Circulating tumour DNA in metastatic breast cancer to guide clinical trial enrolment and precision oncology: A cohort study

Autoři: Andjelija Zivanovic Bujak aff001;  Chen-Fang Weng aff001;  Maria João Silva aff001;  Miriam Yeung aff001;  Louisa Lo aff001;  Sarah Ftouni aff001;  Cassandra Litchfield aff001;  Yi-An Ko aff001;  Keilly Kuykhoven aff001;  Courtney Van Geelen aff001;  Sushma Chandrashekar aff001;  Mark A. Dawson aff001;  Sherene Loi aff001;  Stephen Q. Wong aff001;  Sarah-Jane Dawson aff001
Působiště autorů: Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia aff001;  Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia aff002;  Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia aff003
Vyšlo v časopise: Circulating tumour DNA in metastatic breast cancer to guide clinical trial enrolment and precision oncology: A cohort study. PLoS Med 17(10): e32767. doi:10.1371/journal.pmed.1003363
Kategorie: Research Article
doi: 10.1371/journal.pmed.1003363



Metastatic breast cancer (mBC) is a heterogenous disease with increasing availability of targeted therapies as well as emerging genomic markers of therapeutic resistance, necessitating timely and accurate molecular characterization of disease. As a minimally invasive test, analysis of circulating tumour DNA (ctDNA) is well positioned for real-time genomic profiling to guide treatment decisions. Here, we report the results of a prospective testing program established to assess the feasibility of ctDNA analysis to guide clinical management of mBC patients.

Methods and findings

Two hundred thirty-four mBC patients (median age 54 years) were enrolled between June 2015 and October 2018 at the Peter MacCallum Cancer Centre, Melbourne, Australia. Median follow-up was 15 months (range 1–46). All patient samples at the time of enrolment were analysed in real time for the presence of somatic mutations. Longitudinal plasma testing during the course of patient management was also undertaken in a subset of patients (n = 67, 28.6%), according to clinician preference, for repeated molecular profiling or disease monitoring. Detection of somatic mutations from patient plasma was performed using a multiplexed droplet digital PCR (ddPCR) approach to identify hotspot mutations in PIK3CA, ESR1, ERBB2, and AKT1. In parallel, subsets of samples were also analysed via next-generation sequencing (targeted panel sequencing and low-coverage whole-genome sequencing [LC-WGS]). The sensitivity of ddPCR and targeted panel sequencing to identify actionable mutations was compared. Results were discussed at a multidisciplinary breast cancer meeting prior to treatment decisions. ddPCR and targeted panel sequencing identified at least 1 actionable mutation at baseline in 80/234 (34.2%) and 62/159 (39.0%) of patients tested, respectively. Combined, both methods detected an actionable alteration in 104/234 patients (44.4%) through baseline or serial ctDNA testing. LC-WGS was performed on 27 patients from the cohort, uncovering several recurrently amplified regions including 11q13.3 encompassing CCND1. Increasing ctDNA levels were associated with inferior overall survival, whether assessed by ddPCR, targeted sequencing, or LC-WGS. Overall, the ctDNA results changed clinical management in 40 patients including the direct recruitment of 20 patients to clinical trials. Limitations of the study were that it was conducted at a single site and that 31.3% of participants were lost to follow-up.


In this study, we found prospective ctDNA testing to be a practical and feasible approach that can guide clinical trial enrolment and patient management in mBC.

