Next-generation sequencing of disseminated tumor cells

Frontiers in Oncology

Volumn 3 DEC, Issue , 2013, Pages

  Møller, Elen K ^a,b   Kumar, Parveen ^c   Voet, Thierry ^c,d   Peterson, April ^e   Van Loo, Peter ^d,f   Mathiesen, Randi R ^a   Fjelldal, Renathe ^a   Grundstad, Jason ^e   Borgen, Elin ^a   Baumbusch, Lars O ^a,b   Naume, Bjørn ^a,b   Børresen Dale, Anne Lise ^a,b   White, Kevin P ^e   Nord, Silje ^a,b   Kristensen, Vessela N ^a,b,g  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

^c UNIVERSITY HOSPITALS LEUVEN   (Belgium)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e UNIVERSITY OF CHICAGO   (United States)

^f UNIVERSITY OF LEUVEN   (Belgium)

^g AKERSHUS UNIVERSITY HOSPITAL   (Norway)

Author keywords

Circulating tumor cells; Clonal evolution; Disseminating tumor cells; Single tumor cell sequencing; Tumor heterogeneity

Indexed keywords

ALLELE; ARTICLE; BONE MARROW; CASE REPORT; CHROMOSOME 13; CHROMOSOME 16Q; CHROMOSOME 1Q; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA SEQUENCE; GENE AMPLIFICATION; GENE MAPPING; GENOME; HUMAN; HUMAN CELL; IMMUNOCYTOCHEMISTRY; METASTASIS; MICROMANIPULATION; MICROMETASTASIS; NUCLEOTIDE SEQUENCE;

EID: 84892393752     PISSN: None     EISSN: 2234943X     Source Type: Journal    
DOI: 10.3389/fonc.2013.00320     Document Type: Article

References (36)

