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Catalog of genetic progression of human cancers: breast cancer

Abstract

With the rapid development of next-generation sequencing, deeper insights are being gained into the molecular evolution that underlies the development and clinical progression of breast cancer. It is apparent that during evolution, breast cancers acquire thousands of mutations including single base pair substitutions, insertions, deletions, copy number aberrations, and structural rearrangements. As a consequence, at the whole genome level, no two cancers are identical and few cancers even share the same complement of “driver” mutations. Indeed, two samples from the same cancer may also exhibit extensive differences due to constant remodeling of the genome over time. In this review, we summarize recent studies that extend our understanding of the genomic basis of cancer progression. Key biological insights include the following: subclonal diversification begins early in cancer evolution, being detectable even in in situ lesions; geographical stratification of subclonal structure is frequent in primary tumors and can include therapeutically targetable alterations; multiple distant metastases typically arise from a common metastatic ancestor following a “metastatic cascade” model; systemic therapy can unmask preexisting resistant subclones or influence further treatment sensitivity and disease progression. We conclude the review by describing novel approaches such as the analysis of circulating DNA and patient-derived xenografts that promise to further our understanding of the genomic changes occurring during cancer evolution and guide treatment decision making.

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References

  1. Hudson, T. J., Anderson, W., Artez, A., Barker, A. D., Bell, C., Bernabe, R. R., et al. (2010). International network of cancer genome projects. Nature, 464(7291), 993–998.

    CAS  Article  PubMed  Google Scholar 

  2. Tomczak, K., Czerwinska, P., & Wiznerowicz, M. (2015). The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemporary Oncology (Pozn), 19(1A), A68–A77.

    Google Scholar 

  3. Banerji, S., Cibulskis, K., Rangel-Escareno, C., Brown, K. K., Carter, S. L., Frederick, A. M., et al. (2012). Sequence analysis of mutations and translocations across breast cancer subtypes. Nature, 486(7403), 405–409.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. Ciriello, G., Gatza, M. L., Beck, A. H., Wilkerson, M. D., Rhie, S. K., Pastore, A., et al. (2015). Comprehensive molecular portraits of invasive lobular breast cancer. Cell, 163(2), 506–519.

    CAS  Article  PubMed  Google Scholar 

  5. Cancer Genome Atlas Network. (2012). Comprehensive molecular portraits of human breast tumours. Nature, 490(7418), 61–70.

    Article  Google Scholar 

  6. Nik-Zainal, S., Van Loo, P., Wedge, D. C., Alexandrov, L. B., Greenman, C. D., Lau, K. W., et al. (2012). The life history of 21 breast cancers. Cell, 149(5), 994–1007.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. Shah, S. P., Roth, A., Goya, R., Oloumi, A., Ha, G., Zhao, Y., et al. (2012). The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature, 486(7403), 395–399.

    CAS  PubMed  Google Scholar 

  8. Stephens, P. J., Tarpey, P. S., Davies, H., Van Loo, P., Greenman, C., Wedge, D. C., et al. (2012). The landscape of cancer genes and mutational processes in breast cancer. Nature, 486(7403), 400–404.

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Curtis, C., Shah, S. P., Chin, S. F., Turashvili, G., Rueda, O. M., Dunning, M. J., et al. (2012). The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature, 486(7403), 346–352.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Ellis, M. J., Ding, L., Shen, D., Luo, J., Suman, V. J., Wallis, J. W., et al. (2012). Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature, 486(7403), 353–360.

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Alexandrov, L. B., Nik-Zainal, S., Wedge, D. C., Aparicio, S. A., Behjati, S., Biankin, A. V., et al. (2013). Signatures of mutational processes in human cancer. Nature, 500(7463), 415–421.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  12. Stephens, P. J., McBride, D. J., Lin, M. L., Varela, I., Pleasance, E. D., Simpson, J. T., et al. (2009). Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature, 462(7276), 1005–1010.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. Yates, L. R., Gerstung, M., Knappskog, S., Desmedt, C., Gundem, G., Van Loo, P., et al. (2015). Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nature Medicine, 21(7), 751–759.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. Nik-Zainal, S., Alexandrov, L. B., Wedge, D. C., Van Loo, P., Greenman, C. D., Raine, K., et al. (2012). Mutational processes molding the genomes of 21 breast cancers. Cell, 149(5), 979–993.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. Roy, R., Chun, J., & Powell, S. N. (2012). BRCA1 and BRCA2: different roles in a common pathway of genome protection. Nature Reviews Cancer, 12(1), 68–78.

