What are secondary findings from genetic testing?

Secondary findings are genetic test results that provide information about changes (variants) in a gene unrelated to the primary purpose for the testing.
When a clinician orders a genetic test  to discover the genetic cause of a particular condition, the test will often sequence one or a few genes that seem most likely to be associated with that individual’s set of signs and symptoms. However, if the individual’s signs and symptoms do not have an obvious genetic cause, a clinician might order a test that sequences all of the pieces of an individual's DNA that provide instructions for making proteins (called an exome) or a test that sequences all of an individual’s DNA building blocks (nucleotides), called a genome. 
Many more genetic changes can be identified with whole exome and whole genome sequencing than by sequencing just one or a few genes. Sometimes, testing finds a variant that is associated with a condition other than the one for which testing was originally indicated. This is called a secondary finding. Some individuals with a secondary finding may not yet have any of the symptoms associated with the condition, but may be at risk of developing it later in life. For example, a person with a variant in the BRCA1 gene, which is associated with an increased risk of breast and ovarian cancer, may not have developed cancer.
Other individuals with secondary findings may have a known medical condition, such as extremely high cholesterol, but receive results that indicate a genetic cause for that condition, such as a variant in the LDLR gene.
In 2013 (and again in 2017), the American College of Medical Genetics and Genomics (ACMG) recommended that all labs performing whole exome and whole genome sequencing tests include the reporting of secondary findings, in addition to any variants that are found related to the primary purpose of the testing. The ACMG proposed a list of 59 genes that are associated with a variety of conditions, from cancer to heart disease. The 59 genes for which secondary findings are reported were chosen because they are associated with conditions that have a definable set of clinical features, the possibility of early diagnosis, a reliable clinical genetic test, and effective intervention or treatment. The goal of reporting these secondary findings to an individual is to provide medical benefit by preventing or better managing health conditions. The variants that are reported are known to cause disease. Variants of unknown significance on page 25, whose involvement in disease at the current time is unclear, are not reported.
The information provided by secondary findings can be very important because it may help prevent a disease from occurring or guide the management of signs and symptoms if the disease develops or is already present. However, as with any type of medical diagnosis, the news of an unexpected potential health problem may lead to additional health costs and stress for individuals and their families. On the basis of secondary findings, additional testing to confirm results, ongoing screening tests, or preventive care may be advised. Individuals receiving whole exome or whole genome sequencing can choose to “opt out” of analysis of the 59 secondary finding genes and not receive variant results. As whole exome and whole genome sequencing become more common, it is important for individuals to understand what type of information they may learn and how it can impact their medical care.