Retrospective comparison between breast cancer tissue- and blood-based next-generation sequencing results in detection of PIK3CA, AKT1, and PTEN alterations

Abstract

Background: Based on the CAPItello-291 phase III trial results, capivasertib in combination with fulvestrant has been approved for patients with hormone receptor-positive/human epidermal growth factor receptor 2-negative advanced breast cancer harboring one or more PIK3CA, AKT1, and/or PTEN alterations. Given the growing interest in circulating tumor DNA (ctDNA) next-generation sequencing (NGS) to detect PIK3CA/AKT1/PTEN alterations, we retrospectively compared blood-based FoundationOne®Liquid CDx versus tumor tissue-based FoundationOne®CDx real-world data from patients with various breast cancer subtypes.

Methods: We utilized a database of patients profiled with FoundationOne®CDx and/or FoundationOne®Liquid CDx during routine clinical care. Analytical comparison of all pathogenic alterations in PIK3CA, AKT1, AKT2, AKT3, and PTEN, including alterations defined in the CAPItello-291 protocol (CAPItello-defined alterations), was performed in paired data from 289 patients with both tissue and liquid biopsies sampled within 90 days of each other.

Results: Overall positive percent agreement (PPA) for short variants across ctDNA tumor fraction (TF) subgroups in paired biopsy samples was: ctDNA TF ≥ 10%: PIK3CA, 93.9%; AKT1, 100%; PTEN, 100%; ctDNA TF 1%-10%: PIK3CA, 96.3%; AKT1, 100%; PTEN, 100%; ctDNA TF < 1%: PIK3CA, 34.7%; AKT1, 50.0%; PTEN, 37.5%. PPA for CAPItello-defined alterations was: ctDNA TF ≥ 10%: 92.5%; ctDNA TF 1%-10%: 97.1%; ctDNA TF < 1%: 33.9%. For PTEN homozygous deletions, PPA was 50.0% in cases with ctDNA TF ≥ 10%. Overall PPA for AKT2 and AKT3 copy number variations (CNVs) was 66.7% and 0%, respectively.

Conclusions: Blood-based NGS could offer a minimally invasive option to identify clinically relevant PIK3CA/AKT1/PTEN short variants in cases with ctDNA TF ≥ 1%. Confirmatory tissue-based NGS should be performed when blood-based NGS results are negative, especially when ctDNA TF is < 1% and for enhanced detection of CNVs in general.

Keywords: AKT inhibitor; Breast cancer; Capivasertib; Circulating tumor DNA; HR-positive/HER2-negative; Next-generation sequencing; Targeted therapy.

Fig. 1

Prevalence of (A) all pathogenic alterations and (B) pathogenic SVs in the tissue and liquid biopsy cohorts, and number of alterations (SVs, CNVs, and rearrangements) detected in (C) the tissue biopsy cohort and (D) the liquid biopsy cohort. **P < .01; ***P < .001. Please note that information on hormone receptor and human epidermal growth factor receptor 2 status (including hormone receptor-positive and triple-negative breast cancers) was not routinely available. (A, B) N = total number of samples; (C, D) N = total number of detected alterations per gene. AKT1, Akt serine/threonine kinase 1; AKT2, Akt serine/threonine kinase 2; AKT3, Akt serine/threonine kinase 3; CNV, copy number variant; PIK3CA, phosphatidylinositol-3-kinase catalytic subunit alpha; PTEN, phosphatase and tensin homolog; SV, short variant

Fig. 2

Positive predictive agreement in detection of pathogenic alterations between tissue and liquid biopsies according to (A) ctDNA TF and (B) collection intervals between paired biopsies. Please note that information on hormone receptor and human epidermal growth factor receptor 2 status (including hormone receptor-positive and triple-negative breast cancers) was not routinely available. Additionally, one sample may be counted in more than one category, e.g. both in ‘shared positive’ and ‘tissue-only positive’ for different alterations detected within this sample. Therefore, the total N shown here may exceed the number of samples (n = 289). PPA = shared positive / (shared positive + tissue-only positive). AKT1, Akt serine/threonine kinase 1; CNV, copy number variant; ctDNA, circulating tumor DNA; NA, not applicable; PIK3CA, phosphatidylinositol-3-kinase catalytic subunit alpha; PPA, positive percent agreement; PTEN, phosphatase and tensin homolog; SV, short variant; TF, tumor fraction

Fig. 3

Co-occurring alterations in liquid biopsies. A Prevalence of co-occurring alterations in other clinically relevant genes. Prevalence is presented for pathogenic alterations in PIK3CA, AKT1, and PTEN, and in genes for which the prevalence of mutations was ≥ 5% in the cohort with CAPItello-defined alterations. Mutations in DNMT3A, TET2, and ASXL1 are not presented, as they are likely associated with clonal hematopoiesis. B Breakdown of ESR1 alterations in samples with CAPItello-defined alterations, and any pathogenic alterations in PIK3CA, AKT1, and PTEN. Prevalence is presented for alterations detected in ≥ 5 samples in the cohort with CAPItello-defined alterations and for individual grouped driver mutations irrespective of positive sample count. C Prevalance of co-occurring CAPItello-defined alterations in liquid biopsies with ESR1 alterations. Please note that information on hormone receptor and human epidermal growth factor receptor 2 status (including hormone receptor-positive and triple-negative breast cancers) was not routinely available. ^aGrouped driver mutations include the following: E380Q, S463P, P535H, L536R, L536Q, L536H, L536P, Y537S, Y537N, Y537C, and D538G. AKT1, Akt serine/threonine kinase 1; CNV, copy number variant; ESR1, estrogen receptor 1; NA, not applicable; PIK3CA, phosphatidylinositol-3-kinase catalytic subunit alpha; PTEN, phosphatase and tensin homolog; SV, short variant