Neil Winegarden

CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome

An effective tool for the global analysis of both DNA methylation status and protein–chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regions. We have obtained 20 736 clones from a CGI Library and used these to construct CGI arrays. The utility of this library requires proper annotation and assessment of the clones, including CpG content, genomic origin and proximity to neighboring genes. Alignment of clone sequences to the human genome (UCSC hg17) identified 9595 distinct genomic loci; 64% were defined by a single clone while the remaining 36% were represented by multiple, redundant clones. Approximately 68% of the loci were located near a transcription start site. The distribution of these loci covered all 23 chromosomes, with 63% overlapping a bioinformatically identified CGI. The high representation of genomic CGI in this rich collection of clones supports the utilization of microarrays produced with this library for the study of global epigenetic mechanisms and protein–chromatin interactions. A browsable database is available on-line to facilitate exploration of the CGIs in this library and their association with annotated genes or promoter elements.

In vivo optical imaging of tumor and microvascular response to ionizing radiation.

Radiotherapy is a widely used cancer treatment. However, understanding how ionizing radiation affects tumor cells and their vasculature, particularly at cellular, subcellular, genetic, and protein levels, has been limited by an inability to visualize the response of these interdependent components within solid tumors over time and in vivo. Here we describe a new preclinical experimental platform combining intravital multimodal optical microscopy for cellular-level longitudinal imaging, a small animal x-ray microirradiator for reproducible spatially-localized millimeter-scale irradiations, and laser-capture microdissection of ex vivo tissues for transcriptomic profiling. Using this platform, we have developed new methods that exploit the power of optically-enabled microscopic imaging techniques to reveal the important role of the tumor microvasculature in radiation response of tumors. Furthermore, we demonstrate the potential of this preclinical platform to study quantitatively - with cellular and sub-cellular details - the spatio-temporal dynamics of the biological response of solid tumors to ionizing radiation in vivo.

Gene expression signatures prognostic for relapse in stage I testicular germ cell tumours

To identify differentially expressed genes between relapsed and non‐relapsed clinical stage I testicular germ cell tumours (TGCTs).

Toward the Realization of the Promise of Microarrays in Oncology

Microarrays have long been promised to be a tool that might one day revolutionize oncology research and drug development. Despite the tremendous potential, however, there have been few breakthroughs that can be directly attributed to microarray-based profiling. While many researchers now say that microarrays have been over-hyped, it is more likely that early experiments were simply conducted in a naive manner. Many believe that as technology and our understanding of experimental design improves, so too will the end results. We believe that with new approaches, particularly the use of pure cell populations potentially coupled with new and improved RNA amplification methodologies, the promise of microarrays for oncology finally will be realized.