Hybrid capture-based genomic profiling of circulating tumor DNA from patients with estrogen receptor-positive metastatic breast cancer

Abstract Background Following the PALOMA-3 study results, the combination of palbociclib, a CDK4/6 inhibitor, with fulvestrant, a selective estrogen receptor degrader, has become a standard therapy in women with estrogen receptor-positive (ER+) HER2-negative (HER2−) metastatic breast cancer (MBC). Palbociclib has been shown to increase the progression-free survival (PFS) overall but no predictive biomarker of palbociclib efficacy has been validated so far. We thus evaluated whether early changes of circulating tumor DNA (ctDNA) levels are associated with palbociclib plus fulvestrant efficiency. Methods ER+ HER2− MBC patients were included in a prospective observational cohort before treatment initiation. Tumor response was assessed by radiological evaluation (RECIST v1.1) every 3 months. Plasma samples were collected before treatment (baseline), at day 15 (D15), at day 30 (D30), and at disease progression. We searched for somatic mutations from archived tumor tissues by targeted deep sequencing. For patients with somatic mutations identified, circulating tumor DNA (ctDNA) was tracked using digital droplet PCR. Ratios of ctDNA levels ([D15/baseline] and [D30/baseline]) were then correlated with prospectively registered patient characteristics and outcomes. Results Twenty-five of the 61 patients enrolled had a somatic mutation testable in plasma (NPIK3CA = 21, NTP53 = 2, NAKT1 = 2). At baseline, 84% of patients had detectable ctDNA levels but ctDNA levels had no prognostic impact on PFS (p = 0.10). Among those patients, ctDNA was still detected in 82% at D15 and 68% at D30. ctDNA clearance observed at day 30 was associated with longer PFS (HR = 7.2, 95% CI = 1.5–32.6, p = 0.004). On the contrary, a [D30/baseline] ctDNA ratio > 1 was associated with a shorter PFS (HR = 5.1, 95% CI = 1.4–18.3, p = 0.02) and all 5 patients with increased ctDNA levels at D30 showed disease progression after 3 months under palbociclib-fulvestrant. Finally, at the time of radiological tumor progression, ctDNA was detected in all patients tested. Conclusion Our study demonstrates that the efficiency of palbociclib and fulvestrant can be monitored by serial analyses of ctDNA before radiological evaluation and that early ctDNA variation is a prognostic factor of PFS.

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Hybrid capture-based genomic profiling of circulating tumor DNA from patients with metastatic breast cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.e12569 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. e12569-e12569

Author(s):

Xiaoxiang Guan ◽

Hong Zhu ◽

Wenzhuan Xie ◽

Jing Zhao ◽

Guoqiang Wang ◽

...

Keyword(s):

Breast Cancer ◽

Metastatic Breast Cancer ◽

Metastatic Breast ◽

Circulating Tumor Dna ◽

Internal Tissue ◽

Genomic Alterations ◽

Invasive Approach ◽

Hybrid Capture ◽

Female Patients ◽

Tumor Dna

e12569 Background: Breast cancer is the most common malignancy among women worldwide. It is particularly important to provide precise therapies based on genomic alterations, especially for metastatic breast cancers (MBC), which exhibit a high tumor heterogeneity and dynamic changes during the course of disease progression. However, genomic sampling upon metastatic tissue biopsy frequently encountered difficulties due to its inherent invasive approach such as insufficient samples and clinical risks. Our study aims to assess the genomic alternation landscape of metastatic breast cancer detected by blood-based circulating tumor DNA (ctDNA) and evaluate the assay performance. Methods: We performed hybrid capture-based next-generation sequencing (NGS) of 150 genes on ctDNA from 203 female patients with MBC. The mean sequencing depth was more than 3000×. The results were compared with our internal tissue genomic database (297 female patients with MBC) tested by NGS and TCGA database (N=982) tested by whole exome sequencing. Genomic alterations including single nucleotide variation (SNV), insertions/deletions, copy number variations, gene rearrangement and fusions were assessed. Results: Genomic data from 203 female patients with metastatic breast cancer were analyzed via ctDNA [median age 53 years (range, 46–61 years)]. Evidence of ctDNA as estimated by the maximum somatic allele frequency (MSAF) was detected in 95.6% of the patients (median=7.1 alterations/patient), and 97.0% of the patients had at least one characterized altered gene. The most frequently mutated genes identified for SNV occurred in TP53 (47.8%), PIK3CA (36.0%), and ESR1 (16.3%) upon ctDNA analysis and TP53 (73.2%), PIK3CA (38.4%), and ESR1 (4.0%) from our internal tissue database. However, in TCGA cohort, where most patients were presented with early stage diseases, the most mutated gene in terms of SNV was PIK3CA (32.5%), followed by TP53 (30.7%) and TTN (16.0%). The status of ERBB2 amplifications had a high concordance among ctDNA (14.8%), tissue (14.9%), and TCGA database (13.5%). The MSAF level was significantly higher for the fusion-present cases (P=0.048) or amplification cases (p<0.0001) than non-fusion or non-amplification cases. Conclusions: Our study has suggested that ctDNA profiling is a feasible approach for the molecular analysis in metastatic breast cancer and may better capture the mutational landscape of MBC for further clinical implications.

