 g/kg of carrots (diet 6, 7.3% dose), 226 g/kg of peas (diet 7, 22.6% dose); or 31 g/kg of onions (diet 8, 3.1% dose). The vegetable mixture used in diets 2 to 4 consisted of the 4 individual vegetables used in diets 5 to 8: cauliflower (30% wet wt), carrots (30% wet wt), peas (30% wet wt), and onions (10% wet wt). To assess gene expression changes, colonic mucosal cells were collected after the mice were killed. Total RNA was isolated and microarray technology was used to measure the expression levels of 602 genes simultaneously. For 39 genes, significant dose-dependent effects were found, although in general the relations were not linear. For 15 genes, the altered expression could indeed explain reduced cancer risk at various stages of CRC development. Eleven genes were modulated by the vegetable mixture as well as by one or more of the individual vegetables. For 7 of the genes, the modulation by the mixture was due to the effect of a particular vegetable. These genes are of particular interest because they were consistently affected and could be involved in the prevention of CRC by vegetable consumption.

Animals↗

PubMed2004

Pseudo-likelihood estimation for a marginal multivariate survival model.

In this paper, we propose a multivariate Plackett-Dale model for survival outcomes. A pseudo-likelihood method for the estimation of the parameters is proposed and these ideas are applied to two case studies. The modelling approach is similar in spirit but different from Parner's approach. The first study is in AIDS, where the overall survival time and different opportunistic infections in HIV-infected patients are studied. The second study is on adoption data where the association of the survival times within families is modelled, illustrating the use of the proposed methodology for the context of population genetics.

Acquired Immunodeficiency Syndrome↗

PubMed2004

Efficacy of oral adjuvant therapy after resection of colorectal cancer: 5-year results from three randomized trials.

PURPOSE: Adjuvant therapy of colorectal cancer with oral fluorinated pyrimidines is attractive because of its ease of administration and good tolerability. The purpose of this meta-analysis is to assess the survival and disease-free survival benefits of treating patients after surgical resection of a primary colorectal tumor with oral fluoropyrimidines for 1 year. PATIENTS AND METHODS: This meta-analysis was performed on individual data from three randomized trials conducted by the Japanese Foundation for Multidisciplinary Treatment for Cancer involving a total of 5,233 patients with stages I to III colorectal cancer. RESULTS: The overall hazard ratio in favor of oral therapy was 0.89 for survival (95% CI, 0.80 to 0.99; P =.04), and 0.85 for disease-free survival (95% CI, 0.77 to 0.93; P <.001). Thus oral therapy reduced the risk of death by 11% and the risk of recurrence or death by 15%. There was no significant heterogeneity between trials, nor did the benefit of oral therapy depend on tumor stage (I, II, or III), tumor site (rectum or colon), patient age, or patient sex. CONCLUSION: Oral fluoropyrimidines improve disease-free survival and survival of patients after resection of early-stage colorectal cancer. These observations support the use of these agents alone after resection of early-stage disease, as well as further testing of oral agents in combination with new drugs that have recently shown antitumor activity in advanced colorectal cancer.

Administration, Oral↗

PubMed2004

Axillary sentinel node and tumour-related factors associated with non-sentinel node involvement in breast cancer.

BACKGROUND: After completion of axillary dissection, many breast cancer patients with axillary sentinel nodal involvement are found to have regional disease limited to the sentinel nodes. These patients are exposed to the morbidity of axillary clearance without any expected therapeutic benefit. METHODS: Sentinel node biopsy was performed either with Patent blue dye or with a combined dye, radiocolloid and gamma-probe-guided method involving peritumoral tracer administration. For a series of 150 consecutive patients with involved axillary sentinel nodes and axillary dissection, factors associated with non-sentinel nodal involvement were analysed in a multivariate analysis based on logistic regression with the use of fractional polynomials. RESULTS: The following variables were found to be potentially associated with non-sentinel node metastases: tumour size, sentinel node metastasis size, number of examined sentinel nodes, percentage of involved sentinel nodes (the latter two were found to be significant only when in combination), and extracapsular perinodal spread. CONCLUSIONS: Isolated tumour cells and micrometastases in axillary sentinel nodes carry a low risk of non-sentinel node metastasis. The risk of metastasis to further echelon nodes is higher with macrometastases, especially if there is extracapsular growth and the proportion of involved sentinel nodes is high.

Axilla↗

PubMed2004

Prentice's approach and the meta-analytic paradigm: a reflection on the role of statistics in the evaluation of surrogate endpoints.

We put a perspective on the strengths and limitations of statistical methods for the evaluation of surrogate endpoints. Whereas using several trials overcomes some of the limitations of a single-trial framework (Prentice, 1989, Statistics in Medicine 8, 431-440), arguably the evaluation of surrogate endpoints can never be done using only statistical evidence but such evidence should be seen as but one component in a decision-making process that involves, among others, a number of clinical and biological considerations. We briefly present a hierarchical framework that incorporates ideas from Prentice's work and is uniformly applicable to different types of surrogate and true clinical outcomes.

Biometry↗

PubMed2004

A perspective on surrogate endpoints in controlled clinical trials.

