Table 10.1 Techniques to study lymphoma genetics.

Cytogenetic analysis

Southern blot analysis

Polymerase chain reaction (PCR) analysis

Fluorescent in situ hybridization (FISH)

Comparative genomic hybridization (CGH)

CGH microarray

Gene expression profiling

Proteomic profiling

As with all cancers, lymphomas were originally categorized primarily on morphology and clinical behavior. The use of antibodies against cell surface markers allowed the study of lymphoma specimens with antibody panels that could, along with morphological criteria, usually place a given lymphoma into a diagnostic category. Even within a given lymphoma category, however, there is considerable heterogeneity of clinical behavior. A prominent example is the category of diffuse large B-cell lymphomas, of which approximately 40% are cured with chemotherapy but 60% of patients die of disease, usually within a few years of diagnosis. In this case, as with many of the lymphomas, a prognostic index (the International Prognostic Index or IPI) based on a few pretreatment criteria is able to subdivide the category and provide very useful prognostic information. However, even within IPI classes, significant clinical heterogeneity persists. Furthermore, it is likely that the IPI defines subclasses of lymphomas according to biological differences among these lymphomas. Studies of genetic abnormalities are proving important tools for the improved classification and prognostication of diseases. In addition, a better understanding of the molecular patho-physiology of the disease will likely lead to improvements in treatment of lymphoma.

Techniques for studying genetic abnormalities in tumor specimens have undergone a revolution in the past 5-10 years (Table 10.1). Initial genetic analyses were based on the technique of chromosomal study by Giemsa-trypsin banding. In these studies, cells are grown in short-term culture, usually in the presence of mitogens. Colcemid treatment results in the accumulation of cells in metaphase, at which point the cells are fixed and dropped onto glass slides. The slides are treated with trypsin followed by Giemsa to give a banding pattern. An experienced cytogenetic technician can then identify normal chromosomes, translocations, numerical abnormalities, and sometimes more subtle deletions. The technique can identify only genetic changes large enough to disrupt a Giemsa-stained band.

More modern techniques are able to detect abnormalities with greater sensitivity. Southern hybridization starts with the electrophoretic separation of tumor DNA on a gel, followed by transfer to a membrane. This membrane is then probed with radioactively labeled polynucleotide probes specific for certain genes of interest. Changes in the expected size or intensity of the band of interest can indicate mutation, translocation, amplification, or deletion of the gene of interest.

Polymerase chain reaction (PCR) technology has allowed the detection of genetic abnormalities using only a small amount of tumor DNA. PCR for the detection of lymphoma cells is discussed in more detail in Chapter 6. Using primers designed to flank the genomic region of interest, repetitive cycles of annealing, DNA polymerization and thermal melting eventually yield a PCR product. The presence and size of this product may be analyzed by gel electrophoresis to determine

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