Somatic gene mutation analysis of triple negative breast cancers

Breast

Volumn 29, Issue , 2016, Pages 202-207

  Dillon, J L ^a,b   Mockus, S M ^c   Ananda, G ^c   Spotlow, V ^c   Wells, W A ^a,b   Tsongalis, G J ^a,b,c   Marotti, J D ^a,b  

^a NORRIS COTTON CANCER CENTER   (United States)

^b DARTMOUTH MEDICAL SCHOOL   (United States)

^c JACKSON LABORATORY   (United States)

Author keywords

Myc; Next generation sequencing; Triple negative breast cancer

Indexed keywords

NUCLEOTIDE; PROTEIN P53; VASCULOTROPIN RECEPTOR 2; AURKA PROTEIN, HUMAN; AURORA A KINASE; DNA; KDR PROTEIN, HUMAN; TP53 PROTEIN, HUMAN;

ADULT; AGED; ARTICLE; CLINICAL ARTICLE; COPY NUMBER VARIATION; DATA BASE; DIAGNOSTIC EQUIPMENT; DNA ISOLATION; FEMALE; GENE AMPLIFICATION; GENE DELETION; GENE INSERTION; HISTOPATHOLOGY; HUMAN; MUTATIONAL ANALYSIS; NEXT GENERATION SEQUENCING; ONCOGENE C MYC; PRIORITY JOURNAL; SOMATIC MUTATION; TRIPLE NEGATIVE BREAST CANCER; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MIDDLE AGED; MUTATION; VERY ELDERLY;

ADULT; AGED; AGED, 80 AND OVER; AURORA KINASE A; DNA, NEOPLASM; FEMALE; GENE AMPLIFICATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MIDDLE AGED; MUTATION; TRIPLE NEGATIVE BREAST NEOPLASMS; TUMOR SUPPRESSOR PROTEIN P53; VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR-2;

EID: 84989948878     PISSN: 09609776     EISSN: 15323080     Source Type: Journal    
DOI: 10.1016/j.breast.2016.06.018     Document Type: Article

References (33)

