314P - The impact of changes in tumor mutational landscape during neoadjuvant therapy on tumor-informed ctDNA testing in breast cancer patients

Background

The I-SPY2 trial showed that patients (pts) with residual cancer burden (RCB-II/III) after neoadjuvant therapy (NAT) who tested negative for ctDNA during and after treatment had significantly lower risk of metastatic recurrence compared to ctDNA-positive pts. To understand the lack of ctDNA detection in pts with RCB-II/III, we examined the prevalence of somatic variants included in ctDNA assays in matched serial non-responding tumors.

Methods

We assessed whether the 16 variants selected for tumor-informed ctDNA testing (Signatera™, Natera, Inc.) were conserved in the tumor over time using whole exome sequencing (WES) data from 101 consecutively selected I-SPY2 pts with RCB-II/III (46 hormone receptor+/HER2-, 44 triple-negative, and 11 HER2+). WES was performed on tumors collected pre-NAT (BIO0, n=101), 3 weeks after NAT initiation (BIO1, n=83), and post-NAT at surgery (BIO3, n=72). ctDNA testing was performed pre-NAT (T0), during (3 and 12 weeks, T1 and T2), and post-NAT before surgery (T3).

Results

ctDNA dynamics in response to NAT included: persistently ctDNA+ (n=30, 30%), ctDNA+ at T0 but cleared at T1, T2, or T3 (n=45, 45%), persistently ctDNA- (n=12, 12%), and mixed pattern (n=14, 14%). When analyzing all gene mutations in serial tumor samples at the population level, only 39% and 23% were conserved between BIO0 and BIO1 (n=83 pairs) and BIO0 and BIO3 (n=72 pairs), respectively, indicating changes in the tumor mutational landscape. At the patient level, a median of 25% (5-45%) of gene mutations were conserved between BIO0 and BIO1 and 23% (3-41%) between BIO0 and BIO3. In contrast, we observed high conservation of variants included in ctDNA assays in paired serial tumors from the same pts: BIO0 vs. BIO1 (median 16 out of 16, IQR 14-16), BIO0 vs. BIO3 (median 15 out of 16, IQR 13-16).

Conclusions

Despite changes in the tumor mutational landscape, assay variants selected from pretreatment tumor DNA sequencing were highly conserved in serial tumor samples over time. Understanding the biology of ctDNA shedding in response to NAT may inform the use of this biomarker in predicting clinical outcomes.

Clinical trial identification

NCT01042379.

Editorial acknowledgement

Legal entity responsible for the study

Quantum Leap Health Care.

Funding

NIH/NCI (grant R01CA255442) NIH/NCI I-SPY2+ (grant PO1-CA210961) NIH/NCI Imaging (grant 28XS197 P-0518835) NIH/NCI Cancer Cell Map Initiative (CCMI) (grant U54CA209891) NIH/NCI Cancer Center Support Grant (CCSG) (grant P30-CA82103), NIH/NHGRI Big Data (grant U54-HG007990), Breast Cancer Research Foundation (grant BCRF-23-142) Breast Cancer Research Foundation (grant BCRF-23-165) Breast Cancer Research – Atwater Trust Stand Up to Cancer California Breast Cancer Research Program Give Breast Cancer the Boot Natera provided the ctDNA assay at no cost. Quantum Leap Healthcare Collaborative, sponsor of the I-SPY2 trial, provided specimens and clinical data.

Disclosure

S. Rivero-Hinojosa: Financial Interests, Personal, Full or part-time Employment: Natera, Inc.; Financial Interests, Personal, Stocks/Shares: Natera, Inc. T. Tin: Financial Interests, Personal, Full or part-time Employment: Natera, Inc.; Financial Interests, Personal, Stocks/Shares: Natera, Inc. E. Kalashnikova: Financial Interests, Personal, Full or part-time Employment: Natera, Inc.; Financial Interests, Personal, Stocks/Shares: Natera, Inc. C. Yau: Financial Interests, Institutional, Other: NCI/NIH, University of California; Financial Interests, Personal, Other: Quantum Leap Healthcare Collaborative. C. Isaacs: Financial Interests, Institutional, Advisory Board: Tesaro/GSK, Seattle Genetics, Pfizer, AZ, BMS, Genentech, Novartis, Regeneron, BMS; Financial Interests, Personal, Advisory Board: UptoDate, McGraw Hill, AstraZeneca, Biotheranostic, EISAI, Genentech, Gilead, ION, Novartis, Pfizer, PUMA, Seagen, Novartis, ideOut Foundation, Pfizer. R.A. Shatsky: Financial Interests, Institutional, Local PI: OBI Pharmaceuticals, Quantum Leap Healthcare Collaborative, AstraZeneca, Gilead; Financial Interests, Personal, Advisory Board: AstraZeneca, Stemline; Financial Interests, Personal, Speaker’s Bureau: Gilead. C.C. Palsuledesai: Financial Interests, Personal, Full or part-time Employment: Natera, Inc.; Financial Interests, Personal, Stocks/Shares: Natera, Inc. A.A. Rodriguez: Financial Interests, Personal, Full or part-time Employment: Natera, Inc.; Financial Interests, Personal, Stocks/Shares: Natera, Inc. M.C. Liu: Financial Interests, Personal, Full or part-time Employment: Natera, Inc.; Financial Interests, Personal, Stocks/Shares: Natera, Inc.; Financial Interests, Personal, Other: AstraZeneca, Genomic Health, Ionis; Financial Interests, Institutional, Research Grant: Eisai, Exact Sciences, Genentech, Genomic Health, GRAIL, Ionis, Merck, Novartis, Seattle Genetics, Tesaro; Financial Interests, Institutional, Advisory Board: AstraZeneca, Celgene, Roche/Genentech, Genomic Health, GRAIL, Ionis, Merck, Pfizer, Seattle Genetics, Syndax. P.R. Pohlmann: Financial Interests, Institutional, Advisory Board: Genentech/Roche, Fabre-Kramer, Advanced Cancer Therapeutics, Caris Centers of Excellence, Pfizer, Pieris Pharmaceuticals, Cascadian Therapeutics, BOLT, Byondis, Seagen, Orum Therapeutics, Carisma Therapeutics, Personalized Cancer Therapy, OncoPlex Diagnostics, mmunonet BioSciences, Pfizer, HERON, Puma Biotechnology, Sirtex, CARIS Lifesciences, Immunonet BioSciences, Pfizer, HERON, Puma Biotechnology, Sirtex, CARIS Lifesciences, Bolt Biotherapeutics, Abbvie, Dava Oncology, OncLive/MJH Life Sciences, Frontiers - Publisher, SABCS, Genentech/Roche, Immunonet BioSciences. L. Esserman: Financial Interests, Institutional, Advisory Board: Merck & Co., Blue Cross Blue Shield; Financial Interests, Personal, Advisory Board: UpToDate. H.S. Rugo: Financial Interests, Advisory Board: Astellas Pharma, AstraZeneca, Daiichi Sankyo, F Hoffmann-La Roche–Genentech, Gilead Sciences, GSK, Lilly, Merck, Novartis Pharmaceuticals Corporation, OBI Pharma, Pfizer, Pionyr, Napo Pharmaceutical, Puma Biotechnology, Blueprint, Scorpion Therapeutics, Daiichi Sankyo, Mylan. A. DeMichele: Financial Interests, Institutional, Advisory Board: Novartis, Pfizer, Genentech, Neogenomics, ASCO. L.J. Van't Veer: Financial Interests, Personal, Advisory Role: Exai BIo; Financial Interests, Personal, Full or part-time Employment: Agendia. All other authors have declared no conflicts of interest.