Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress
Clinical Collections
Advances in Alzheimer’s

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.
ADVANCED SEARCH
Log in
Top
Breast Cancer Research
Published in: Breast Cancer Research 4/2014

Open Access 01-08-2014 | Research article

The dynamic range of circulating tumor DNA in metastatic breast cancer

Authors: Maryam Heidary, Martina Auer, Peter Ulz, Ellen Heitzer, Edgar Petru, Christin Gasch, Sabine Riethdorf, Oliver Mauermann, Ingrid Lafer, Gunda Pristauz, Sigurd Lax, Klaus Pantel, Jochen B Geigl, Michael R Speicher

Published in: Breast Cancer Research | Issue 4/2014

Login to get access

Abstract

Introduction

The management of metastatic breast cancer needs improvement. As clinical evaluation is not very accurate in determining the progression of disease, the analysis of circulating tumor DNA (ctDNA) has evolved to a promising noninvasive marker of disease evolution. Indeed, ctDNA was reported to represent a highly sensitive biomarker of metastatic cancer disease directly reflecting tumor burden and dynamics. However, at present little is known about the dynamic range of ctDNA in patients with metastatic breast cancer.

Methods

In this study, 74 plasma DNA samples from 58 patients with metastasized breast cancer were analyzed with a microfluidic device to determine the plasma DNA size distribution and copy number changes in the plasma were identified by whole-genome sequencing (plasma-Seq). Furthermore, in an index patient we conducted whole-genome, exome, or targeted deep sequencing of the primary tumor, metastases, and circulating tumor cells (CTCs). Deep sequencing was done to accurately determine the allele fraction (AFs) of mutated DNA fragments.

Results

Although all patients had metastatic disease, plasma analyses demonstrated highly variable AFs of mutant fragments. We analyzed an index patient with more than 100,000 CTCs in detail. We first conducted whole-genome, exome, or targeted deep sequencing of four different regions from the primary tumor and three metastatic lymph node regions, which enabled us to establish the phylogenetic relationships of these lesions, which were consistent with a genetically homogeneous cancer. Subsequent analyses of 551 CTCs confirmed the genetically homogeneous cancer in three serial blood analyses. However, the AFs of ctDNA were only 2% to 3% in each analysis, neither reflecting the tumor burden nor the dynamics of this progressive disease. These results together with high-resolution plasma DNA fragment sizing suggested that differences in phagocytosis and DNA degradation mechanisms likely explain the variable occurrence of mutated DNA fragments in the blood of patients with cancer.