Klíčová slova:

Biopsy – Breast cancer – Cancer genomics – Cancer treatment – Circulating tumor DNA – Gene sequencing – Metastasis – Mutation detection


1. Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M, et al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer. 2015;136(5):E359–86. doi: 10.1002/ijc.29210 25220842

2. Hyman DM, Smyth LM, Donoghue MTA, Westin SN, Bedard PL, Dean EJ, et al. AKT Inhibition in Solid Tumors With AKT1 Mutations. J Clin Oncol. 2017;35(20):2251–9. doi: 10.1200/JCO.2017.73.0143 28489509

3. Andre F, Ciruelos E, Rubovszky G, Campone M, Loibl S, Rugo HS, et al. Alpelisib for PIK3CA-Mutated, Hormone Receptor-Positive Advanced Breast Cancer. N Engl J Med. 2019;380(20):1929–40. doi: 10.1056/NEJMoa1813904 31091374

4. Hyman DM, Piha-Paul SA, Won H, Rodon J, Saura C, Shapiro GI, et al. HER kinase inhibition in patients with HER2- and HER3-mutant cancers. Nature. 2018;554(7691):189–94. doi: 10.1038/nature25475 29420467

5. Fribbens C, O'Leary B, Kilburn L, Hrebien S, Garcia-Murillas I, Beaney M, et al. Plasma ESR1 Mutations and the Treatment of Estrogen Receptor-Positive Advanced Breast Cancer. J Clin Oncol. 2016;34(25):2961–8. doi: 10.1200/JCO.2016.67.3061 27269946

6. Schiavon G, Hrebien S, Garcia-Murillas I, Cutts RJ, Pearson A, Tarazona N, et al. Analysis of ESR1 mutation in circulating tumor DNA demonstrates evolution during therapy for metastatic breast cancer. Sci Transl Med. 2015;7(313):313ra182. doi: 10.1126/scitranslmed.aac7551 26560360

7. Toy W, Weir H, Razavi P, Lawson M, Goeppert AU, Mazzola AM, et al. Activating ESR1 Mutations Differentially Affect the Efficacy of ER Antagonists. Cancer Discov. 2017;7(3):277–87. doi: 10.1158/2159-8290.CD-15-1523 27986707

8. Murtaza M, Dawson SJ, Pogrebniak K, Rueda OM, Provenzano E, Grant J, et al. Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer. Nat Commun. 2015;6:8760. doi: 10.1038/ncomms9760 26530965

9. Savas P, Teo ZL, Lefevre C, Flensburg C, Caramia F, Alsop K, et al. The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE". PLoS Med. 2016;13(12):e1002204. doi: 10.1371/journal.pmed.1002204 28027312

10. Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013;497(7447):108–12. doi: 10.1038/nature12065 23563269

11. Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, et al. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017;17(4):223–38. doi: 10.1038/nrc.2017.7 28233803

12. Mattos-Arruda L, Weigelt B, Cortes J, Won HH, Ng CKY, Nuciforo P, et al. Capturing intra-tumor genetic heterogeneity by de novo mutation profiling of circulating cell-free tumor DNA: a proof-of-principle. Ann Oncol. 2018;29(11):2268. doi: 10.1093/annonc/mdx804 29718117

13. Kim ST, Banks KC, Lee S-H, Kim K, Park JO, Park SH, et al. Prospective Feasibility Study for Using Cell-Free Circulating Tumor DNA–Guided Therapy in Refractory Metastatic Solid Cancers: An Interim Analysis. JCO Precis Oncol. 2017(1):1–15.

14. Rothwell DG, Ayub M, Cook N, Thistlethwaite F, Carter L, Dean E, et al. Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study. Nat Med. 2019;25(5):738–43. doi: 10.1038/s41591-019-0380-z 31011204

15. Sánchez NS, Kahle MP, Bailey AM, Wathoo C, Balaji K, Demirhan ME, et al. Identification of Actionable Genomic Alterations Using Circulating Cell-Free DNA. JCO Precision Oncology. 2019(3):1–10.