1. Braun S, Kentenich C, Janni W, Hepp F, de Waal J, Willgeroth F, et al. Lack of effect of adjuvant chemotherapy on the elimination of single dormant tumor cells in bone marrow of high-risk breast cancer patients. J Clin Oncol (2000) 18(1):80-6.
2. Stathopoulou A. Molecular detection of cytokeratin-19-positive cells in the peripheral blood of patients with operable breast cancer: evaluation of their prognostic significance. J Clin Oncol (2002) 20(16):3404-12. doi: 10.1200/JCO.2002.08.135.
3. Wiedswang G, Borgen E, Karesen R, Kvalheim G, Nesland JM, Qvist H, et al. Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer. J Clin Oncol (2003) 21(18):3469-78. doi:10.1200/JCO.2003.02.009.
4. Xenidis N, Perraki M, Kafousi M, Apostolaki S, Bolonaki I, Stathopoulou A, et al. Predictive and prognostic value of peripheral blood cytokeratin-19 mRNA-positive cells detected by real-time polymerase chain reaction in node-negative breast cancer patients. J Clin Oncol (2006) 24(23):3756-62. doi:10.1200/JCO.2005.04.5948.
5. Pantel K, Brakenhoff RH. Dissecting the metastatic cascade. Nat Rev Cancer (2004) 4(6):448-56. doi:10.1038/nrc1370.
6. Klein CA. Parallel progression of primary tumours and metastases. Nat Rev Cancer (2009) 9(4):302-12. doi:10.1038/nrc2627.
7. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, et al. Tumour evolution inferred by single-cell sequencing. Nature (2011) 472(7341):90-4. doi:10.1038/nature09807.
8. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med (2012) 366(10):883-92. doi:10.1056/NEJMoa1113205.
9. Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD, Lau KW, et al. The life history of 21 breast cancers. Cell (2012) 149(5):994-1007. doi:10.1016/j.cell.2012.04.023.
10. Lindstrom LS, Karlsson E, Wilking UM, Johansson U, Hartman J, Lidbrink EK, et al. Clinically used breast cancer markers such as estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 are unstable throughout tumor progression. J Clin Oncol (2012) 30(21):2601-8. doi:10.1200/JCO.2011.37.2482.
11. Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature (2009) 461(7265):809-13. doi:10.1038/nature08489.
12. Zhang J, Shi Y, Lalonde E, Li L, Cavallone L, Ferenczy A, et al. Exome profiling of primary, metastatic and recurrent ovarian carcinomas in a BRCA1-positive patient. BMC Cancer (2013) 13:146. doi:10.1186/1471-2407-13-146.
13. Early Breast Cancer Trialists' Collaborative Group (EBCTCG). Relevance of breast cancer hormone receptors and other factors to the efficacy of adjuvant tamoxifen: patient-level meta-analysis of randomised trials. Lancet (2011) 378(9793):771-84. doi:10.1016/S0140-6736(11)60993-8.
14. Early Breast Cancer Trialists' Collaborative Group (EBCTCG). Comparisons between different polychemotherapy regimens for early breast cancer: meta-analyses of long-term outcome among 100 000 women in 123 randomised trials. Lancet (2012) 379(9814):432-44. doi:10.1016/S0140-6736(11)61625-5.
15. Gundry M, Li W, Maqbool SB, Vijg J. Direct, genome-wide assessment of DNA mutations in single cells. Nucleic Acids Res (2012) 40(5):2032-40. doi:10.1093/nar/gkr949.
16. Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, et al. Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 148(5):873-85. doi:10.1016/j.cell.2012.02.028.
17. Li Y, Xu X, Song L, Hou Y, Li Z, Tsang S, et al. Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer. Gigascience (2012) 1(1):12. doi:10.1186/2047-217X-1-12.
18. Wang J, Fan HC, Behr B, Quake SR. Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell (2012) 150(2):402-12. doi:10.1016/j.cell.2012.06.030.
19. Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, et al. Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 148(5):886-95. doi:10.1016/j.cell.2012.02.025.
20. Zong C, Lu S, Chapman AR, Xie XS. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science (2012) 338(6114):1622-6. doi:10.1126/science.1229164.
21. Heitzer E, Auer M, Gasch C, Pichler M, Ulz P, Hoffmann EM, et al. Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res (2013) 73(10):2965-75. doi:10.1158/0008-5472.CAN-12-4140.
22. Voet T, Kumar P, Van Loo P, Cooke SL, Marshall J, Lin ML, et al. Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res (2013) 41(12):6119-38. doi:10.1093/nar/gkt345.
23. Schmidt-Kittler O, Ragg T, Daskalakis A, Granzow M, Ahr A, Blankenstein TJ, et al. From latent disseminated cells to overt metastasis: genetic analysis of systemic breast cancer progression. Proc Natl Acad Sci USA (2003) 100(13):7737-42. doi:10.1073/pnas.1331931100.
24. Fiegler H, Geigl JB, Langer S, Rigler D, Porter K, Unger K, et al. High resolution array-CGH analysis of single cells. Nucleic Acids Res (2007) 35(3):e15. doi:10.1093/nar/gkl1030.
25. Mathiesen RR, Fjelldal R, Liestol K, Due EU, Geigl JB, Riethdorf S, et al. High-resolution analyses of copy number changes in disseminated tumor cells of patients with breast cancer. Int J Cancer (2012) 131(4):E405-15. doi:10.1002/ijc.26444.
26. Baslan T, Kendall J, Rodgers L, Cox H, Riggs M, Stepansky A, et al. Genome-wide copy number analysis of single cells. Nat Protoc (2012) 7(6):1024-41. doi:10.1038/nprot.2012.039.
27. Nilsen G, Liestol K, Van Loo P, Moen Vollan HK, Eide MB, Rueda OM, et al. Copynumber: efficient algorithms for single-and multi-track copy number segmentation. BMC Genomics (2012) 13:591. doi:10.1186/1471-2164-13-591.
28. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 25(14):1754-60. doi:10.1093/bioinformatics/btp324.
29. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 26(6):841-2. doi:10.1093/bioinformatics/btq033.
30. Van Loo P, Nordgard SH, Lingjaerde OC, Russnes HG, Rye IH, Sun W, et al. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci USA (2010) 107(39):16910-5. doi:10.1073/pnas.1009843107.
31. Fuhrmann C, Schmidt-Kittler O, Stoecklein NH, Petat-Dutter K, Vay C, Bockler K, et al. High-resolution array comparative genomic hybridization of single micrometastatic tumor cells. Nucleic Acids Res (2008) 36(7):e39. doi:10.1093/nar/gkn101.
32. Geigl JB, Obenauf AC, Waldispuehl-Geigl J, Hoffmann EM, Auer M, Hormann M, et al. Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays. Nucleic Acids Res (2009) 37(15):e105. doi:10.1093/nar/gkp526.
33. Tirkkonen M, Tanner M, Karhu R, Kallioniemi A, Isola J, Kallioniemi OP. Molecular cytogenetics of primary breast cancer by CGH. Genes Chromosomes Cancer (1998) 21(3):177-84.
34. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell (2011) 144(1):27-40. doi:10.1016/j.cell.2010.11.055.
35. Naume B, Zhao X, Synnestvedt M, Borgen E, Russnes HG, Lingjaerde OC, et al. Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer. Mol Oncol (2007) 1(2):160-71. doi:10.1016/j.molonc.2007.03.004.
36. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, et al. Molecular portraits of human breast tumours. Nature (2000) 406(6797):747-52. doi:10.1038/35021093.