    CAS  Article  Google Scholar 

  16. Abkevich, V., Timms, K. M., Hennessy, B. T., Potter, J., Carey, M. S., Meyer, L. A., et al. (2012). Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer. British Journal of Cancer, 107(10), 1776–1782.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. Birkbak, N. J., Wang, Z. C., Kim, J. Y., Eklund, A. C., Li, Q., Tian, R., et al. (2012). Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents. Cancer Discovery, 2(4), 366–375.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. Popova, T., Manie, E., Rieunier, G., Caux-Moncoutier, V., Tirapo, C., Dubois, T., et al. (2012). Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. Cancer Research, 72(21), 5454–5462.

    CAS  Article  PubMed  Google Scholar 

  19. Watkins, J. A., Irshad, S., Grigoriadis, A., & Tutt, A. N. (2014). Genomic scars as biomarkers of homologous recombination deficiency and drug response in breast and ovarian cancers. Breast Cancer Research, 16(3), 211.

    Article  PubMed  PubMed Central  Google Scholar 

  20. Watkins, J., Weekes, D., Shah, V., Gazinska, P., Joshi, S., Sidhu, B., et al. (2015). Genomic complexity profiling reveals that HORMAD1 overexpression contributes to homologous recombination deficiency in triple-negative breast cancers. Cancer Discovery, 5(5), 488–505.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. Lawrence, M. S., Stojanov, P., Mermel, C. H., Robinson, J. T., Garraway, L. A., Golub, T. R., et al. (2013). Discovery and saturation analysis of cancer genes across 21 tumour types. Nature, 505(7484), 495–501.

    Article  Google Scholar 

  22. Zack, T. I., Schumacher, S. E., Carter, S. L., Cherniack, A. D., Saksena, G., Tabak, B., et al. (2013). Pan-cancer patterns of somatic copy number alteration. Nature Genetics, 45(10), 1134–1140.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. Desmedt, C., Zoppoli, G., Gundem, G., Pruneri, G., Larsimont, D., Fornili, M., et al. (2016). Genomic characterization of primary invasive lobular breast cancer.  Journal of Clinical Oncology. doi:10.1200/JCO.2015.64.0334.

  24. Denisov, E. V., Litviakov, N. V., Zavyalova, M. V., Perelmuter, V. M., Vtorushin, S. V., Tsyganov, M. M., et al. (2014). Intratumoral morphological heterogeneity of breast cancer: neoadjuvant chemotherapy efficiency and multidrug resistance gene expression. Science Reports, 4, 4709.

    Google Scholar 

  25. Lee, H. J., Kim, J. Y., Park, S. Y., Park, I. A., Song, I. H., Yu, J. H., et al. (2015). Clinicopathologic significance of the intratumoral heterogeneity of HER2 gene amplification in HER2-positive breast cancer patients treated with adjuvant trastuzumab. American Journal of Clinical Pathology, 144(4), 570–578.

    Article  PubMed  Google Scholar 

  26. Madaras, L., Szasz, M. A., Baranyak, Z., Tokes, A. M., Szittya, L., Lotz, G., et al. (2012). Morphological and immunophenotypical heterogeneity in breast cancers of young and elderly women. Magyar Onkologia, 56(2), 75–78.

    PubMed  Google Scholar 

  27. Desmedt, C., Fumagalli, D., Pietri, E., Zoppoli, G., Brown, D., & Nik-Zainal, S., et al. (2015). Uncovering the genomic heterogeneity of multifocal breast cancer. The Journal of Pathology, 236(4), 457–466.

  28. Ng, C. K., Martelotto, L. G., Gauthier, A., Wen, H. C., Piscuoglio, S., Lim, R. S., et al. (2015). Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification. Genome Biology, 16, 107.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Navin, N., Kendall, J., Troge, J., Andrews, P., Rodgers, L., McIndoo, J., et al. (2011). Tumour evolution inferred by single-cell sequencing. Nature, 472(7341), 90–94.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  30. Wang, Y., Waters, J., Leung, M. L., Unruh, A., Roh, W., Shi, X., et al. (2014). Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature, 512(7513), 155–160.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. Yates, L. R., & Campbell, P. J. (2012). Evolution of the cancer genome. Nature Reviews Genetics, 13(11), 795–806.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. Bea, S., Valdes-Mas, R., Navarro, A., Salaverria, I., Martin-Garcia, D., Jares, P., et al. (2013). Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. Proceedings of the National Academy of Sciences of the United States of America, 110(45), 18250–18255.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. Gerlinger, M., Horswell, S., Larkin, J., Rowan, A. J., Salm, M. P., Varela, I., et al. (2014). Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nature Genetics, 46(3), 225–233.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Cooper, C. S., Eeles, R., Wedge, D. C., Van Loo, P., Gundem, G., Alexandrov, L. B., et al. (2015). Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nature Genetics, 47(4), 367–372.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  35. Gerlinger, M., Rowan, A. J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., et al. (2012). Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. New England Journal of Medicine, 366(10), 883–892.