16. Lok SW, Whittle JR, Vaillant F, Teh CE, Lo LL, Policheni AN, et al. A Phase Ib Dose-Escalation and Expansion Study of the BCL2 Inhibitor Venetoclax Combined with Tamoxifen in ER and BCL2-Positive Metastatic Breast Cancer. Cancer Discov. 2019;9(3):354–69. doi: 10.1158/2159-8290.CD-18-1151 30518523

17. Yeh P, Dickinson M, Ftouni S, Hunter T, Sinha D, Wong SQ, et al. Molecular disease monitoring using circulating tumor DNA in myelodysplastic syndromes. Blood. 2017;129(12):1685–90. doi: 10.1182/blood-2016-09-740308 28126926

18. Dawson SJ, Rueda OM, Aparicio S, Caldas C. A new genome-driven integrated classification of breast cancer and its implications. EMBO J. 2013;32(5):617–28. doi: 10.1038/emboj.2013.19 23395906

19. Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 2012;486(7403):405–9. doi: 10.1038/nature11154 22722202

20. Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012;486(7403):353–60. doi: 10.1038/nature11143 22722193

21. Pereira B, Chin SF, Rueda OM, Vollan HK, Provenzano E, Bardwell HA, et al. The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nat Commun. 2016;7:11479. doi: 10.1038/ncomms11479 27161491

22. Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, et al. The landscape of cancer genes and mutational processes in breast cancer. Nature. 2012;486(7403):400–4. doi: 10.1038/nature11017 22722201

23. Bertucci F, Ng CKY, Patsouris A, Droin N, Piscuoglio S, Carbuccia N, et al. Genomic characterization of metastatic breast cancers. Nature. 2019;569(7757):560–4. doi: 10.1038/s41586-019-1056-z 31118521

24. Chakravarty D, Gao J, Phillips SM, Kundra R, Zhang H, Wang J, et al. OncoKB: A Precision Oncology Knowledge Base. JCO Precis Oncol. 2017;2017.

25. Dawson S-J, Wein L, Silva MJ, Luen SJ, VanGeelen C, Moodie K, et al. Plasma and tumor genomic correlates of response to BYL719 in PI3KCA mutated metastatic ER-positive breast cancer (ER+/HER2- BC). J Clin Oncol. 2018;36(15_suppl):1055.

26. Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013; 368(13):1199–1209. doi: 10.1056/NEJMoa1213261 23484797

27. Stover DG, Parsons HA, Ha G, Freeman SS, Barry WT, Guo H, et al. Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. J Clin Oncol. 2018;36(6):543–53. doi: 10.1200/JCO.2017.76.0033 29298117

28. Schwaederle M, Chattopadhyay R, Kato S, Fanta PT, Banks KC, Choi IS, et al. Genomic Alterations in Circulating Tumor DNA from Diverse Cancer Patients Identified by Next-Generation Sequencing. Cancer Res. 2017;77(19):5419–27. doi: 10.1158/0008-5472.CAN-17-0885 28807936

29. Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun. 2017;8(1):1324. doi: 10.1038/s41467-017-00965-y 29109393

30. Pritchard CC, Salipante SJ, Koehler K, Smith C, Scroggins S, Wood B, et al. Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. J Mol Diagn. 2014;16(1):56–67. doi: 10.1016/j.jmoldx.2013.08.004 24189654

Článek vyšel v časopise

PLOS Medicine

2020 Číslo 10

Nejčtenější v tomto čísle

Tomuto tématu se dále věnují…


Zvyšte si kvalifikaci online z pohodlí domova

Antiseptika a prevence ve stomatologii
nový kurz
Autoři: MUDr. Ladislav Korábek, CSc., MBA

Diagnostika a léčba deprese pro ambulantní praxi
Autoři: MUDr. Jan Hubeňák, Ph.D

Snímatelné zubní náhrady a fixační krémy
Autoři: doc. MUDr. Hana Hubálková, Ph.D.

Nová éra v léčbě migrény
Autoři: MUDr. Eva Medová, MUDr. Tomáš Nežádal, Ph.D.

Význam nutraceutik u kardiovaskulárních onemocnění

Všechny kurzy
Zapomenuté heslo

Nemáte účet?  Registrujte se

Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.


Nemáte účet?  Registrujte se