Abstract P4-02-08: Global quantitative measures using next-generation sequencing for breast cancer presence outperform individual tumor markers in plasma
Authors: Beasley Ellen M , Abramson Richard D , Alexander Gregory E , Chan David , Bradley Kristen , Collin Francois , Crager Michael , Dei Rossi Andrew , Dorado Joseph , Friedman Adam , Gibb William J , Jeong Jennie , Jones Col , Ku C J , Ma Yan , Morlan John , Qu Kunbin , Rao Aibing , Scott Aaron , Tezcan Haluk 
Published: May 2015

Abstract
Background: Analytically and clinically validated non-invasive blood tests that quantify breast cancer burden and clinical drug response/resistance are greatly needed. Many groups have successfully detected tumor markers in blood using a variety of technologies, including next generation sequencing (NGS). We performed a comprehensive NGS study on a small number of patients to evaluate the value of global versus individual markers for the quantitation of tumor-derived cell free DNA (cfDNA) in plasma.
Methods: DNA isolated from formalin-fixed primary tumor, buffy coat cells, and plasma from 2 patients with metastatic breast cancer were characterized simultaneously for copy number aberrations (CNAs) and differentially methylated regions (DMRs) using whole genome bisulfite sequencing (WBGS), and targeted sequencing-based genotyping of 346 cancer-associated single nucleotide variations (SNVs). CNA and DMR regions were identified from log normalized, GC content corrected counts and DMR data using Poisson and binomial distribution theory and false discovery rate controlling methods. Percent tumor in cfDNA was estimated from the normalized ratio (plasma: primary tumor) of CNA or DMR compared to buffy coat, aggregating over genomic regions. Sample sets from 8 non-metastatic patients were also profiled using the targeted SNV panel in order to compare SNVs between samples and estimate percent tumor cfDNA.
Results: WGBS detected tumor specific alterations in each primary tumor compared to buffy coat. By analyzing the genome using 100 Kb bins, we observed over 1000 bins with detectable CNA signal and, among 56 million CpG sites, over 30,000 DMRs. As expected, 5 or fewer informative somatic SNVs were detected in each patient. Analysis of these somatic changes in plasma revealed that the tumor fraction estimated from SNV detected in cfDNA varied widely between sites originally discovered in the patient’s primary tumor. In contrast, similar estimates of tumor fraction in cfDNA were obtained using CNA and DMR profiles within each patient; both methods yielded similar estimates of over 50% in one patient and less than 10% in the other. For the patient with high tumor fraction, both CNA and DMR profiles contained examples of individual large genomic regions that displayed additional clear aberrations in the plasma compared to the original tumor, such as a striking loss of a &gt;25 Mb region of chromosome 4.
Conclusions: Although individual somatic SNV in cfDNA can be detected in metastatic disease, calculated allelic fraction based on individual SNVs varies greatly within the same patient. Measuring and integrating CNA or DMR across the genome provided more consistent and reliable estimates of tumor DNA fraction in plasma, and also revealed alterations in plasma from patients with metastatic disease that were not prominent in the primary tumor.
Citation Format: Ellen M Beasley, Richard D Abramson, Gregory E Alexander, David Chan, Kristen Bradley, Francois Collin, Michael Crager, Andrew Dei Rossi, Joseph Dorado, Adam Friedman, William J Gibb, Jennie Jeong, Col Jones, C J Ku, Yan Ma, John Morlan, Kunbin Qu, Aibing Rao, Aaron Scott, Haluk Tezcan. Global quantitative measures using next-generation sequencing for breast cancer presence outperform individual tumor markers in plasma [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-02-08.