Biomedical subjects

T L Bergemann

Publications and source records attributed to T L Bergemann.

4 recordsLinked to original sources

PubMed2005

Linear parameter haplotype models with stratification.

OBJECTIVES: The question of interest is estimating the relationship between haplotypes and an outcome measure, based upon unphased genotypes. The outcome of interest might be predicting the presence of disease in a logistic model, predicting a numeric drug response in a linear model, or predicting survival time in a parametric survival model with censoring. Explanatory variables may include phased haplotype design variables, environmental variables, or interactions between them. METHODS: We extend existing generalized linear haplotype models to parametric survival outcomes. To improve the stability of model variance estimates, a profile likelihood solution is proposed. An adjustment for population stratification is also considered. Here we investigate data sampled from known 'strata' (e.g., gender or ethnicity) that influence haplotype prior probabilities and thus the regression model weights. Differing linear model variance estimates, and the effect of stratification and departures from Hardy-Weinberg Equilibrium (HWE) on parameter estimates, are compared and contrasted via simulation. RESULTS: From simulations, we observed an improvement in statistical power when using a solution to profile likelihood equations. We also saw that stratification had little impact on estimates. Haplotypes that are not in HWE had a negative impact on power to test hypotheses. Finally, profile likelihood solutions for haplotypes deviating from HWE had improved power and confidence interval coverage of regression model coefficients.

Carcinoma, Squamous Cell↗

PubMed2004

A statistically driven approach for image segmentation and signal extraction in cDNA microarrays.

The increasing use of cDNA microarrays necessitates the development of methods for extracting quality data. Here, we set forth hurdles to overcome in image analysis of microarrays. We emphasize the importance of objective data extraction methods resulting in reliable signal estimates. Based on statistical principles, we describe a method for automated grid alignment, spot detection, background estimation, flagging, and signal extraction. A software application that we call SignalViewer has been implemented for this method. We identify areas where we improved upon current methods used for array image analysis at each step in the process. Finally, we give examples to illustrate the performance of our algorithms on raw data.

Algorithms↗

PubMed2003

SignalViewer: analyzing microarray images.

Microarray technology is now routinely used to monitor genome-wide expression profiles. However, current microarray imaging and analysis packages typically require manual intervention and assumptions on alignments. Unfortunately, limitations and assumptions are typically undisclosed and methods are not published. To facilitate exploration of image data, we developed SignalViewer. This paper presents a description of the application.

Artifacts↗

PubMed2001

Intravascular extension of Wilms tumor.

OBJECTIVE: To define the incidence and manifestations of and optimal therapy for children with intravascular extension of Wilms tumor. METHODS: Children on a collaborative study of Wilms tumor who had intravascular extension into the inferior vena cava (IVC) or atrium were identified. Surgical checklists and surgical and pathology reports were reviewed. RESULTS: One hundred sixty-five of 2,731 patients had intravascular extension of Wilms tumor. The level of extension was IVC in 134 and atrium in 31. Sixty-nine had received preoperative therapy (55 with IVC extension and 14 with atrial extension) for a median of 8 weeks. Complications during preoperative chemotherapy were seen in five patients (tumor embolism and tumor progression in one each, and three with adult respiratory distress syndrome, one of which was fatal). The intravascular extension of the tumor regressed in 39 of 49 children with comparable pre- and posttherapy radiographic studies, including 7 of 12 in whom the tumor regressed from an atrial location, thus obviating the need for cardiopulmonary bypass. Surgical complications occurred in 36.7% of the children in the atrial group and 17.2% in the IVC group. The frequency of surgical complications was 26% in the primary resection group versus 13.2% in children with preoperative therapy. When all the complications of therapy were considered, including those that occurred during the interval of preoperative chemotherapy (one of the five also had a surgical complication), the incidence of complications among those receiving preoperative therapy was not statistically different from the incidence among those who underwent primary resection. The difference in 3-year relapse-free survival (76.9% for 165 patients with intravascular extension, 80.3% for 1,622 patients with no extension) was not statistically significant whether or not it was adjusted for stage and histology. CONCLUSIONS: Preoperative treatment of these children may facilitate resection by decreasing the extent of the tumor thrombus, but the overall frequency of complications is similar in both groups.

Child↗