cfDNA-whole exome sequencing analysis tracks cancer evolution in early stage breast cancer - 11th International Symposium on Circulating Nucleic Acids in Plasma and Serum (CNAPS)

Hsin-Ta Wu ¹ Robert K. Hastings ⁵ Karen Page ⁴ Mustafa Balcioglu ¹ Anne Armstrong ⁵ Samreen Ahmed ⁶ Anna-Rita Boydell ³ Misha Agarwal ¹ Antony Tin ¹ Derrick Renner ¹ Scott Dashner ¹ Bradley James Toghill ⁴ Luke Martinson ⁴ Daniel Fernandez-Garcia ⁴ Kelly LT Gleason ³ Raheleh Salari ¹ Dave S. Guttery ⁴ Maggie Louie ² Himanshu Sethi ¹ Bernhard G. Zimmermann ¹ Raoul C. Coombes ³ Jacqueline A. Shaw ⁴

¹R&D, Natera, Inc., San Carlos, CA, USA
²Oncology, Natera, Inc., San Carlos, CA, USA
³Medical Oncology, Imperial College London,, London, UK
⁴Cancer Research Centre, The University of Leicester, Leicester, UK
⁵Medical Oncology, The Christie Foundation NHS Trust, Manchester, UK
⁶Medical Oncology, Leicester Royal Infirmary, Leicester, UK

Background: Whole-exome sequencing of plasma cell-free DNA (cfDNA-WES) is an emerging technology for investigating genomic mutational signatures and clonal evolution in patients with advanced cancers and patients with high circulating tumour DNA (ctDNA) burden. Here we demonstrate the use of cfDNA-WES for profiling pre-clinical metastasis in patients with primary breast cancer.

Methods: Forty-nine primary breast cancer patients were recruited following surgery and adjuvant therapy. Serial plasma samples were collected every six months for bespoke ctDNA analysis. In parallel, whole exome sequencing was performed on plasma cfDNA from all 17 relapsed patients before and around the time of clinical relapse. The concordance between variants identified in plasma and primary tumor tissue was used to track tumor evolution during disease progression.

Results: Preliminary analysis of cfDNA-WES for the first three relapsed patients showed variable concordance with primary tumor WES. Over 62% of somatic single nucleotide variants and short Indels detected from cfDNA-WES were not present in the paired primary tumor WES suggesting tumor evolution or heterogeneity. However, genomic copy number variants (CNVs) showed alignment between plasma and primary tumor suggesting these were early clonal events. The cfDNA WES showed close agreement with the 16-plex personalized assays for detection of ctDNA in the plasma samples. In particular, 26 out of 27 personalized variants were also identified by cfDNA-WES and showed highly concordant variant allele frequencies (VAF). The one variant that was not detected by cfDNA-WES was detected by the 16-plex assay at a 0.2% VAF.

Conclusions: Plasma cfDNA-WES captures mutational signatures in breast cancer patients. Moreover, analysis of cfDNA-WES provides evidence of tumor evolution, which may be important for treatment decision making.