Conclusions

The dynamic range of ctDNA varies substantially in patients with metastatic breast cancer. This has important implications for the use of ctDNA as a predictive and prognostic biomarker.
Appendix
Available only for authorised users
Literature
1.
Duffy MJ, Evoy D, McDermott EW: CA 15-3: uses and limitation as a biomarker for breast cancer. Clin Chim Acta. 2010, 411: 1869-1874. 10.1016/j.cca.2010.08.039.CrossRefPubMed
2.
Crowley E, Di Nicolantonio F, Loupakis F, Bardelli A: Liquid biopsy: monitoring cancer-genetics in the blood. Nat Rev Clin Oncol. 2013, 10: 472-484. 10.1038/nrclinonc.2013.110.CrossRefPubMed
3.
4.
Speicher MR, Pantel K: Tumor signatures in the blood. Nat Biotechnol. 2014, 32: 441-443. 10.1038/nbt.2897.CrossRefPubMed
5.
Pantel K, Brakenhoff RH, Brandt B: Detection, clinical relevance and specific biological properties of disseminating tumour cells. Nat Rev Cancer. 2008, 8: 329-340. 10.1038/nrc2375.CrossRefPubMed
6.
Cristofanilli M, Budd GT, Ellis MJ, Stopeck A, Matera J, Miller MC, Reuben JM, Doyle GV, Allard WJ, Terstappen LW, Hayes DF: Circulating tumor cells, disease progression, and survival in metastatic breast cancer. N Engl J Med. 2004, 351: 781-791. 10.1056/NEJMoa040766.CrossRefPubMed
7.
Cristofanilli M, Hayes DF, Budd GT, Ellis MJ, Stopeck A, Reuben JM, Doyle GV, Matera J, Allard WJ, Miller MC, Fritsche HA, Hortobagyi GN, Terstappen LW: Circulating tumor cells: a novel prognostic factor for newly diagnosed metastatic breast cancer. J Clin Oncol. 2005, 23: 1420-1430. 10.1200/JCO.2005.08.140.CrossRefPubMed
8.
Schwarzenbach H, Hoon DS, Pantel K: Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer. 2011, 11: 426-437. 10.1038/nrc3066.CrossRefPubMed
9.
Kidess E, Jeffrey SS: Circulating tumor cells versus tumor-derived cell-free DNA: rivals or partners in cancer care in the era of single-cell analysis?. Genome Med. 2013, 5: 70-10.1186/gm474.CrossRefPubMedPubMedCentral
10.
Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, Thornton K, Agrawal N, Sokoll L, Szabo SA, Kinzler KW, Vogelstein B, Diaz LA: Circulating mutant DNA to assess tumor dynamics. Nat Med. 2008, 14: 985-990. 10.1038/nm.1789.CrossRefPubMed
11.
Leary RJ, Kinde I, Diehl F, Schmidt K, Clouser C, Duncan C, Antipova A, Lee C, McKernan K, De La Vega FM, Kinzler KW, Vogelstein B, Diaz LA, Velculescu VE: Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med. 2010, 2: 20ra14-10.1126/scitranslmed.3000702.CrossRefPubMedPubMedCentral
12.
McBride DJ, Orpana AK, Sotiriou C, Joensuu H, Stephens PJ, Mudie LJ, Hamalainen E, Stebbings LA, Andersson LC, Flanagan AM, Durbecq V, Ignatiadis M, Kallioniemi O, Heckman CA, Alitalo K, Edgren H, Futreal PA, Stratton MR, Campbell PJ: Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors. Gene Chromosome Canc. 2010, 49: 1062-1069. 10.1002/gcc.20815.CrossRef
13.
Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, Dunning MJ, Gale D, Forshew T, Mahler-Araujo B, Rajan S, Humphray S, Becq J, Halsall D, Wallis M, Bentley D, Caldas C, Rosenfeld N: Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013, 368: 1199-1209. 10.1056/NEJMoa1213261.CrossRefPubMed
14.
Chan KC, Jiang P, Zheng YW, Liao GJ, Sun H, Wong J, Siu SS, Chan WC, Chan SL, Chan AT, Lai PB, Chiu RW, Lo YM: Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin Chem. 2013, 59: 211-224. 10.1373/clinchem.2012.196014.CrossRefPubMed
15.
Heitzer E, Auer M, Hoffmann EM, Pichler M, Gasch C, Ulz P, Lax S, Waldispuehl-Geigl J, Mauermann O, Mohan S, Pristauz G, Lackner C, Höfler G, Eisner F, Petru E, Sill H, Samonigg H, Pantel K, Riethdorf S, Bauernhofer T, Geigl JB, Speicher MR: Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer. Int J Cancer. 2013, 133: 346-356. 10.1002/ijc.28030.CrossRefPubMedPubMedCentral
16.
Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D, O'shaughnessy J, Kinzler KW, Parmigiani G, Vogelstein B, Diaz LA, Velculescu VE: Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med. 2012, 4: 162ra154-10.1126/scitranslmed.3004742.CrossRefPubMedPubMedCentral
17.
Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin SF, Kingsbury Z, Wong AS, Marass F, Humphray S, Hadfield J, Bentley D, Chin TM, Brenton JD, Caldas C, Rosenfeld N: Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013, 497: 108-112. 10.1038/nature12065.CrossRefPubMed
18.
Heitzer E, Ulz P, Belic J, Gutschi S, Quehenberger F, Fischereder K, Benezeder T, Auer M, Pischler C, Mannweiler S, Pichler M, Eisner F, Haeusler M, Riethdorf S, Pantel K, Samonigg H, Hoefler G, Augustin H, Geigl JB, Speicher MR: Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing. Genome Med. 2013, 5: 30-10.1186/gm434.CrossRefPubMedPubMedCentral
19.
Mohan S, Heitzer E, Ulz P, Lafer I, Lax S, Auer M, Pichler M, Gerger A, Eisner F, Hoefler G, Bauernhofer T, Geigl JB, Speicher MR: Changes in colorectal carcinoma genomes under anti-EGFR therapy identified by whole-genome plasma DNA sequencing. PLoS Genet. 2014, 10: e1004271-10.1371/journal.pgen.1004271.CrossRefPubMedPubMedCentral
20.
Diaz LA, Williams RT, Wu J, Kinde I, Hecht JR, Berlin J, Allen B, Bozic I, Reiter JG, Nowak MA, Kinzler KW, Oliner KS, Vogelstein B: The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 2012, 486: 537-540.PubMedPubMedCentral
21.
Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DW, Kaper F, Dawson SJ, Piskorz AM, Jimenez-Linan M, Bentley D, Hadfield J, May AP, Caldas C, Brenton JD, Rosenfeld N: Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med. 2012, 4: 136ra168-10.1126/scitranslmed.3003726.CrossRef
22.
Misale S, Yaeger R, Hobor S, Scala E, Janakiraman M, Liska D, Valtorta E, Schiavo R, Buscarino M, Siravegna G, Bencardino K, Cercek A, Chen CT, Veronese S, Zanon C, Sartore-Bianchi A, Gambacorta M, Gallicchio M, Vakiani E, Boscaro V, Medico E, Weiser M, Siena S, Di Nicolantonio F, Solit D, Bardelli A: Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature. 2012, 486: 532-536.PubMedPubMedCentral
23.
Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, Bartlett BR, Wang H, Luber B, Alani RM, Antonarakis ES, Azad NS, Bardelli A, Brem H, Cameron JL, Lee CC, Fecher LA, Gallia GL, Gibbs P, Le D, Giuntoli RL, Goggins M, Hogarty MD, Holdhoff M, Hong SM, Jiao Y, Juhl HH, Kim JJ, Siravegna G, Laheru DA, et al: Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014, 6: 224ra224-10.1126/scitranslmed.3007094.CrossRef
24.
Heitzer E, Auer M, Gasch C, Pichler M, Ulz P, Hoffmann EM, Lax S, Waldispuehl-Geigl J, Mauermann O, Lackner C, Höfler G, Eisner F, Sill H, Samonigg H, Pantel K, Riethdorf S, Bauernhofer T, Geigl JB, Speicher MR: Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res. 2013, 73: 2965-2975. 10.1158/0008-5472.CAN-12-4140.CrossRefPubMed
25.
Riethdorf S, Fritsche H, Muller V, Rau T, Schindlbeck C, Rack B, Janni W, Coith C, Beck K, Janicke F, Jackson S, Gornet T, Cristofanilli M, Pantel K: Detection of circulating tumor cells in peripheral blood of patients with metastatic breast cancer: a validation study of the Cell Search system. Clin Cancer Res. 2007, 13: 920-928. 10.1158/1078-0432.CCR-06-1695.CrossRefPubMed
26.
Fiegler H, Geigl JB, Langer S, Rigler D, Porter K, Unger K, Carter NP, Speicher MR: High resolution array-CGH analysis of single cells. Nucleic Acids Res. 2007, 35: e15-10.1093/nar/gkl1030.CrossRefPubMed
27.
Geigl JB, Obenauf AC, Waldispuehl-Geigl J, Hoffmann EM, Auer M, Hormann M, Fischer M, Trajanoski Z, Schenk MA, Baumbusch LO, Speicher MR: Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays. Nucleic Acids Res. 2009, 37: e105-10.1093/nar/gkp526.CrossRefPubMedPubMedCentral
28.