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Abstract P5-01-05: Genomic alterations detected by circulating tumor DNA and correlation with response to treatment with elacestrant, an oral selective estrogen receptor degrader, in phase 1 trials in postmenopausal women with ER+/HER2- advanced/metastatic breast cancer

10.1158/1538-7445.sabcs19-p5-01-05 ◽

2020 ◽

Author(s):

Teeru Bihani ◽

JungAh Jung ◽

Hitisha K Patel ◽

Aditya Bardia ◽

Peter Kabos ◽

...

Keyword(s):

Breast Cancer ◽

Estrogen Receptor ◽

Metastatic Breast Cancer ◽

Postmenopausal Women ◽

Phase 1 ◽

Metastatic Breast ◽

Circulating Tumor Dna ◽

Response To Treatment ◽

Genomic Alterations ◽

Tumor Dna

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305P Patterns of acquired mutations in estrogen receptor-positive metastatic breast cancer (MBC) patients identified by comprehensive genomic profiling (CGP)

Annals of Oncology ◽

10.1016/j.annonc.2020.08.407 ◽

2020 ◽

Vol 31 ◽

pp. S364

Author(s):

K. McGregor ◽

J.S. Ross ◽

N.A. Danziger ◽

E.S. Sokol ◽

J. Venstrom ◽

...

Keyword(s):

Breast Cancer ◽

Estrogen Receptor ◽

Metastatic Breast Cancer ◽

Metastatic Breast ◽

Genomic Profiling ◽

Estrogen Receptor Positive ◽

Comprehensive Genomic Profiling

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Abstract P3-05-02: Detection of activating estrogen receptor 1 (ESR1) in circulating tumor DNA (ctDNA) in hormone-receptor positive metastatic breast cancer (MBC)

10.1158/1538-7445.sabcs15-p3-05-02 ◽

2016 ◽

Author(s):

L Austin ◽

A Rodriguez ◽

R Jaslow ◽

P Fortina ◽

R Nagy ◽

...

Keyword(s):

Breast Cancer ◽

Estrogen Receptor ◽

Metastatic Breast Cancer ◽

Hormone Receptor ◽

Metastatic Breast ◽

Circulating Tumor Dna ◽

Hormone Receptor Positive ◽

Estrogen Receptor 1 ◽

Tumor Dna

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Early, On-Treatment Levels and Dynamic Changes of Genomic Instability in Circulating Tumor DNA Predict Response to Treatment and Outcome in Metastatic Breast Cancer Patients

Cancers ◽

10.3390/cancers13061331 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1331

Author(s):

Adriana Aguilar-Mahecha ◽

Josiane Lafleur ◽

Susie Brousse ◽

Olga Savichtcheva ◽

Kimberly A. Holden ◽

...

Keyword(s):

Breast Cancer ◽

Metastatic Breast Cancer ◽

Genomic Instability ◽

Metastatic Cancer ◽

Metastatic Breast ◽

Circulating Tumor Dna ◽

Response To Treatment ◽

Breast Cancer Patients ◽

T1 And T2 ◽

Tumor Dna

Background: Circulating tumor DNA (ctDNA) offers high sensitivity and specificity in metastatic cancer. However, many ctDNA assays rely on specific mutations in recurrent genes or require the sequencing of tumor tissue, difficult to do in a metastatic disease. The purpose of this study was to define the predictive and prognostic values of the whole-genome sequencing (WGS) of ctDNA in metastatic breast cancer (MBC). Methods: Plasma from 25 patients with MBC were taken at the baseline, prior to treatment (T0), one week (T1) and two weeks (T2) after treatment initiation and subjected to low-pass WGS. DNA copy number changes were used to calculate a Genomic Instability Number (GIN). A minimum predefined GIN value of 170 indicated detectable ctDNA. GIN values were correlated with the treatment response at three and six months by Response Evaluation Criteria in Solid Tumours assessed by imaging (RECIST) criteria and with overall survival (OS). Results: GIN values were detectable (>170) in 64% of patients at the baseline and were significantly prognostic (41 vs. 18 months OS for nondetectable vs. detectable GIN). Detectable GIN values at T1 and T2 were significantly associated with poor OS. Declines in GIN at T1 and T2 of > 50% compared to the baseline were associated with three-month response and, in the case of T1, with OS. On the other hand, a rise in GIN at T2 was associated with a poor response at three months. Conclusions: Very early measurements using WGS of cell-free DNA (cfDNA) from the plasma of MBC patients provided a tumor biopsy-free approach to ctDNA measurement that was both predictive of the early tumor response at three months and prognostic.

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