Policy Guidelines
Background
Advancements in technology and availability of sequencing, previously constrained by limitations of sequential single-gene testing on limited patient samples, have led to significant strides in our understanding of the genetic basis of inherited and somatic conditions. Variants detected by genetic testing include inherited germline variants and somatic mutations (Konnick & Pritchard, 2016).
Spontaneous mutations accumulate in somatic cells over a lifetime. While the majority of these mutations are inconsequential, others alter key cellular functions (Martincorena & Campbell, 2015). Genetic variations may be activating, resulting in a gain of function or loss of regulation of a protein, or inactivating, such as nonsense, splice-site, and frameshift insertion/deletion mutations, thereby causing a loss of function. They can range from single-nucleotide variants (SNVs) that cause a missense, silent, or nonsense amino acid substitution, or a splice site alteration affecting normal splicing of the mRNA transcript, to one or more nucleotides involved in duplications, deletions, insertions, or even a more complex pattern (Li et al., 2017). Also common is a change in copy number, as well as structural rearrangements, including chromosome translocations, deletions, duplication, or inversions (Li et al., 2017).
Early somatic mutations can cause developmental disorders, whereas the progressive accumulation of mutations throughout life can lead to cancer and contribute to aging (Martincorena & Campbell, 2015). Molecular profiles of tumors have been found to have clinical utility in guiding the clinical management of cancer patients, providing diagnostic or prognostic information, or identifying a potential treatment regimen or targeted therapy(Li et al., 2017). Increasingly, somatic mutations are being identified in diseases other than cancer, including neurodevelopmental diseases (Poduri, Evrony, Cai, & Walsh, 2013).
Applicable Federal Regulations
N/A
Guidelines and Recommendations
Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists
The Joint Commission recommended that somatic variants be categorized by and reported based on their impact on clinical care as follows(Li et al., 2017):
“Somatic variants include SNVs, indels, fusion genes resulting from genomic rearrangements, and CNVs. Unlike interpretation of germline sequence variations, which focuses on pathogenicity of a variant for a specific disease or disease causality, interpretation of somatic variants should be focused on their impact on clinical care. A variant can be considered a biomarker that affects clinical care if it predicts sensitivity, resistance, or toxicity to a specific therapy, alters the function of the gene, which can be targeted by approved or investigational drugs, serves as an inclusion criterion for clinical trials, influences disease prognosis, assists in establishing a diagnosis of a cancer, or warrants implementing surveillance measures for early cancer detection. Clinical impacts should, therefore, include therapeutic, prognostic, diagnostic, and preventive actions. The clinical impact of a given variant should be determined according to currently available evidence. Evidence used for variant categorization can be weighed differently based on its significance in clinical decision making. On the basis of literature review and Working Group consensus, we propose to group clinical and experimental evidence into four levels:
- Level A, biomarkers that predict response or resistance to US FDA-approved therapies for a specific type of tumor or have been included in professional guidelines as therapeutic, diagnostic, and/or prognostic biomarkers for specific types of tumors;
- Level B, biomarkers that predict response or resistance to a therapy based on well-powered studies with consensus from experts in the field, or have diagnostic and/or prognostic significance of certain diseases based on well-powered studies with expert consensus;
- Level C, biomarkers that predict response or resistance to therapies approved by FDA or professional societies for a different tumor type (ie, off-label use of a drug), serve as inclusion criteria for clinical trials, or have diagnostic and/or prognostic significance based on the results of multiple small studies;
- Level D, biomarkers that show plausible therapeutic significance based on preclinical studies, or may assist disease diagnosis and/or prognosis themselves or along with other biomarkers based on small studies or multiple case reports with no consensus.”
NCCN Guidelines
Multiple somatic mutations have been incorporated into the diagnostic workups recommended by the NCCN. Furthermore, the NCCN has several guidelines which recommend that gene expression profiling, or multiple gene testing may be helpful, more efficient and/or cost-effective for selected patients (NCCN, 2017). Please see “Related Policies”.