Capturing intra-tumor genetic heterogeneity by de novo mutation profiling of circulating cell-free tumor DNA: A proof-of-principle

Annals of Oncology

Volumn 25, Issue 9, 2014, Pages 1729-1735

  De Mattos Arruda, L ^a,b,c   Weigelt, B ^c   Cortes, J ^a   Won, H H ^c   Ng, C K Y ^c   Nuciforo, P ^a   Bidard, F C ^c,d   Aura, C ^a   Saura, C ^a   Peg, V ^e   Piscuoglio, S ^c   Oliveira, M ^a   Smolders, Y ^c   Patel, P ^f   Norton, L ^c   Tabernero, J ^a,b   Berger, M F ^c   Seoane, J ^a,b,g   Reis Filho, J S ^c  

^a VALL D HEBRON UNIVERSITY HOSPITAL   (Spain)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^d INSTITUT CURIE   (France)

^e HOSPITAL UNIVERSITARI VALL D HEBRON   (Spain)

^f GENENTECH INC   (United States)

^g INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

Breast cancer; Cell free tumor DNA; Disease monitoring; Intra tumor heterogeneity; Massively parallel sequencing

Indexed keywords

CELL FREE TUMOR DNA; CYCLIN DEPENDENT KINASE INHIBITOR 2A; DNA; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; IPATASERTIB; JANUS KINASE 3; UNCLASSIFIED DRUG; UVOMORULIN; VASCULOTROPIN RECEPTOR 3; ERBB2 PROTEIN, HUMAN; PROTEIN KINASE B; TUMOR MARKER; ANTHRACYCLINE; CAPECITABINE; FIZZY RELATED PROTEIN; PACLITAXEL; PROTEIN P53;

AGED; AKT1 GENE; ARTICLE; BONE METASTASIS; BREAST CANCER; CASE REPORT; CDH1 GENE; CDKN2A GENE; COMPUTER ASSISTED TOMOGRAPHY; CTNNB1 GENE; FEMALE; FLT4 GENE; GENETIC HETEROGENEITY; HUMAN; HUMAN CELL; HUMAN TISSUE; JAK3 GENE; LIVER METASTASIS; MASSIVELY PARALLEL SEQUENCING; MML3 GENE; MOLECULARLY TARGETED THERAPY; MONOTHERAPY; NF1 GENE; PHARMACODYNAMICS; PHASE 1 CLINICAL TRIAL (TOPIC); POSITRON EMISSION TOMOGRAPHY; PRIORITY JOURNAL; PROGRESSION FREE SURVIVAL; SEQUENCE ANALYSIS; SOMATIC MUTATION; TUMOR GENE; TUMOR SUPPRESSOR GENE; ANTAGONISTS AND INHIBITORS; BLOOD; BONE TUMOR; BREAST NEOPLASMS; CELL FREE SYSTEM; CLINICAL TRIAL; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; HIGH THROUGHPUT SEQUENCING; LIVER TUMOR; METABOLISM; MIDDLE AGED; NUCLEOTIDE SEQUENCE; PAGET NIPPLE DISEASE; PATHOLOGY; PHASE 1 CLINICAL TRIAL; SECONDARY; BREAST CARCINOMA; DNA EXTRACTION; GENE; GENE MUTATION; GENETIC PROCEDURES; TP53 GENE; TSC1 GENE;

BASE SEQUENCE; BONE NEOPLASMS; BREAST NEOPLASMS; CARCINOMA, DUCTAL, BREAST; CELL-FREE SYSTEM; DNA, NEOPLASM; FEMALE; GENETIC HETEROGENEITY; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LIVER NEOPLASMS; MIDDLE AGED; PROTO-ONCOGENE PROTEINS C-AKT; RECEPTOR, ERBB-2; RECEPTORS, ESTROGEN; SEQUENCE ANALYSIS, DNA; TUMOR MARKERS, BIOLOGICAL;

EID: 84906890825     PISSN: 09237534     EISSN: 15698041     Source Type: Journal    
DOI: 10.1093/annonc/mdu239     Document Type: Article

References (31)