The last couple of decades have seen a large amount of activity in the area of surrogate marker and surrogate endpoint validation, both from a clinical and a statistical perspective. Prentice made a pivotal contribution in the context of a single trial. Subsequently, the framework he proposed has been discussed, criticized, and extended. An important class of extensions considers several rather than a single trial. Recently, a lot of work has been done in this so-called hierarchical or meta-analytic framework. In this paper, we review both the single trial and the hierarchical framework. A number of applications, scattered throughout the literature, are brought together. We outline the statistical issues involved in trying to validate surrogate endpoints. Clearly statistical evidence should only be seen as a component in a decision making process that also involves a number of clinical and biological considerations.

Antineoplastic Agents, Hormonal↗

PubMed2004

Predicted and observed thyroid cancer incidence in Poland after year 1986.

Chmielarczyk et al. analyzed thyroid cancer incidence in Poland between the years 1986 and 1994. Both for males and for females they found exponential increase of the directly standardized total incidence rates. The exponential growth could also be concluded for several age-specific rates in both sexes. Following the suggestion by Chmielarczyk et al., in this paper an attempt to verify their conclusions is undertaken. To this aim thyroid cancer incidence rates observed in Poland in 1995-2000 are compared with the predictions obtained from the models used by Chmielarczyk et al. to analyze the 1986-1994 data. The results of the comparison indicate that the predictions for the exponential growth model are consistent with the data observed in 1995-2000 for females. For males, however, an alternative possibility of a linear increase of incidence rates might also be applicable. To reach a more definite conclusion in this case, further follow up is needed.

Adult↗

PubMed2003

Using the expected survival to explain differences between the results of randomized trials: a case in advanced ovarian cancer.

PURPOSE: A meta-analysis of randomized trials in advanced ovarian cancer showed a longer survival with cyclophosphamide, doxorubicin, and cisplatin (CAP) than with cyclophosphamide and cisplatin (CP; P =.009). In contrast, the results of the large International Collaborative Ovarian Neoplasm Study (ICON2) showed no survival difference between CAP and carboplatin (P =.98). In this article, we show how these discrepant results can be reconciled through the estimation of expected survival curves. MATERIALS AND METHODS: A proportional hazards model, fitted to the meta-analysis data, was used to construct the expected survival curve for each treatment arm of the ICON2 trial. Expected survival curves were compared with observed survival curves in the ICON2 trial at all time points using a nonparametric test. RESULTS: The prognostic model for survival obtained in the meta-analysis included extent of residual disease, age, histologic grade, and International Federation of Gynecology and Obstetrics stage. When this model was applied to the ICON2 data, there was no difference between the expected and observed curves in the CAP arm. In contrast, the observed survival curve for carboplatin was far superior to the expected survival curve for CP (P <.01). CONCLUSION: These analyses provide indirect evidence that better results are achieved with carboplatin alone at an optimally tolerated dose, compared with the CP combination at a cisplatin dose of 50 to 60 mg/m2. The expected survival may provide valuable insight when direct comparisons between randomized groups yield discrepant results across different studies.

Adult↗

PubMed2003

Multivariate analysis of risk factors for development of duodenal ulcer in Helicobacter pylori-infected patients.

BACKGROUND: Although Helicobacter pylori is a significant etiologic factor of peptic ulcer disease, it remains unknown why ulcers develop only in the minority of infected individuals. AIM: The aim of this cross-sectional study was to evaluate the association between the presence of duodenal ulcer in H. pylori-infected patients and different risk factors. METHODS: A total of 122 H. pylori-infected patients were enrolled; 79 had duodenal ulcer and 43 gastritis. Univariate analysis was conducted using either Fisher's exact test or exact Cochrane-Armitage trend test. In multivariate analysis the logistic model was used. RESULTS: Univariate analysis indicated six factors (male sex, smoking, antral H. pylori density, CAGA presence in antrum, and VACA s1a presence in antrum and corpus). Four factors (sex, smoking-alcohol index, H. pylori density index, and CAGA index) were found to be significant in multivariate analysis. The best model predicting duodenal ulcer included male sex, smoking, presence of H. PYLORI on histopathology in antrum and CAGA presence in corpus. CONCLUSION: Although several risk factors were significantly associated with duodenal ulcer, we failed in the identification of either a single risk factor or a set of factors that can unequivocally differentiate patients with ulcer from those with gastritis.

Adolescent↗

PubMed2003

Functional form of the effect of the numbers of axillary nodes on survival in early breast cancer.

The change in survival in function of the numbers of involved and uninvolved axillary nodes in early breast cancer - i.e. the functional form - was investigated to search for prognostic cutoffs and to assess if ratio-based characterization of node involvement is a significant prognostic factor or not. Women aged 40-69, diagnosed in 1988-1997 with T1-T2 invasive breast carcinoma, who underwent axillary dissection, are selected from the SEER public database. The method determines the functional form by applying smoothed plots to the martingale residuals obtained from a proportional hazards model. The results on 55,267 selected patients find that the ratio of involved nodes on examined nodes, in a multivariate model that takes into account known prognostic factors (age, race, tumor size, topography, histology, grade, hormone receptors), is associated with a relative mortality hazard of 1.012 (95% confidence interval 1.010-1.014; relative increase of mortality of 1.2% for each 1% increase in the percentage of involved nodes). The functional form for the number of uninvolved nodes shows that the relative mortality hazard initially steeply decreases and then tends to level off beyond 5-10 uninvolved nodes. For the number of involved nodes, the relative mortality hazard continues to increase with each involved node without any obvious cutpoint. Even when the number of involved nodes is already large, each additional involved node increases the relative mortality hazard by at least 1.3%.

Adult↗