Comparative analysis of <i>PIK3CA</i> mutation detection methods in the first-in-human phase 1/1b study of inavolisib.

Abstract

e13058 Background: Mutations (mut) in the alpha catalytic subunit of PI3K (p110α, PIK3CA gene) occur in ~35-40% of patients with HR+, HER2- metastatic breast cancer (mBC). Until the recent approvals of therapies targeting PI3K/AKT, PIK3CA mut screening was not included in breast cancer clinical biomarker testing guidelines, and cross-assay concordance studies are limited. Here, we compared PIK3CA mut detection among blood and tissue-based PCR and NGS assays used in the first-in-human phase I/Ib trial (NCT03006172) of the recently FDA-approved p110α-inhibitor, inavolisib. Methods: Biomarker eligibility required at least 1 of 17 oncogenic amino acid substitutions in PIK3CA , determined by blood- or tissue-based PCR or NGS testing performed locally at participating sites (184/190 [96.8%] patients) or by Sponsor central testing of tumor tissue with the cobas PIK3CA Mutation Test (cobas PCR) (6/190 [3.2%]). For concordance analyses, available archival or fresh tumor tissue was retrospectively sequenced with the cobas PCR test (n = 111) and/or FoundationOne (n = 155); available pre-study plasma-derived circulating tumor (ct)DNA was sequenced with the FoundationACT or FoundationOne Liquid CDx (n = 131) NGS assays at Foundation Medicine, Inc (FMI ctDNA). Overall concordance – agreement + disagreement for detection of a study-eligible PIK3CA mut between assays – is reported, unless noted otherwise. Results: PIK3CA mut status was confirmed by central cobas PCR for 97/111 (87.4%) local test enrolled patients: 71.4% (10/14) for blood-based tests; 90.2% (46/51) for tissue-based tests; 100% (20/20) for tissue-based PCR; 80.8% (21/26) for other tests. For 14 participants for whom the locally determined PIK3CA mut status was not centrally confirmed, the type of local test included NGS on tissue (5/14), NGS on blood (3/14), PCR on blood (1/14), and unspecified (5/14). PIK3CA mut detection concordance between cobas PCR and FoundationOne tissue testing was 96.2% (100/104). Concordance between cobas PCR and FMI ctDNA testing was 81.1% (77/95). Similarly, the concordance between FoundationOne and FMI ctDNA testing was 80.2% (85/106). Among 18 patients with discordant results between cobas PCR and FMI ctDNA, discrepancies were not attributed to a single assay, with 11 detected by cobas PCR but not FMI ctDNA, and 7 by FMI ctDNA but not cobas PCR. Conclusions: These results, albeit from a small study, demonstrate the ability of both tissue- and blood-based PCR and NGS assays to robustly identify a similar patient population with PIK3CA mut HR+, HER2- mBC, who may benefit from an inavolisib-based therapy regimen. Differences in PIK3CA mut detection concordance between tissue- vs. blood-based assays may reflect mutational profiling of a single-biopsied lesion vs. a multi-lesion representative blood sample, or insufficient ctDNA shedding; reflex testing on an alternative sample may prove useful in such cases.