    CAS  Article  PubMed  Google Scholar 

  36. Sottoriva, A., Kang, H., Ma, Z., Graham, T. A., Salomon, M. P., Zhao, J., et al. (2015). A Big Bang model of human colorectal tumor growth. Nature Genetics, 47(3), 209–216.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  37. Yachida, S., & Iacobuzio-Donahue, C. A. (2013). Evolution and dynamics of pancreatic cancer progression. Oncogene, 32(45), 5253–5260.

    CAS  Article  PubMed  Google Scholar 

  38. Yachida, S., Jones, S., Bozic, I., Antal, T., Leary, R., Fu, B., et al. (2010). Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature, 467(7319), 1114–1117.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. Cottu, P. H., Asselah, J., Lae, M., Pierga, J. Y., Dieras, V., Mignot, L., et al. (2008). Intratumoral heterogeneity of HER2/neu expression and its consequences for the management of advanced breast cancer. Annals of Oncology, 19(3), 595–597.

    CAS  Article  PubMed  Google Scholar 

  40. Janiszewska, M., Liu, L., Almendro, V., Kuang, Y., Paweletz, C., Sakr, R. A., et al. (2015). In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer. Nature Genetics, 47(10), 1212–1219.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  41. Seol, H., Lee, H. J., Choi, Y., Lee, H. E., Kim, Y. J., Kim, J. H., et al. (2012). Intratumoral heterogeneity of HER2 gene amplification in breast cancer: its clinicopathological significance. Modern Pathology, 25(7), 938–948.

    CAS  Article  PubMed  Google Scholar 

  42. Cowell, C. F., Weigelt, B., Sakr, R. A., Ng, C. K., Hicks, J., King, T. A., et al. (2013). Progression from ductal carcinoma in situ to invasive breast cancer: revisited. Molecular Oncology, 7(5), 859–869.

    Article  PubMed  Google Scholar 

  43. Gorringe, K. L., Hunter, S. M., Pang, J. M., Opeskin, K., Hill, P., Rowley, S. M., et al. (2015). Copy number analysis of ductal carcinoma in situ with and without recurrence. Modern Pathology, 28(9), 1174–1184.

    CAS  Article  PubMed  Google Scholar 

  44. Waldman, F. M., DeVries, S., Chew, K. L., Moore, D. H., 2nd, Kerlikowske, K., & Ljung, B. M. (2000). Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences. Journal of the National Cancer Institute, 92(4), 313–320.

    CAS  Article  PubMed  Google Scholar 

  45. Solin, L. J., Gray, R., Baehner, F. L., Butler, S. M., Hughes, L. L., Yoshizawa, C., et al. (2013). A multigene expression assay to predict local recurrence risk for ductal carcinoma in situ of the breast. Journal of the National Cancer Institute, 105(10), 701–710.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  46. Hernandez, L., Wilkerson, P. M., Lambros, M. B., Campion-Flora, A., Rodrigues, D. N., Gauthier, A., et al. (2012). Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intra-tumour genetic heterogeneity and clonal selection. Journal of Pathology, 227(1), 42–52.

    CAS  Article  PubMed  Google Scholar 

  47. Heselmeyer-Haddad, K., Berroa Garcia, L. Y., Bradley, A., Ortiz-Melendez, C., Lee, W. J., Christensen, R., et al. (2012). Single-cell genetic analysis of ductal carcinoma in situ and invasive breast cancer reveals enormous tumor heterogeneity yet conserved genomic imbalances and gain of MYC during progression. American Journal of Pathology, 181(5), 1807–1822.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  48. Cummings, M. C., Simpson, P. T., Reid, L. E., Jayanthan, J., Skerman, J., Song, S., et al. (2014). Metastatic progression of breast cancer: insights from 50 years of autopsies. Journal of Pathology, 232(1), 23–31.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  49. Kuukasjarvi, T., Karhu, R., Tanner, M., Kahkonen, M., Schaffer, A., Nupponen, N., et al. (1997). Genetic heterogeneity and clonal evolution underlying development of asynchronous metastasis in human breast cancer. Cancer Research, 57(8), 1597–1604.

