Detection of somatic variants in peripheral blood lymphocytes using a next generation sequencing multigene pan cancer panel

- Next generation sequencing detects germline and somatic variants.
- Pathogenic variants (PVs) evaluated in individuals undergoing 25-gene panel testing.
- Likely somatic PVs detected in 0.06% of individuals, mostly in TP53, CHEK2, and ATM.
- Likely somatic PVs accounted for 40% of PVs in TP53; <1% of PVs in most other genes.
- Likely somatic PVs more frequently identified in older individuals (p < 0.001).

Next Generation Sequencing (NGS) multigene panels, which are routinely used to assess hereditary cancer risk, can detect both inherited germline variants and somatic variants in cancer-risk genes. We evaluated the frequency and distribution of likely somatic Pathogenic and Likely Pathogenic variants (PVs) detected in >220,000 individuals who underwent clinical testing with a 25-gene panel between September 2013 and March 2016. Likely somatic PVs are defined as variants with NGS read frequencies from 10% to 30%. Overall, 137 (0.06%) individuals were identified as carrying likely somatic PVs, most commonly in TP53 (73), CHEK2 (27), and ATM (20). Among this group, a second PV with a NGS read frequency consistent with a germline variant within the same gene or a different gene on the panel was detected in 21 individuals (15.3%), which is similar to the detection rate in our general testing population. Likely somatic PVs accounted for 38.8% of all PVs in TP53. In comparison, likely somatic PVs accounted for <1% of PVs in most other genes. Likely somatic PVs were more frequently identified in older individuals (p < 0.001). Additional studies are ongoing to further investigate the incidence and clinical implications of somatic variants, enabling the appropriate medical management for these patients.