Geigl JB, Speicher MR: Single-cell isolation from cell suspensions and whole genome amplification from single cells to provide templates for CGH analysis. Nat Protoc. 2007, 2: 3173-3184. 10.1038/nprot.2007.476.CrossRefPubMed
29.
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25: 1754-1760. 10.1093/bioinformatics/btp324.CrossRefPubMedPubMedCentral
30.
Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G: Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013, 31: 213-219. 10.1038/nbt.2514.CrossRefPubMedPubMedCentral
31.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20: 1297-1303. 10.1101/gr.107524.110.CrossRefPubMedPubMedCentral
32.
Cazier JB, Holmes CC, Broxholme J: GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples. Bioinformatics. 2012, 28: 2981-2982. 10.1093/bioinformatics/bts547.CrossRefPubMedPubMedCentral
33.
34.
35.
Burke JE, Perisic O, Masson GR, Vadas O, Williams RL: Oncogenic mutations mimic and enhance dynamic events in the natural activation of phosphoinositide 3-kinase p110alpha (PIK3CA). Proc Natl Acad Sci U S A. 2012, 109: 15259-15264. 10.1073/pnas.1205508109.CrossRefPubMedPubMedCentral
36.
37.
Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S, Diaz LA, Goodman SN, David KA, Juhl H, Kinzler KW, Vogelstein B: Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci U S A. 2005, 102: 16368-16373. 10.1073/pnas.0507904102.CrossRefPubMedPubMedCentral
38.
Lo YM, Zhang J, Leung TN, Lau TK, Chang AM, Hjelm NM: Rapid clearance of fetal DNA from maternal plasma. Am J Hum Genet. 1999, 64: 218-224. 10.1086/302205.CrossRefPubMedPubMedCentral
39.
Balko JM, Stricker TP, Arteaga CL: The genomic map of breast cancer: which roads lead to better targeted therapies?. Breast Cancer Res. 2013, 15: 209-10.1186/bcr3435.CrossRefPubMedPubMedCentral
40.
41.
Lo YM, Chan KC, Sun H, Chen EZ, Jiang P, Lun FM, Zheng YW, Leung TY, Lau TK, Cantor CR, Chiu RW: Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med. 2010, 2: 61ra91-10.1126/scitranslmed.3001720.CrossRefPubMed
Metadata
Title
The dynamic range of circulating tumor DNA in metastatic breast cancer
Authors
Maryam Heidary
Martina Auer
Peter Ulz
Ellen Heitzer
Edgar Petru
Christin Gasch
Sabine Riethdorf
Oliver Mauermann
Ingrid Lafer
Gunda Pristauz
Sigurd Lax
Klaus Pantel
Jochen B Geigl
Michael R Speicher
Publication date
01-08-2014
Publisher
BioMed Central
Published in
Breast Cancer Research / Issue 4/2014
Electronic ISSN: 1465-542X
DOI
https://doi.org/10.1186/s13058-014-0421-y

Other articles of this Issue 4/2014

Breast Cancer Research 4/2014 Go to the issue

Research article

Nestin positively regulates the Wnt/β-catenin pathway and the proliferation, survival and invasiveness of breast cancer stem cells

Research article

Physical activity and telomere length in early stage breast cancer survivors

Review

Current and upcoming approaches to exploit the reversibility of epigenetic mutations in breast cancer

Research article

Relationships between computer-extracted mammographic texture pattern features and BRCA1/2mutation status: a cross-sectional study

Research article

Peroxiredoxin-1 protects estrogen receptor α from oxidative stress-induced suppression and is a protein biomarker of favorable prognosis in breast cancer

Research article

Identification of a novel AMPK-PEA15 axis in the anoikis-resistant growth of mammary cells
Webinar | 19-02-2024 | 17:30 (CET)

Keynote webinar | Spotlight on antibody–drug conjugates in cancer

Watch now

Antibody–drug conjugates (ADCs) are novel agents that have shown promise across multiple tumor types. Explore the current landscape of ADCs in breast and lung cancer with our experts, and gain insights into the mechanism of action, key clinical trials data, existing challenges, and future directions.

Dr. Véronique Diéras
Prof. Fabrice Barlesi
Developed by: Springer Medicine
Image Credits