    CAS  PubMed  Google Scholar 

  50. Moelans, C. B., van der Groep, P., Hoefnagel, L. D., van de Vijver, M. J., Wesseling, P., Wesseling, J., et al. (2013). Genomic evolution from primary breast carcinoma to distant metastasis: few copy number changes of breast cancer related genes. Cancer Letters, 344(1), 138–146.

    Article  PubMed  Google Scholar 

  51. Meric-Bernstam, F., Frampton, G. M., Ferrer-Lozano, J., Yelensky, R., Perez-Fidalgo, J. A., Wang, Y., et al. (2014). Concordance of genomic alterations between primary and recurrent breast cancer. Molecular Cancer Therapeutics, 13(5), 1382–1389.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  52. Brastianos, P. K., Carter, S. L., Santagata, S., Cahill, D. P., Taylor-Weiner, A., & Jones, R. T., et al. (2015). Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets. Cancer Discovery.

  53. Ding, L., Ellis, M. J., Li, S., Larson, D. E., Chen, K., Wallis, J. W., et al. (2010). Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature, 464(7291), 999–1005.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  54. Shah, S. P., Morin, R. D., Khattra, J., Prentice, L., Pugh, T., Burleigh, A., et al. (2009). Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 461(7265), 809–813.

    CAS  Article  PubMed  Google Scholar 

  55. Naxerova, K., & Jain, R. K. (2015). Using tumour phylogenetics to identify the roots of metastasis in humans. Nature Reviews. Clinical Oncology, 12(5), 258–272.

    CAS  Article  PubMed  Google Scholar 

  56. Desmedt, C., Brown, D., Szekely, B., Smeets, D., Szasz, M. A., & Adnet, P. Y., et al. (2014). Unraveling breast cancer progression through geographical and temporal sequencing [abstract]. In: Proceedings: AACR Annual Meeting 2014; April 5–9, 2014; San Diego, a986.

  57. Juric, D., Castel, P., Griffith, M., Griffith, O. L., Won, H. H., Ellis, H., et al. (2014). Convergent loss of PTEN leads to clinical resistance to a PI(3)K alpha inhibitor. Nature, 518(7538), 240–244.

    Article  PubMed  PubMed Central  Google Scholar 

  58. Aceto, N., Bardia, A., Miyamoto, D. T., Donaldson, M. C., Wittner, B. S., Spencer, J. A., et al. (2014). Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell, 158(5), 1110–1122.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  59. Gundem, G., Van Loo, P., Kremeyer, B., Alexandrov, L. B., Tubio, J. M., Papaemmanuil, E., et al. (2015). The evolutionary history of lethal metastatic prostate cancer. Nature, 520(7547), 353–357.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  60. Alkner, S., Tang, M. H., Brueffer, C., Dahlgren, M., Chen, Y., Olsson, E., et al. (2015). Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing. Breast Cancer Research, 17(1), 102.

    Article  PubMed  PubMed Central  Google Scholar 

  61. Klevebring, D., Lindberg, J., Rockberg, J., Hilliges, C., Hall, P., Sandberg, M., et al. (2015). Exome sequencing of contralateral breast cancer identifies metastatic disease. Breast Cancer Research and Treatment, 151(2), 319–324.

    CAS  Article  PubMed  Google Scholar 

  62. Chen, Y., Thompson, W., Semenciw, R., & Mao, Y. (1999). Epidemiology of contralateral breast cancer. Cancer Epidemiology, Biomarkers & Prevention, 8(10), 855–861.

    CAS  Google Scholar 

  63. Malone, K. E., Begg, C. B., Haile, R. W., Borg, A., Concannon, P., Tellhed, L., et al. (2010). Population-based study of the risk of second primary contralateral breast cancer associated with carrying a mutation in BRCA1 or BRCA2. Journal of Clinical Oncology, 28(14), 2404–2410.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  64. Almendro, V., Cheng, Y. K., Randles, A., Itzkovitz, S., Marusyk, A., Ametller, E., et al. (2014). Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell Reports, 6(3), 514–527.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  65. Balko, J. M., Giltnane, J. M., Wang, K., Schwarz, L. J., Young, C. D., Cook, R. S., et al. (2013). Molecular profiling of the residual disease of triple-negative breast cancers after neoadjuvant chemotherapy identifies actionable therapeutic targets. Cancer Discovery, 4(2), 232–245.