1. Swanton C. Intratumor heterogeneity: evolution through space and time. Cancer Res 2012; 72: 4875-4882.
2. Gerlinger M, Rowan AJ, Horswell S et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012; 366: 883-892.
3. De Mattos-Arruda L, Bidard FC, Won HH et al. Establishing the origin of metastatic deposits in the setting of multiple primary malignancies: the role of massively parallel sequencing. Mol Oncol 2014; 8: 150-158.
4. Shah SP, Roth A, Goya R et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 2012; 486: 395-399.
5. Nik-Zainal S, Van Loo P, Wedge DC et al. The life history of 21 breast cancers. Cell 2012; 149: 994-1007.
6. Martelotto LG, Ng CK, Piscuoglio S et al. Breast cancer intra-tumor heterogeneity. Breast Cancer Res 2014; 16: 210.
7. Geyer FC, Weigelt B, Natrajan R et al. Molecular analysis reveals a genetic basis for the phenotypic diversity of metaplastic breast carcinomas. J Pathol 2010; 220: 562-573.
8. Navin N, Kendall J, Troge J et al. Tumour evolution inferred by single-cell sequencing. Nature 2011; 472: 90-94.
9. Bidard FC, Weigelt B, Reis-Filho JS. Going with the flow: from circulating tumor cells to DNA. Sci Transl Med 2013; 5: 207ps214.
10. De Mattos-Arruda L, Cortes J, Santarpia L et al. Circulating tumour cells and cellfree DNA as tools for managing breast cancer. Nat Rev Clin Oncol 2013; 10: 377-389.
11. Yap TA, Gerlinger M, Futreal PA et al. Intratumor heterogeneity: seeing the wood for the trees. Sci Transl Med 2012; 4: 127ps110.
12. Powell AA, Talasaz AH, Zhang H et al. Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines. PLoS ONE 2012; 7: e33788.
13. Forshew T, Murtaza M, Parkinson C et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med 2012; 4: 136ra168.
14. Dawson SJ, Rosenfeld N, Caldas C. Circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 2013; 369: 93-94.
15. Bettegowda C, Sausen M, Leary RJ et al. Detection of circulating tumor DNA in early-and late-stage human malignancies. Sci Transl Med 2014; 6: 224ra224.
16. Leary RJ, Sausen M, Kinde I et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med 2012; 4: 162ra154.
17. Murtaza M, Dawson SJ, Tsui DW et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 2013; 497: 108-112.
18. Chan KC, Jiang P, Zheng YWet al. 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.
19. Misale S, Yaeger R, Hobor S et al. Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature 2012; 486: 532-536.
20. Zhang L, Ridgway LD, Wetzel MD et al. The identification and characterization of breast cancer CTCs competent for brain metastasis. Sci Transl Med 2013; 5: 180ra148.
21. Lin J, Sampath D, Nannini MA et al. Targeting activated Akt with GDC-0068, a novel selective Akt inhibitor that is efficacious in multiple tumor models. Clin Cancer Res 2013; 19: 1760-1772.
22. Eisenhauer EA, Therasse P, Bogaerts J et al. New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1). Eur J Cancer 2009; 45: 228-247.
23. Hernandez L, Wilkerson PM, Lambros MB et al. Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intra-tumour genetic heterogeneity and clonal selection. J Pathol 2012; 227: 42-52.
24. Won HH, Scott SN, Brannon AR et al. Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing. J Vis Exp 2013; 80: e50710.
25. Robinson JT, Thorvaldsdottir H, Winckler W et al. Integrative genomics viewer. Nat Biotechnol 2011; 29: 24-26.
26. Von HoffDD, Stephenson JJ, Jr, Rosen P et al. Pilot study using molecular profiling of patients' tumors to find potential targets and select treatments for their refractory cancers. J Clin Oncol 2010; 28: 4877-4883.
27. Polyak K. Tumor heterogeneity confounds and illuminates: a case for Darwinian tumor evolution. Nat Med 2014; 20: 344-346.
28. Li S, Shen D, Shao J et al. Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts. Cell Rep 2013; 4: 1116-1130.
29. Gerlinger M, Horswell S, Larkin J et al. Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat Genet 2014; 46: 225-233.
30. Sottoriva A, Spiteri I, Piccirillo SG et al. Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc Natl Acad Sci USA 2013; 110: 4009-4014.
31. Chandarlapaty S, Sawai A, Scaltriti M et al. AKT inhibition relieves feedback suppression of receptor tyrosine kinase expression and activity. Cancer Cell 2011; 19: 58-71.