Background: Locally advanced breast cancer (BC) is currently treated with neoadjuvant chemotherapy (NACT) followed by surgery. NACT is able to achieve about a 20% rate of pathological complete response (pCR), defined as the absence of invasive cancer in breast and in axillary nodes. To date the pre-surgical assessment of clinical complete response (cCR) is mostly based, even though with suboptimal accuracy, on magnetic resonance imaging (MRI). Knowledge of cCR is useful to guide the surgical management of post-NACT BC. The study of plasma cell-free DNA integrity (DI) has shown serious potential for providing useful information in neoplastic patients in regard to early diagnosis, recurrence, and response to therapy. The aim of the present study is to estimate the accuracy of an electrophoresis-based method for DI assessment in the evaluation of the response to the systemic treatment in BC patients undergoing NACT. Methods: 62 BC patients undergoing anthracycline/taxane based NACT followed by surgery were recruited. Plasma samples were collected from each patient at diagnosis (T0), after anthracycline administration (T1), and after NACT completion before surgery (T2). After cfDNA extraction, cfDNA fragmentation profiling (DFP) was performed for each sample by automated electrophoresis on an Agilent Tapestation 2200 device. The concentration of differently sized cfDNA fragments, respectively of 90-150 base pairs (bp), 150-220 bp, 221-320 bp, 100-300 bp, and 321-1000 bp was assessed. cfDNA fragments size ranges evaluated as the most informative of the response to NACT were finally selected to calculate a normalized measure of DI, namely cfDNA integrity index (DII), expressed as the ratio of 321-1000 bp sized fragments concentration to 150-220 bp sized fragments one. DII was finally used to build an explorative classifier for BC response to NACT, directly comparing its performance with MRI, via bootstrapped logistic regression. Results: After preliminary essays to identify the most promising time point, DFP was performed on 38 plasma samples collected from as many patients at T2, with a 70/30 ratio between pCR and non pCR patients. DII showed an overall accuracy in correctly predicting the achievement of pCR of 81.6, with a cutoff above 2.71 having sensitivity = 81.8 and specificity = 81.5. MRI overall accuracy in the same cohort amounted to 77.1, with a sensitivity and a specificity of 72.7 and 81.5 respectively. The performance of the two techniques combined, in case of concordance, achieved an overall accuracy of 92.6 with a predictive value of complete response of 87.5 and a predictive value of absence of complete response of 94.7. Conclusions: DII measured before surgery after NACT completion shows great potential to correctly predict the achievement of pCR in BC patients. The evaluation of its use in combination with MRI is warranted in prospective studies.

Citation Format: Gabriella Cirmena, Lorenzo Ferrando, Francesco Ravera, Anna Garuti, Valentina Barbero, Fabio Ferrando, Piero Fregatti, Lucia Del Mastro, Alessandro Garlaschi, Daniele Friedman, Alberto Ballestrero, Gabriele Zoppoli. Plasma cell-free DNA integrity predicts the achievement of pathological complete response to neoadjuvant chemotherapy in breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB063.