Genetic Testing of the Tumor Genome

Personalized cancer care begins with genetic testing of the tumor genome followed by identification of prognostic markers and therapeutic targets. Molecular testing can be performed at any time during the disease course, but is most helpful at the time of diagnosis so that information about the tumor genome can be incorporated into therapy decisions such as surgery, chemotherapy, and radiation. Prediction of disease course can often be made at the time of diagnosis and is particularly useful for forms of cancer such as chronic lymphocytic leukemia (CLL) and prostate cancer, which are often treated using a “watch and wait” approach. 

What is tested by genetic methods?

In some genetic tests, tumor cells are opened to retrieve the nucleic acids DNA and RNA, while other tests examine proteins encoded by nucleic acids in blood and/or tissue. Approximately 3 billion base pairs of DNA, 30,000 genes and 500,000 proteins characterize the normal human genome. In cancer, many of these normal genome features are disrupted and reorganized by the tumor into a malignant clone (or clones) of cells which escape normal control and regulation mechanisms. This process can occur in any cell, organ, or tissue of the body, and the aggressiveness of the tumor will depend in large part on the extent that the tumor genome differs from the normal genome. In order to get a “good look” at the tumor, the pathologist will use microscopic or laboratory methods to ensure that tissue containing the tumor genome (and not normal tissue) is sent for molecular testing.
However, in some cases molecular testing of the patient’s normal genome is performed to look for information about how the patient may or may not respond to chemotherapy. This is called pharmacogenomics and examples are genetic testing of patients for mutations of genes that help determine how well patients will be able to metabolize or process medications such as CYP2D6, CYP450, TPMT, and UGT1A1.  If a patient is found to have a mutation that prevents a drug from being toxic or ineffective, then a different drug can be chosen prior to starting treatment increasing the chances of treatment response and decreasing the chances of deleterious side effects.

What kinds of molecular tests are used for tumor genome testing?

Many of the methods currently used for clinical laboratory testing of tumor genomes were developed during the Human Genome Sequencing project. The method chosen for a particular case will often depend on the type of tumor and the clinical question being asked. The most commonly used techniques are listed below:

Fluorescent in situ hybridization (FISH): used to investigate whether a specific gene is lost, normal, or amplified in the tumor. Examples are amplifications of the HER2 gene in breast , ovarian and other cancers and loss of the TP53 tumor suppressor gene in CLL, multiple myeloma and other solid tumors.

Polymerase chain reaction (PCR): used to find deletions and amplifications of single genes as well as detect fusions where one gene attaches to another and forms and aberrant protein. An example is the BCR/ABL fusion gene in chronic myelogenous leukemia (CML).

Array comparative genomic hybridization (array CGH): used to obtain genome-scale information about the tumor as well as identify gains and losses of specific genes. Examples are array CGH analysis of breast cancer for subtyping and HER2 gene status, and scanning of the CLL genome to identify prognostic markers.

References:

Utilizing the molecular gateway: the path to personalized cancer management. Clinical Chemistry 2009;55:684-697

Discussion or the applicability of microarrays: profiling of leukemias. Methods in Molecular Biology 2009;509:15-33

Genomic strategies for personalized cancer therapy. Human Molecular Genetics. 2007;16:226-232