This chapter details methods used for analysis of DNA copy-number changes in breast tumor tissues through the use of fluorescence in situ hybridization. The specific DNA probe described herein is the oncogene c-myc, although the tissue fluorescence in situ hybridization methodology p ...
This chapter discusses the complementary methodologies of fluorescence in situ hybridization and comparative genomic hybridization. Fluorescence in situ hybridization uses fluorescently labeled DNA probes (whole chromosomes, centromere, or locus-specific seque ...
The determination of the protein content of urokinase-type plasminogen activator (uPA) and its inhibitor, PAI-1, in breast cancer tissue extracts is used clinically to identify patients at risk to experience disease recurrence (metastasis) or early death. The serine protease uPA, in co ...
Proteomics has emerged as a powerful approach for studying disease-associated changes in protein levels. The most commonly used method in proteomics studies remains two-dimensional gel electrophoresis, but the methodology, standardization, and interpretation of the resul ...
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting to detect proteins and glycoproteins is one of the most widely used and broadly useful techniques in cancer research, allowing the proteins in a complex sample—such as a blood fsample, aspira ...
Lectins are naturally occurring, carbohydrate-binding molecules that can be isolated from diverse biological sources and used in the laboratory to investigate the presence of carbohydrate structures in or on cells, in much the same way as antibodies can be used to probe cells and tissues for ...
The outcome of breast cancer in an individual patient can be predicted by assessing a range of factors relating to the particular cancer. This assessment can be used to select treatments that are most likely to be successful, and to avoid futile or unnecessarily aggressive procedures. Histopa ...
Over the last few years, great advances in our understanding in tumor neovascularization have emerged, with several new mechanisms of neovascularization being proposed. Solid tumors establish a vasculature through angiogenesis, vasculogenesis, vascular remodeling, co-o ...
Apoptosis is a physiological process that occurs in cells during development and normal cellular processes. The useless, unwanted, or damaged cells die during the apoptotic process. However, if signals instructing cells to carry out apoptosis are lost, a variety of malignant disorders m ...
The estrogen receptor (ER) status and, to a lesser extent, progesterone receptor status have been recommended by recently published guidelines as important for routine prognostic and predictive evaluation of breast cancer. Although the clinical utility of ER status has been largely v ...
Nodal staging is the most important prognostic factor in the management of patients with breast cancer. Sentinel lymph node (SLN) procedure enables selective targeting of the first lumph node that drains the tumor when the initial metastases occur. A negative sentinel node predicts the ab ...
Sentinel lymph node biopsy is now a widely accepted method of axillary lymph node staging for invasive breast cancer. This review encompasses the historical perspective of surgical management of the axilla; the data that has emerged over the last decade highlighting the accuracy, safety, a ...
One of the major challenges in molecular analysis of breast cancer specimens is tissue heterogeneity. The admixture of contaminating bystander cells might distort the results of quantitative molecular analyses. Therefore, pure tumor cell populations have to be isolated in order to o ...
A method for producing high-molecular-weight DNA from pulverized tissue, nuclear fractions, or cultured cells. This isolation method relies on the powerful proteolytic activity of proteinase K combined with the denaturing ability of the ionic detergent sodium dodecyl sulfate. Et ...
The guanidinium acid-phenol method of RNA extraction is relatively fast (4 h) and is useful for the processing of large numbers of samples, without the need for ultracentrifugation. This protocol produces total RNA that includes ribosomal, transfer, and messenger RNA. This high-quality R ...
This chapter outlines methods for the preparation of several different cellular fractions from whole samples of tumor and normal tissue.
Tissue microarrays have been used effectively to study representative tissue from large groups of patients, with minimal technical and reagent costs. The construction of these arrays may appear complex, but with the use of a semiautomated tissue arrayer and a degree of manual dexterity, sy ...
Taking a series of repeat biopsies or fine needle aspirates of a tumor during the course of therapy can provide information about treatment-induced changes in tumor biomarkers and help monitor patient response to adjuvant therapy. It is hoped that analysis of biomarkers in serial biopsies w ...
This chapter describes some simple standard operating procedures for the regular collection of samples from surgical resections and their rapid preservation by freezing for long-term cryogenic storage.
A “tumor bank” provides a resource tool that can efficiently address the limitations of other tissue resources, such as clinical archives and research study collections. A tumor bank allows formal accreditation of ethics and security procedures, and through a dedicated management, pr ...

