Detection of Tumor PIK3CA Status in Metastatic Breast Cancer Using Peripheral Blood

Abstract

Purpose We sought to evaluate the feasibility of detecting PIK3CA mutations in circulating tumor DNA (ctDNA) from plasma of patients with metastatic breast cancer using a novel technique called BEAMing. Experimental Design In a retrospective analysis, 49 tumor and temporally matched plasma samples from patients with breast cancer were screened for PIK3CA mutations by BEAMing. We then prospectively screened the ctDNA of 60 patients with metastatic breast cancer for PIK3CA mutations by BEAMing and compared the findings with results obtained by screening corresponding archival tumor tissue DNA using both sequencing and BEAMing. Results The overall frequency of PIK3CA mutations by BEAMing was similar in both patient cohorts (29% and 28.3%, respectively). In the retrospective cohort, the concordance of PIK3CA mutation status by BEAMing between formalin-fixed, paraffin-embedded (FFPE) samples and ctDNA from temporally matched plasma was 100% (34 of 34). In the prospective cohort, the concordance rate among 51 evaluable cases was 72.5% between BEAMing of ctDNA and sequencing of archival tumor tissue DNA. When the same archival tissue DNA was screened by both sequencing and BEAMing for PIK3CA mutations (n = 41 tissue samples), there was 100% concordance in the obtained results. Conclusions Analysis of plasma-derived ctDNA for the detection of PIK3CA mutations in patients with metastatic breast cancer is feasible. Our results suggest that PIK3CA mutational status can change upon disease recurrence, emphasizing the importance of reassessing PIK3CA status on contemporary (not archival) biospecimens. These results have implications for the development of predictive biomarkers of response to targeted therapies.

MultiplexKRASG12/G13 mutation testing of unamplified cell-free DNA from the plasma of patients with advanced cancers using droplet digital polymerase chain reaction

“…previously published studies despite the fact that we used a very low amount of cfDNA, which in most cases was isolated from much less than 0.5 ml of plasma [17][18][19][20][21]. Collectively, there is increasing evidence that the mutation analysis results for cfDNA are highly concordant with those for archival tumor tissue for concordantly, but not discordantly, collected samples, which may be explained by tumor biology, including heterogeneity and evolution over time [10,21].…”

“…A certain level of discordance can be anticipated if the tumor tissue and plasma are not obtained at the same time. Higgins et al [17] found 100% agreement between PIK3CA mutation testing of plasma cfDNA with BEAMing PCR and tumor tissue collected in a cohort of patients with advanced breast cancer and simultaneous collection. However, the concordance between the methods decreased to 79% in a cohort of patients whose tumor and plasma cfDNA samples were obtained at different times, which is consistent with Figure 2.…”

Analysing the Mutational Status of PIK3CA in Circulating Tumor Cells from Metastatic Breast Cancer Patients

“…In order to investigate PIK3CA mutations which concentrate within only few hot spots this is feasible, since up to 10 SNPs can be screened at once. As aforementioned the sensitivity of the SNaPshot methodology was reported to be approximately 5% (Hurst et al, 2009); an even higher detection rate (up to 0.01%) might be achieved by the recently published BEAMing technology (Beads, Emulsification, Amplification, and Magnetics; Higgins et al, 2012) which is also based on PCR amplification of hot spot regions. However, neither the SNaPshot nor the BEAMing technique allows for the discovery of unknown mutations.…”

Detection of the <i>PIK3CA</i> Mutation in Circulating Tumor DNA as a Possible Predictive Indicator for Poor Prognosis of Early-Stage Breast Cancer

“…On the other hand, mutated proteins observed in cancer, including H1047R, E545K and E542K, activate AKT signaling to oncogenic growth of cancer cells. Previous study has reported that PIK3CA mutations were detected in ctDNA from patients with metastatic breast cancer using digital PCR [8]. The levels of the mutated PIK3CA in ctDNA showed a larger dynamic range and more significant correlation with the tumor burden than other known tumor markers in metastatic breast cancer [9].…”