1. [1] Venkitaraman, V., Triple-negative/basal-like breast cancer: clinical, pathologic and molecular features. Expert Rev Anticancer Ther 10:2 (2010), 199–207.
2. [2] Kalimutho, M., Parsons, K., Mittal, D., López, J.A., Srihari, S., Khanna, K.K., Targeted therapies for triple-negative breast cancer: combating a stubborn disease. Trends Pharmacol Sci 36 (2015), 822–846.
3. [3] Lehmann, B.D., Bauer, J.A., Chen, X., Sanders, M.E, Chakravarthy, A.B., Shyr, Y., et al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Investig 121 (2011), 2750–2767.
4. [4] Patterson, S.E., Liu, R., Statz, C.M., Durkin, D., Lakshminarayana, A., Mockus, S.M., The clinical trial landscape in oncology and connectivity of somatic mutations profiles to targeted therapies. Hum Genom, 10, 2016, 4.
5. [5] Lips, E.H., Michaut, M., Hoogstraat, M., Mulder, L., Besselink, N.J.M., Koudijs, M.J., et al. Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response. Breast Cancer Res, 17, 2015, 134.
6. [6] Siu, L.L., Conley, B.A., Boerner, S., LoRusso, P.M., Next-generation sequencing to guide clinical trials. Clin Cancer Res 21 (2015), 4536–4544.
7. [7] Hammond, M.E., Hayes, D.F., Dowsett, M., Allred, D.C., Hagerty, K.L., Badve, S., et al. American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer. Arch Pathol Lab Med 134 (2010), e48–72.
8. [8] Wolff, A.C., Hammond, M.E., Hicks, D.G., Dowsett, M., McShange, L.M., Allison, K.H., et al. Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. Arch Pathol Lab Med 138 (2014), 241–256.
9. [9] Livasy, C.A., Karaca, G., Nanda, R., Tretiakova, M.S., Olopade, O.I., Moore, D.T., et al. Phenotypic evaluation of the basal-like subtype of invasive breast carcinoma. Mod Pathol 19 (2006), 264–271.
10. [10] Ananda, G., Mockus, S., Lundquist, M., Spotlow, V., Simons, A., Mitchell, T., et al. Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors. Exp Mol Pathol 98 (2015), 106–112.
11. [11] McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20 (2010), 1297–12303.
12. [12] DePristo, M.A., Banks, E., Poplin, R., Garimella, K.V., Maguire, J.R., Hartl, C., et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43 (2011), 491–498.
13. [13] Ye, K., Schulz, M.H., Long, Q., Apweiler, R., Ning, Z., Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25 (2009), 2865–2871.
14. [14] Li, J., Lupat, R., Amarasinghe, K.C., Thompson, E.R., Doyle, M.A., Ryland, G.L., et al. CONTRA: copy number analysis for targeted resequencing. Bioinformatics 28 (2012), 1307–1313.
15. [15] Mi, H., Muruganujan, A., Thomas, P.D., PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 41 (2013), D377–D386.
16. [16] Xu, J., Chen, Y., Olopade, O.I., MYC and breast cancer. Genes Cancer 1 (2010), 629–640.
17. [17] Liao, D.J., Dickson, R.B., c-MYC in breast cancer. Endocr Relat 7 (2000), 143–164.
18. [18] Badve, S., Dabbs, D.J., Schnitt, S.J., Baehner, F.L., Decker, T., Eusebi, V., et al. Basal-like and triple-negative breast cancers: a critical review with an emphasis on the implications for pathologists and oncologists. Mod Pathol 24 (2011), 157–167.
19. [19] Shah, S.P., Roth, A., Goya, R., Oloumi, A., Ha, G., Zhao, Y., et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486 (2012), 395–399.
20. [20] Weisman, P.S., Ng, C.K., Brogi, E., Eisenberg, R.E., Won, H.H., Piscuoglio, S., et al. Genetic alterations of triple negative breast cancer by targeted next-generation sequencing and correlation with tumor morphology. Mod Pathol 29 (2016), 476–488.
21. [21] Roy-Chowdhuri, S., de Melo Gagliato, D., Routbort, M.J., Patel, K.P., Singh, R.R., Broaddus, R., et al. Multigene clinical mutational profile of breast carcinoma using next-generation sequencing. Am J Clin Pathol 144 (2015), 713–721.
22. [22] Cancer Genome Atlas Network, Comprehensive molecular portraits of human breast tumours. Nature 490 (2012), 61–70.
23. [23] Tsimberidou, A.M., Iskander, N.G., Hong, D.S., Wheler, J.J., Falchook, G.S., Fu, S., et al. Personalized medicine in phase I clinical trials program: the MD Anderson Cancer Center initiative. Clin Cancer Res 18 (2012), 6373–6383.
24. [24] Andre, F., Bachelot, T., Commo, F., Campone, M., Arnedos, M., Dieras, V., et al. Comparative genomic hybridization array and DNA sequencing to direct treatment of metastatic breast cancer: a multicenter, prospective trial (SAFIR01/UNICANCER). Lancet Oncol 15 (2014), 267–274.
25. [25] ClinicalTrials.gov. AURORA: Aiming to Understand the Molecular Aberrations in Metastatic Breast Cancer. (AURORA). https://clinicaltrials.gov/ct2/show/NCT02102165 [accessed 06.10.16].
26. [26] Tafe, L.J., Gorlov, I.P., De Abreu, F.B., Lefferts, J.A., Liu, X., Pettus, J.R., et al. Implementation of a molecular tumor board: the impact on treatment decisions for 35 patients evaluated at Dartmouth-Hitchcock Medical Center. Oncologist 20 (2015), 1011–1018.
27. [27] Dai, Z.J., Kang, H.F., Wang, X.J., Shao, Y.P., Lin, S., Zhao, Y., et al. Association between genetic polymorphisms in AURKA (rs2273535 and rs1047972) and breast cancer risk: a meta-analysis involving 37,221 subjects. Cancer Cell Int, 14, 2014, 91.
28. [28] Kimura, M.T., Mori, T., Conroy, J., Nowak, N.J., Satomi, S., Tamai, K., et al. Two functional coding single nucleotide polymorphisms in STK15 (Aurora-A) coordinately increase esophageal cancer risk. Caner Res 65 (2005), 3548–3554.
29. [29] Ewart-Toland, A., Briassouli, P., de Koning, J.P., Mao, J.H., Yuan, J., Chan, F., et al. Identification of Stk6/STK15 as a candidate low-penetrance tumor-susceptibility gene in mouse and human. Nat Genet 34 (2003), 403–412.
30. [30] Zheng, F., Yue, C., Li, G., He, B., Cheng, W., Wang, X., et al. Nuclear AURKA acquires kinase-independent transactivating function to enhance breast cancer stem cell phenotype. Nat Commun, 7, 2016, 10180.
31. [31] Opyrchal, M., Divya Guruswamy Sangameswaran, K., Khoury, T., Boland, P., Galanis, E., Haddad, T.C., et al. Aurora kinase inhibitors in breast cancer treatment. Am J Hematol/Oncol 11 (2015), 14–18.
32. [32] Silva, I.P., Salhi, A., Giles, K.M., Vogelsang, M., Han, S.W., Ismaili, N., et al. Identification of a novel pathogenic germline KDR variant in melanoma. Clin Cancer Res 22 (2016), 2377–2385.
33. [33] Glubb, D.M., Cerri, E., Giese, A., Zhang, W., Mirza, O., Thompson, E.E., et al. Novel functional germline variants in the VEGF receptor 2 gene and their effect on gene expression and microvessel density in lung cancer. Clin Cancer Res 17 (2011), 5257–5267.