Abstract 3138: Changes in tumor cell-free DNA copy number instability (CNI) predict therapeutic response in metastatic cancers
Authors: Weiss Glen J. , Beck Julia , Braun Donald P. , Bornemann-Kolatzki Kirsten , Barilla Heather , Cubello Rhiannon , Sangal Ashish , Whitehead Robert P. , Kundranda Madappa , Khemka Vivek , Urnovitz Howard B. , Schutz Ekkehard 
Published: July 2016

Abstract
Background: Tumor cell-free DNA (cfDNA) has the potential to provide minimally invasive patient specific biomarkers to monitor tumor burden. Gains and losses of chromosomal regions - as a hallmark of cancer - have been detected in plasma as copy number aberrations (CNAs), and for several cancers a relation to tumor size has been reported. Longitudinal observations during anti-cancer therapy have been mostly anecdotal. We measured CNAs changes during treatment by computing a genomic copy number instability index (CNI) of cfDNA to evaluate its potential to predict cytotoxic chemotherapy (chemo) response. Methods: 24 patients (pts) with advanced esophageal cancer (EC; n = 2), colorectal cancer (CRC; n = 3), non-Hodgkin lymphoma (NHL; n = 3), pancreatic ductal adenocarcinomas (PDAC; n = 4), and non-small cell lung cancer (NSCLC; n = 12) were included and assessable for response. DNA was extracted from pre-treatment plasma samples at baseline and sequentially for up to six cycles of chemotherapy. Copy-numbers were called from shotgun sequencing (Illumina) after mapping and quality filtering reads were counted in 5.5MBp windows (sliding) yielding a read coverage of 24,000-fold per bin. The read counts were transformed into log2 ratios and converted into a score based on Gaussian transformations. Concentration of total cfDNA was determined by digital PCR. Treatment response by imaging was recorded by RECIST 1.1 or EORTC PET/CT criteria. For pts with baseline CNI&gt;40 (representing the 99.99% level for non-cancer healthy controls), CNI change was considered predictive of response or stable disease when there was a reduction of CNI ≥50% relative to baseline. Disease progression was demonstrated when: 1) CNI was ≥50% over nadir and &lt;80% reduction relative to baseline; OR, 2) CNI was ≥5 fold the nadir; OR, 3) CNI demonstrated an absolute increase by 1,000 above baseline CNI. For pts with baseline CNI≤40, CNI change was considered predictive of response or stable disease when CNI remained ≤40, and PD when CNI≥2X above the baseline CNI. CNI was an early predictor of response if these results were observed by ∼3-8 weeks prior to imaging or a major change in pt's clinical status. Results: CNI was measured in 124 samples. Median baseline cfDNA was 7,238 cp/mL (range 2,319-91,978) and CNI was 171 (range 26-10,170). In general, NHL and tumors with high lymph node disease burden had highest baseline cfDNA and CNI, whereas overall the CNI was not correlated to the cfDNA content. 22 of 24 pts (91.7%) had CNI changes that were predictive of treatment response. For at least 15 pts, CNI change predicted response ∼3-8 weeks prior to scan results demonstrating response or PD. Conclusions: CNI change may serve as predictor (potentially early predictor) of therapeutic response to standard chemo for the investigated cancer types. Highest baseline cfDNA and CNI appear to be present in lymph node predominant disease, suggesting more readily shed DNA into the circulation.
Citation Format: Glen J. Weiss, Julia Beck, Donald P. Braun, Kirsten Bornemann-Kolatzki, Heather Barilla, Rhiannon Cubello, Ashish Sangal, Robert P. Whitehead, Madappa Kundranda, Vivek Khemka, Howard B. Urnovitz, Ekkehard Schutz. Changes in tumor cell-free DNA copy number instability (CNI) predict therapeutic response in metastatic cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3138.