Minimally interventional study on prevalence of emerging ESR1 mutations in liquid biopsy in three cohorts of patients with breast cancer (with and without prior therapies in metastatic setting, and during first-line aromatase inhibitor plus CDK4/6 inhibitor therapy) in comparison with patient's baseline ESR1 mutation status as defined by tissue profiling.
This is a prospective minimally interventional biomarker cohort study. Biomarkers: 1. GS Focus Liquid Breast (liquid biopsy sequencing test, covering mutations in ESR1, PIK3CA, AKT1, PTEN, ERBB2, BRCA1, BRCA2, PALB2); 2. GS Focus Breast (tissue sequencing assay performed on basal tissue biopsy from the primary tumour or metastatic lesion not exposed to any systemic therapy, covering the same gene panel); 3. ESR1 mutation by πCode (PlexBioTM), which covers hotspot variants (K303R, E380Q, S463P, P535H, L536P, L536H, L536Q, L536R, Y537S, Y537N, Y537C and D538G), with analytical sensitivity ranging from 0.1% to 0.5%, depending on the variant; 4. PTEN analysis by IHC (VENTANA SP218). Biomarker assessment will be carried out by NGS methodology in both liquid biopsy and baseline tissue biopsy. Both strategies consider a custom panel covering PIK3CA, AKT1, PTEN, ESR1, BRCA1, BRCA2, PALB2, ERBB2 genes. NGS panels were internally validated and presented sensitivity, specificity and accuracy of 100,00% with a limit of detection of 0,5% VAF for liquid biopsy panel and sensitivity, specificity and accuracy of 100,00% with a limit of detection of 5% VAF for tissue panel. Cohort 3 will be recruited in two phases. The pilot phase will include 30 patients to assess the complexity of recruitment, sample logistics and laboratory operations using the new πCode liquid biopsy assay. If approved by the investigators and the sponsor, recruitment will continue with a further 70 patients for full-scale implementation. For the detection of ESR1 mutations in Cohort 3, πCode microdisc technology (PlexBio™) will be used with the IntelliPlex™ ESR1 Mutation cfDNA Kit. This assay covers hotspot mutations in ESR1 in exons 4, 5, 7 and 8 (12 variants), with a DNA input of 10 ng and a detection limit ranging from 0.1% to 0.5%. In Cohort 3, an initial liquid biopsy NGS assay (GS Focus Liquid) will be collected 6 months after the start of treatment, followed by ctDNA analyses using GS Focus Liquid and the πCode assay every 3 months for each patient, provided there is no evidence of clinical/radiological progression or the emergence of an ESR1 mutation. In parallel, if archived paraffin blocks are available, tissue NGS (GS Focus) and PTEN IHC (see below) will be performed to assess alterations present in primary tissue or metastatic lesions prior to exposure to AI plus CDK4/6i. PTEN IHC will be analyzed in samples from prospective cohorts 1, 2, and 3 with valid NGS results from tissue and residual paraffin blocks. For PTEN staining by IHC, the VENTANA SP218 antibody will be used, which binds to the PTEN protein in FFPE sample sections (OptiView DAB IHC detection kit) run on the Roche-Ventana Benchmark Ultra platform, according to the manufacturer's instructions.
Study Type
OBSERVATIONAL
Enrollment
170
Ensino E Terapia de Inovação Clínica Amo - Ética
Salvador, Estado de Bahia, Brazil
NOT_YET_RECRUITINGIrmandade Da Santa Casa de Misericórdia de Porto Alegre
Porto Alegre, Rio Grande do Sul, Brazil
NOT_YET_RECRUITINGFundação Antonio Prudente - A.C. Camargo Cancer Center
São Paulo, Brazil
NOT_YET_RECRUITINGInstituto D'Or de Pesquisa E Ensino - São Paulo
São Paulo, Brazil
NOT_YET_RECRUITINGResearch Site
São Paulo, Brazil
RECRUITINGSociedade Beneficente Israelita Brasileira Hospital Albert Eisntein
São Paulo, Brazil
NOT_YET_RECRUITINGPrevalence of emerging ESR1 mutations
Primary objective A (Cohorts 1 and 2): to determine the prevalence of emerging ESR1 mutations in liquid biopsy samples from two cohorts of breast cancer patients (with and without prior treatment in the metastatic setting) and to compare this with the baseline ESR1 mutation status as determined by the patient's tissue profile. Primary objective B (Cohort 3): to determine the overall prevalence of emerging ESR1 mutations during first-line treatment with AI plus CDK4/6i in patients without clinical or radiological evidence of progressive disease, using a highly sensitive ctDNA assay.
Time frame: Through study completation, an avarege 2 years
Define the prevalence of PIK3CA, AKT1, PTEN, BRCA1, BRCA2, PALB2, ERBB2 mutations.
To determine the prevalence of mutations in PIK3CA, AKT1, PTEN, BRCA1, BRCA2, PALB2 and ERBB2 in liquid biopsy samples and compare these with the patient's baseline status. To determine the prevalence of ESR1 mutations at different time points during treatment with AI plus CDK4/6i; to validate a highly sensitive and specific ctDNA assay for common ESR1 variants using πCode technology (PlexBioTM).
Time frame: Through study completation, an avarege 2 years
AstraZeneca Clinical Study Information Center
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