    Article  PubMed  PubMed Central  Google Scholar 

  66. Jeselsohn, R., Yelensky, R., Buchwalter, G., Frampton, G., Meric-Bernstam, F., Gonzalez-Angulo, A. M., et al. (2014). Emergence of constitutively active estrogen receptor-alpha mutations in pretreated advanced estrogen receptor-positive breast cancer. Clinical Cancer Research, 20(7), 1757–1767.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  67. Merenbakh-Lamin, K., Ben-Baruch, N., Yeheskel, A., Dvir, A., Soussan-Gutman, L., Jeselsohn, R., et al. (2013). D538G mutation in estrogen receptor-alpha: a novel mechanism for acquired endocrine resistance in breast cancer. Cancer Research, 73(23), 6856–6864.

    CAS  Article  PubMed  Google Scholar 

  68. Robinson, D. R., Wu, Y. M., Vats, P., Su, F., Lonigro, R. J., Cao, X., et al. (2013). Activating ESR1 mutations in hormone-resistant metastatic breast cancer. Nature Genetics, 45(12), 1446–1451.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  69. Toy, W., Shen, Y., Won, H., Green, B., Sakr, R. A., Will, M., et al. (2013). ESR1 ligand-binding domain mutations in hormone-resistant breast cancer. Nature Genetics, 45(12), 1439–1445.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  70. Lai, A., Kahraman, M., Govek, S., Nagasawa, J., Bonnefous, C., Julien, J., et al. (2015). Identification of GDC-0810 (ARN-810), an orally bioavailable selective estrogen receptor degrader (SERD) that demonstrates robust activity in tamoxifen-resistant breast cancer xenografts. Journal of Medicinal Chemistry, 58(12), 4888–4904.

    CAS  Article  PubMed  Google Scholar 

  71. Ignatiadis, M., & Dawson, S. J. (2014). Circulating tumor cells and circulating tumor DNA for precision medicine: dream or reality? Annals of Oncology, 25(12), 2304–2313.

    CAS  Article  PubMed  Google Scholar 

  72. Bettegowda, C., Sausen, M., Leary, R. J., Kinde, I., Wang, Y., Agrawal, N., et al. (2014). Detection of circulating tumor DNA in early- and late-stage human malignancies. Science Translational Medicine, 6(224), 224ra224.

    Article  Google Scholar 

  73. Dawson, S. J., Tsui, D. W., Murtaza, M., Biggs, H., Rueda, O. M., Chin, S. F., et al. (2013). Analysis of circulating tumor DNA to monitor metastatic breast cancer. New England Journal of Medicine, 368(13), 1199–1209.

    CAS  Article  PubMed  Google Scholar 

  74. Leary, R. J., Sausen, M., Kinde, I., Papadopoulos, N., Carpten, J. D., Craig, D., et al. (2012). Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Science Translational Medicine, 4(162), 162ra154.

    Article  PubMed  PubMed Central  Google Scholar 

  75. McBride, D. J., Orpana, A. K., Sotiriou, C., Joensuu, H., Stephens, P. J., Mudie, L. J., et al. (2010). Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors. Genes, Chromosomes & Cancer, 49(11), 1062–1069.

    CAS  Article  Google Scholar 

  76. Lebofsky, R., Decraene, C., Bernard, V., Kamal, M., Blin, A., Leroy, Q., et al. (2015). Circulating tumor DNA as a non-invasive substitute to metastasis biopsy for tumor genotyping and personalized medicine in a prospective trial across all tumor types. Molecular Oncology, 9(4), 783–790.

    CAS  Article  PubMed  Google Scholar 

  77. Rothe, F., Laes, J. F., Lambrechts, D., Smeets, D., Vincent, D., Maetens, M., et al. (2014). Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer. Annals of Oncology, 25(10), 1959–1965.

    CAS  Article  PubMed  Google Scholar 

  78. Murtaza, M., Dawson, S. J., Tsui, D. W., Gale, D., Forshew, T., Piskorz, A. M., et al. (2013). Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature, 497(7447), 108–112.

    CAS  Article  PubMed  Google Scholar 

  79. Garcia-Murillas, I., Schiavon, G., Weigelt, B., Ng, C., Hrebien, S., Cutts, R. J., et al. (2015). Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer. Science Translational Medicine, 7(302), 302ra133.

