Abstract 43: Predictive biomarkers of recurrence may not be useful for deescalating treatment of breast ductal carcinoma in situ due to de novo ipsilateral breast carcinoma development
Authors: Kader Tanjina , Mahale Sakshi , Zethoven Magnus , Saunders Hugo , Lesche Dorothea , Byrne David , Lai Siqi , Tjoeka Lauren , Candido Claire , Pechlevanis Maree , Craig Olivia , Pang Jia-Min , Devereux Lisa , Hendry Shona , House Eloise , Jayasinghe Sureshni , Toss Michael , Miligy Islam M. , Rakha Emad , Fox Stephen , Mann Bruce , Campbell Ian , Gorringe Kylie 
Published: June 2022

Abstract
Introduction: Up to 25% of cases of ductal carcinoma in situ (DCIS) recur, and half of these recur as invasive breast cancer (IBC). There is no biomarker to predict which DCIS cases will recur but it has been suggested that a biomarker would allow de-escalation of the current paradigm of treating most patients with surgery and/or radiotherapy. However, we hypothesize that not all recurrences are genetically similar to the primary DCIS (i.e. non-clonal) and therefore arise de novo. To test this we assembled a large recurrence cohort to explore the clonal relatedness of primary-recurrence tumor pairs prior to proposing a predictive biomarker (Gorringe et al Mod Pathol 2015).
Method: We microdissected and extracted DNA from 65 pairs of primary DCIS and recurrences. Half of these recurrences were IBC. We analyzed 21 pairs by targeted sequencing or low-coverage whole-genome sequencing (LCWGS, 2x depth) and 44 pairs with Whole Exome Sequencing (WES, average depth 95x). We similarly analyzed a set of non-recurrent DCIS cases (n=29) treated with wide local excision and with a minimum of 7 years follow-up. No matched normal samples were available. Several approaches were utilized to investigate clonal relatedness using copy number alterations and mutations (when detected), including the Clonality package (Mauguen et al Biometrics 2018), manual breakpoint inspection (Bollet et al JNCI 2008), and clonality indexes (Schultheis et al JNCI 2016). Phylogenetic analyses were carried out by MEDICC2 (Petkovic et al bioRxiv 2021) on WES samples.
Results: 62% of cases were clonal (40/65), 28% were non-clonal. There were 7/65 that were equivocal, although further validation will be performed. There was no significant difference in clonal relatedness whether the recurrence was IBC or DCIS. IBC recurrent cases showed a significantly higher ploidy than the DCIS recurrences. The final phylogenetic analysis with MEDICC2 will be presented, which will take into account any subclonal whole-genome doubling events. Furthermore, clonal primary DCIS showed a significantly higher number of TP53 mutations compared to non-recurrent and non-clonal primaries (p&lt;0.001, Fisher Exact test) and a higher level of copy number events overall.
Conclusion: Detailed molecular analysis of a large cohort of matched DCIS primary and their recurrences using high sequencing resolution showed a substantial proportion of recurrences were not genetically related to the primary DCIS. Our observations raise the question of whether a tumor intrinsic biomarker alone would be sufficient to predict DCIS recurrences.
Citation Format: Tanjina Kader, Sakshi Mahale, Magnus Zethoven, Hugo Saunders, Dorothea Lesche, David Byrne, Siqi Lai, Lauren Tjoeka, Claire Candido, Maree Pechlevanis, Olivia Craig, Jia-Min Pang, Lisa Devereux, Shona Hendry, Eloise House, Sureshni Jayasinghe, Michael Toss, Islam M. Miligy, Emad Rakha, Stephen Fox, Bruce Mann, Ian Campbell, Kylie Gorringe. Predictive biomarkers of recurrence may not be useful for deescalating treatment of breast ductal carcinoma in situ due to de novo ipsilateral breast carcinoma development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 43.