Abstract P3-08-13: Exploring the role of ctDNA in triple negative breast cancer
Authors: den Brok WD , Kong E , Bates C , Aguirre-Hernandez R , Miller RR , Lum A , Wan A , Shah S , Aparicio S , Gelmon KA 
Published: May 2019

Abstract
BACKGROUND: Previously published work shows that triple negative (TNBC) is a heterogeneous disease with varying levels of genomic instability, where higher genomic instability is associated with poorer prognosis. Subgroups of TNBC patients with distinct patterns of genome aberrations may indicate pathologies in specific genome maintenance/repair processes. Circulating tumor DNA (ctDNA) as assessed by next generation sequencing (NGS) is a relatively non-invasive test that may provide prognostic and predictive information.
AIM OF STUDY: To analyze genomic alterations with serial plasma samples using NGS methods of ctDNA analysis and determine the utility for actionability and disease burden monitoring. We shall also determine whether TNBC subgroups differ in their ctDNA profiles. Shallow whole genome sequencing vs targeted capture at depth will be contrasted to determine sensitivity for relapse detection.
METHODS: Enrollment of a planned cohort of TNBC patients (N=300) with any stage, at diagnosis (dx) or within 2 years of dx, or at relapse of disease with ongoing plasma sampling every 3 -6 months. Patient age, stage, grade, type of chemotherapy, date of relapse and date of last followup are collected. Tumor tissue (FFPE), saliva for germline mutations and serial blood draws for ctDNA are analyzed with two NGS sequencing methods: (i) a high sensitivity small hotspot gene panel (33 genes, 170 hotspots), directed purely at actionable findings (ii) capture sequencing directed at multiple regions of the genome or shallow whole genome sequencing.
RESULTS: Preliminary analysis in 20 patient cases using the targeted hotspot panel. . Median followup 151 days. Two cases had plasma drawn at time of relapsed disease and 1 at the time of de novo metastatic disease; 12 had plasma samples drawn prior to neoadjuvant chemotherapy (clinical T1/T2N1, T3/T4Nany), and 5 had plasma draws after primary surgery (pathologic T1N0, T2N0). Of the neoadjuvant cases, 5 (42%) had a pathologic complete response (pCR); 4 with ctDNA mutations and 1 without. Six (58%) neoadjuvant cases did not achieve a pCR; 3 with ctDNA mutations, 3 without. One patient is awaiting surgery. Twelve (60%) cases had mutations in TP53, one case had 2 different TP53 mutations (no pCR) and one case had 3 mutations: TP53, PIK3CA, KRAS (achieved pCR). Of the cases treated with curative intent, with short followup (FU), there have been no relapses including the case of the sample containing 3 mutations.
CONCLUSION: TP53 mutations may be a marker of higher genomic alteration burden and may have prognostic value in patients with newly diagnosed, non-metastatic TNBC with longer FU. Ongoing analysis of serial plasma samples and FFPE analysis may provide further insight into the prognostic value of ctDNA. Full genome sequencing may be needed identify other mutations that have prognostic and/or predictive value. We have accrued over 200 patients with samples being analyzed and plan to present an interim analysis of the cohort at SABCS 2018.
Citation Format: den Brok WD, Kong E, Bates C, Aguirre-Hernandez R, Miller RR, Lum A, Wan A, Shah S, Aparicio S, Gelmon KA. Exploring the role of ctDNA in triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-08-13.