More than 20,000 protein-coding genes have been identified in the human genome, with 300 to 600 of these genes associated with cancer. The cancer-associated genes can be either oncogenes or tumor-suppressor genes. Most oncogenes lead to active protein products that are unresponsive to normal regulatory signals. Tumor-suppressing genes generally result in slower cell division and function to repair DNA mistakes. They also activate cell death, which results in inactive protein products that cannot function properly. Substitutions, insertions, deletions of nucleotides, gains and losses of whole chromosomes, and gene fusions are common cancer-associated gene variant types. Identification of variants found in tumors is important in cancer diagnosis, treatment, prognosis, and disease management. If a tumor variant has an approved molecularly targeted therapy or if there is one under clinical investigation, then the patient may have improved clinical outcomes.
Next-generation sequencing (NGS) is an alternative to Sanger sequencing, which was the mainstay of tumor genetic testing. Sanger sequencing has a lower cost and faster turnaround time (TAT) than NGS, but NGS has a higher throughput, higher sensitivity, and greater variant resolution and can sequence millions of DNA fragments in a single reaction. The European Society for Medical Oncology recommends NGS be performed for patients with certain cancers, including patients with non–small-cell lung cancer (NSCLC) where it is useful for clinical management. Common identifiable cancer drivers in NSCLC included EGFR L858R and exon 19 deletions, which account for 15% of tumors; ALK fusions, which are found in 5% of NSCLC tumors; and MET exon14 skipping, which has a 3% prevalence in NSCLC. By identifying these actionable tumor variants, the best induction therapy can be chosen to improve overall survival. NGS can also be useful during treatment to identify resistant mutation emergence and for minimal residual disease assays to detect mutations over time or relapsing clones before clinical detection. Clinical NGS assays can either be broad or rapid.
Broad genomic profiling has a long TAT, ranging from 2 to 3 weeks, but it is more informative, whereas rapid NGS has a rapid TAT but may be more limited in the genomic region covered and may not detect complex genomic events. Broad genomic profiling is useful to help detect complex biomarkers, determine the likely etiology of tumor origin, identify the origin of carcinomas of unknown primary origin, and in research, to identify future biomarkers. Rapid genomic profiling is necessary in some clinical cases where treatment needs to be started as soon as possible. In adult patients with resectable NSCLC, the decision to treat with nivolumab in combination with platinum-doublet chemotherapy in the neoadjuvant setting requires a rapid test to detect multiple variants, because patients with EGFR or ALK variants are poor responders to PD-L1 inhibitors, and subsequent treatment with kinase inhibitors increases the risk for serious adverse events. Despite the usefulness of NGS, the cost, complexity, and specialized knowledge needed to implement routine NGS limit its routine use. Technologic advances are slowly overcoming these hurdles, which may make NGS routine clinical practice in the future.
Source: Poveda-Rogers C, Morrissette JJD. Greater expectations: meeting clinical needs through broad and rapid genomic testing. Clin Chem Lab Med. 2022 Dec 6. Published online ahead of print.