Clinical testing is currently available for more than 1500 different genes or genetic conditions (www.genetests.org
). The initial DNA-based tests introduced by clinically-certified genetic testing laboratories focused on identification of previously defined mutations in relatively rare genetic disorders. For example, molecular testing for cystic fibrosis and for multiple endocrine neoplasia type 2 (MEN2) was based on panels of known mutations in the CFTR
(MIM# 602421) and RET
(MIM# 164761) genes, respectively. Genetic tests based on sequencing of the entire coding region were not generally used clinically because of the expense involved in sequencing, the lack of sequence/polymorphism information, as well as the need to improve methodologies to efficiently interpret the sequence traces.
Full sequence analysis of the BRCA1
(MIM# 113705) and BRCA2
(MIM# 600185) genes was introduced in 1996 by Myriad Genetic Laboratories, as one of the first sequence-based tests offered to identify increased risk for an otherwise common cancer (Collins, 1996
). Sequence-based tests are now ubiquitous in genetic testing, due to advancement in high-throughput sequencing technologies and alternative approaches where mutation scanning methodologies are followed by sequencing of the targeted region. The vast majority of DNA sequence changes that result in an increased risk of developing cancer focus on identifying inactivating mutations that can occur throughout the length of the coding region of a tumor suppressor gene.
For sequence-based genetic tests, there are three possible results reported to physicians: (1) positive, in which a mutation that clearly disrupts gene function (and therefore is highly likely to cause clinical consequences) is detected, (2) negative, in which no variation in DNA sequence is detected, and (3) uncertain, in which a sequence “variant of uncertain/unclassified significance” (VUS) or “unclassified variant” (UV, UCV) is detected and it is not known whether the variant has any effect on gene function which might confer an increased cancer risk. One laboratory from the Netherlands reported that from one-third to one-half of the sequence changes reported for BRCA1
, respectively, were such variants (Gomez-Garcia et al., 2005
). Similarly, analysis of the Myriad Genetics Laboratory data revealed that a physician who orders BRCA1
testing has a similar likelihood of receiving a variant result (13%) as one with a pathogenic mutation (Frank et al., 2002
). The likelihood of an unclassified variant result is even higher for individuals from understudied populations who undergo genetic testing due to insufficient information on the common polymorphisms in that population (Kean-Cowdin et al., 2005
; John et al., 2007
). In addition, less well studied or newly identified disease-associated genes present greater challenges for interpretation of sequence-based results.
Appropriate use of genetic testing in daily clinical practice requires clear reporting by laboratories, well informed interpretation by clinicians and clear communication of the consequences to patients. A classification system for variants with recommendations for action coupled to each class would help facilitate this goal. Clinical interpretation of sequence variants is not limited to testing for cancer susceptibility. Genetic testing is used for a variety of purposes from risk prediction, carrier testing and reproductive decision making which may impact how variants are classified. In this paper we focus on genetic testing for autosomal dominant cancer susceptibility with the expectation that success with this clinical application may lead to further expansion to other venues of genetic testing.
The question of how to report out complex data for prediction of cancer association is not unique to genetic testing. There are several clinical classifications systems in oncology that have been generally perceived to be effective in conveying the likelihood of a test result being associated with disease. We briefly review some of these systems, as they serve as a template for our recommendations with regard to genetic testing for cancer susceptibility.