[Variant Allele Frequency Stratification and EGFR Co-mutation Characteristics 
in AKT1 E17K-mutant Non-small Cell...

AKT serine/threonine kinase 1 (AKT1) E17K, the most common activating mutation of AKT1, is an established druggable driver in breast cancer; however, it is exceedingly rare in non-small cell lung cancer (NSCLC), with its clinical significance remaining unclear. Variant allele frequency (VAF) may partially reflect the clonal proportion of a mutation, offering clues to the clonal characteristics of such rare mutations. This study investigated the relationship between AKT1 E17K VAF and co-mutation with classic driver genes such as epidermal growth factor receptor (EGFR) in NSCLC, aiming to explore the potential role of this mutation in tumor clonal evolution.

Next-generation sequencing (NGS) data of lung cancer patients at Beijing Chest Hospital, Capital Medical University from June 2019 to April 2026 were retrospectively analyzed. After deduplication of 13,003 tests, 11,368 unique patients (including small cell lung cancer) were identified, among whom 35 harbored AKT1 E17K mutations (overall detection rate 0.31%), all being NSCLC; 5 external consultation cases were excluded, leaving 30 cases for analysis. Continuous VAF analysis was designated as the primary analysis, with an exploratory cutoff of 10%.

Of the 30 patients, 20 (66.7%) were adenocarcinoma. Median follow-up was 12 months (range: 1-55 months). The EGFR co-mutation rate was lower in the high-VAF group (≥10%, n=17) than in the low-VAF group (<10%, n=13; 11.8% vs 46.2%), reaching nominal significance before correction [P=0.049, odds ratio (OR)=0.156] but not after Bonferroni adjustment (adjusted P=0.246). The median VAF was lower in the EGFR co-mutated group than in the EGFR wild-type group (1.37% vs 13.73%, P=0.071). Continuous analysis showed a negative trend between VAF and EGFR co-mutation (ρ=-0.340, P=0.066). After adjusting for histological type using Firth-corrected Logistic regression, the direction of the association remained unchanged but was no longer nominally significant (OR=0.21, 95%CI: 0.03-1.33, P=0.097).

AKT1 E17K VAF showed a negative trend with EGFR co-mutation; however, the association did not remain significant after correction for multiple comparisons or adjustment for histological type, and may be partly influenced by histological composition. These findings should be regarded as hypothesis-generating and require validation in larger multi-center cohorts.