Abstract P1-05-05: Comparison of genotyping results from tissue and circulating DNA (ctDNA) in patients with metastatic breast cancer
Authors: Malvarosa G , Spring L , Juric D , Moy B , Bardia A 
Published: May 2019

Introduction: Robust clinical genotyping assays are crucial to accelerate development of targeted therapies toward tumor-specific oncogene pathways. Indeed, there has been an explosion in the development of genotyping assays and stratified enrollment in clinical trials based on molecular characteristics of the tumor. However, availability of tissue can be a significant barrier for genotyping, particularly patients with estrogen receptor positive (ER+) breast cancer, who frequently have bone only metastasis. Detection of mutations in circulating tumor DNA (ctDNA) represents an attractive alternate strategy. However, there is a paucity of data comparing genotyping results from tissue and ctDNA, and potential clinical utility for patients with metastatic breast cancer.

Methods: Analysis of ctDNA was based on Guardant 360 panel (2015), a next-generation sequencing (NGS) based assay that covers point mutations in 70 genes (complete or critical exon coverage) with select amplifications, fusions, and indels, using NGS Illumina HiSeq platform, validated to detect alterations in samples with at least 2% ctDNA. Molecular profiling of tissue was based on the institutional lab-developed test “Snapshot-NGS assay”, utilizing a multiplex polymerase chain reaction (PCR) technology called Anchored Multiplex PCR (AMP) for single nucleotide variant (SNV) and insertion/deletion (indel) detection in genomic DNA targeting hotspots and exons in 39 genes using NGS Illumina MiSeq platform, validated to detect SNV and indel variants at 5% allelic frequency or higher in target regions.

Results: In the analytical dataset, a total of 42 patients with metastatic breast cancer (median age 62) at our institution had ctDNA and tissue Snapshot-NGS results available. Out of these, 95% had at least one genetic alteration detected in ctDNA, before start of a new therapy. The common genetic alterations in ER+ disease (n = 33) included PIK3CA (39.4%), ESR1 (27.3%), and AKT1 (15.2%); HER2+ disease (n = 2) included PIK3CA and CCND1; TNBC (n = 7) included TP53 (71.4%). Gene amplifications in FGFR, PIK3CA, CCND1, MYC, and KRAS were also noted. In general, the average number of molecular alterations was higher in ctDNA than the tissue specimen (mean = 5.1 vs 1.1; p &lt; .001). Of 34 patients with actionable alterations detected in ctDNA, 76.5% of these patients did not have actionable alterations detected in tissue. Of 29 patients with actionable alterations detected in tissue (primary or metastatic), 13.8% of these patients did not have any actionable alterations detected in ctDNA.

Conclusion: A significantly higher number of genomic alterations were detected in ctDNA compared to tissue, including actionable alterations linked to potential targeted therapies. Given these findings and the difficulties with tissue-based genotyping assays, blood based biomarker assays might provide an alternative and effective way to obtain a comprehensive molecular profile, and potentially guide management decisions for patients with metastatic breast cancer.

Citation Format: Malvarosa G, Spring L, Juric D, Moy B, Bardia A. Comparison of genotyping results from tissue and circulating DNA (ctDNA) in patients with metastatic breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-05.