By Kathleen Fergus, MS, CGC and Jill Simonsen

Reviewed By Beth Crawford, MS, CGC and Miriam Komaromy, MD

The Test

If doctors or genetic counselors determine that DNA sequencing is appropriate for a given family, they will begin the process with a family member who has already been diagnosed with breast or ovarian cancer. (This person is most likely to have the altered gene causing the family's inherited cancer risk.) That person, called an affected family member, will provide a blood sample so that a testing lab can obtain DNA from their white blood cells. Scientists will then sequence that person's BRCA1 and BRCA2 genes and compare that sequence to the known normal sequence to determine whether there has been a mutation. If DNA sequencing reveals such a mutation, the genetic basis for a family's cancer has been found.

Interpreting the Results

The results of DNA testing are not always easy to interpret. In some cases, the test does reveal a known mutation, but in other cases it produces results that require additional tests in other family members in order to be useful. A DNA test can also miss a mutation, or find a mutation that is not actually present. However, DNA sequencing is usually quite reliable in detecting mutations: One study found that DNA sequencing found a mutation 98 percent of the time when it was there, and falsely "found" a mutation less than 1 percent of the time when one was not really present. It is important to remember that even if a DNA test fails to identify an unambiguous mutation, it does not mean that a family is not at risk for breast or ovarian cancer. It just means that the cause of that family's cancer risk has not yet been found. Results from DNA sequencing include:

Positive Result

If DNA sequencing turns up what researchers term a "known deleterious change," then the genetic culprit for a family's inherited cancer has been found, and other family members can be tested for the same mutation. Other family members can then be testing for this mutation.

	More on Screening for Women With a High Risk of Breast and Ovarian Cancer

Ambiguous Result

Sometimes DNA sequencing turns up a mutation in an individual's BRCA1 or BRCA2 gene that scientists don't know how to interpret. These types of mutations typically don't shorten the BRCA1 or BRCA2 proteins. However, they do occur in regions that could be important for the protein to function properly. Scientists refer to such mutations as variants of unknown significance, or ambiguous results. The bottom line is that although a mutation has been found, it is unknown whether it's responsible for a family's breast and/or ovarian cancers.

Testing additional family members may or may not clarify the results of an ambiguous test. For example, if other family members with cancer also have the mutation, this suggests that maybe the cancer is related to the change. And, if disease-free members of the family do not have the genetic change, this further confirms that mutation's importance. However, there are also some known alterations in BRCA1 and BRCA2 that are present in more than two percent of the population that are not associated with family histories of breast and ovarian cancer. Thus, having a mutation doesn't mean that the mutation necessarily causes breast or ovarian cancer.

Negative Result

There are two types of negative results, neither of which mean that a person is free of breast and ovarian cancer risk, since the pattern of disease in such families is usually too strong to ignore.

• One kind of negative test result is when DNA sequencing detects an alteration that doesn't appear to increase a person's chances of developing breast or ovarian cancer. Such mutations typically do not shorten the BRCA1 or BRCA2 gene's protein, and they tend to occur in regions of the gene that are not thought to be important to protein function. Scientists consider this a negative result because even though a genetic change has been found, it is a change that is seen in families without breast or ovarian cancer as well, and is not believe to be associated with the disease.
• The other kind of negative test result is when DNA sequencing fails to turn up any alterations in the BRCA1 and BRCA2 genes. This still leaves the possibility that there is a change in BRCA1 or BRCA2 but it is not detectable by fully sequencing the gene. It is also possible that another — so far unidentified — gene explains the cancer history in that particular family.

	Undetectable Changes in BRCA1 and BRCA2
	DNA sequencing can fail to detect very large deletions or duplications, some of which have been found in specific populations. One mutation involves a large segment of DNA that is missing in some people of Dutch descent. Another mutation occurs in people of English descent, who carry an entire extra copy of the gene, or extra region of the gene. However, because this duplication has the correct sequence, the DNA sequencing test does not detect any alteration. These types of alterations account for a small percentage of breast and ovarian cancer in families.

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Advantages and Limitations of Sequencing

DNA sequencing can provide important information for families with a high risk for breast and ovarian cancer. If the test does reveal a mutation, then other family members can be tested for the same mutation — a much less costly and time-consuming procedure than sequencing the full BRCA1 and BRCA2 gene. Testing for just this one mutation also produces a much less ambiguous result. Either the mutation is there, or it isn't. In addition, if a family member tests negative for that mutation, this person will know that he or she has not inherited the family's predisposition to cancer and can follow less stringent screening and prevention guidelines.

More on Genetic Testing When the Mutation in the Family is Known

The disadvantage to DNA sequencing is that in addition to providing possibly ambiguous results, DNA sequencing misses some mutations that can occur in the BRCA1 and BRCA2 genes. For this reason, even negative test results are not as straightforward as they sound: If no alteration is detected in a high-risk individual, scientists don't know whether this is because the person truly doesn't have a mutation or because a mutation exists in a region the test doesn't examine. Either way, the negative test result may give a person a false sense of security when, in fact, they are still at very high risk.

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References

Ford, D. et al. (1998). Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am J Hum Genet 62(3): 676-89.

Ganguly, A. et al. (1997). Genetic testing for breast cancer susceptibility: frequency of BRCA1 and BRCA2 mutations. Genet Test 1(2): 85-90.

Geller, G. et al. (1997). Genetic testing for susceptibility to adult-onset cancer. The process and content of informed consent. JAMA 277(18): 1467-74.

Shattuck-Eidens, D. et al. (1997). BRCA1 sequence analysis in women at high risk for susceptibility mutations. Risk factor analysis and implications for genetic testing. JAMA 278(15): 1242-50.

Stoppa-Lyonnet, D. et al. (1999). Genetic testing for breast cancer predisposition in 1999: which molecular strategy and which family criteria? Dis Markers 15(1-3): 67-8.