    Article  PubMed  Google Scholar 

  80. Chu, D., Paoletti, C., Gersch, C., VanDenBerg, D., Zabransky, D., & Cochran, R., et al. (2016). ESR1 mutations in circulating plasma tumor DNA from metastatic breast cancer patients. Clinical Cancer Research, 22(4), 993–999.

  81. Whittle, J. R., Lewis, M. T., Lindeman, G. J., & Visvader, J. E. (2015). Patient-derived xenograft models of breast cancer and their predictive power. Breast Cancer Research, 17, 17.

    Article  PubMed  PubMed Central  Google Scholar 

  82. Eirew, P., Steif, A., Khattra, J., Ha, G., Yap, D., Farahani, H., et al. (2015). Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature, 518(7539), 422–426.

    CAS  Article  PubMed  Google Scholar 

  83. Marangoni, E., Vincent-Salomon, A., Auger, N., Degeorges, A., Assayag, F., de Cremoux, P., et al. (2007). A new model of patient tumor-derived breast cancer xenografts for preclinical assays. Clinical Cancer Research, 13(13), 3989–3998.

    CAS  Article  PubMed  Google Scholar 

  84. Zhang, X., Claerhout, S., Prat, A., Dobrolecki, L. E., Petrovic, I., Lai, Q., et al. (2013). A renewable tissue resource of phenotypically stable, biologically and ethnically diverse, patient-derived human breast cancer xenograft models. Cancer Research, 73(15), 4885–4897.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  85. Li, S., Shen, D., Shao, J., Crowder, R., Liu, W., Prat, A., et al. (2013). Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts. Cell Reports, 4(6), 1116–1130.

    CAS  Article  PubMed  Google Scholar 

  86. Bose, R., Kavuri, S. M., Searleman, A. C., Shen, W., Shen, D., Koboldt, D. C., et al. (2012). Activating HER2 mutations in HER2 gene amplification negative breast cancer. Cancer Discovery, 3(2), 224–237.

    Article  PubMed  PubMed Central  Google Scholar 

  87. Collier, T. S., Diraviyam, K., Monsey, J., Shen, W., Sept, D., & Bose, R. (2013). Carboxyl group footprinting mass spectrometry and molecular dynamics identify key interactions in the HER2-HER3 receptor tyrosine kinase interface. Journal of Biological Chemistry, 288(35), 25254–25264.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  88. Jaiswal, B. S., Kljavin, N. M., Stawiski, E. W., Chan, E., Parikh, C., Durinck, S., et al. (2013). Oncogenic ERBB3 mutations in human cancers. Cancer Cell, 23(5), 603–617.

    CAS  Article  PubMed  Google Scholar 

  89. Littlefield, P., Liu, L., Mysore, V., Shan, Y., Shaw, D. E., & Jura, N. (2014). Structural analysis of the EGFR/HER3 heterodimer reveals the molecular basis for activating HER3 mutations. Science Signaling, 7(354), ra114.

    Article  PubMed  PubMed Central  Google Scholar 

  90. Meric-Bernstam, F., Johnson, A., Holla, V., Bailey, A. M., Brusco, L., & Chen, K., et al. (2015). A decision support framework for genomically informed investigational cancer therapy. Journal of the National Cancer Institute, 107(7).

  91. Zardavas, D., Irrthum, A., Swanton, C., & Piccart, M. (2015). Clinical management of breast cancer heterogeneity. Nature Reviews. Clinical Oncology, 12(7), 381–394.

    CAS  Article  PubMed  Google Scholar 

  92. Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., et al. (2012). The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discovery, 2(5), 401–404.

    Article  PubMed  Google Scholar 

  93. Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., et al. (2013). Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science Signaling, 6(269), pl1.

    Article  PubMed  PubMed Central  Google Scholar 

  94. Arnedos, M., Vicier, C., Loi, S., Lefebvre, C., Michiels, S., & Bonnefoi, H., et al. (2015). Precision medicine for metastatic breast cancer-limitations and solutions. Nature Review Clinical Oncology, 12(12), 693–704.

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Correspondence to Christine Desmedt.

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Les Amis de Bordet, Fondation MEDIC, Susan G. Komen for the Cure, and Fonds National de Recherche Scientifique.

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Desmedt, C., Yates, L. & Kulka, J. Catalog of genetic progression of human cancers: breast cancer. Cancer Metastasis Rev 35, 49–62 (2016). https://doi.org/10.1007/s10555-016-9609-1

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  • DOI: https://doi.org/10.1007/s10555-016-9609-1

Keywords

  • Breast cancer
  • Progression
  • Genomics
  • Sequencing