TY - JOUR AU - Arnedos, M. AU - Vicier, C. AU - Loi, S. AU - Lefebvre, C. AU - Michiels, S. AU - Bonnefoi, H. PY - 2015 DA - 2015// TI - Precision medicine for metastatic breast cancer--limitations and solutions JO - Nat Rev Clin Oncol VL - 12 UR - https://doi.org/10.1038/nrclinonc.2015.123 DO - 10.1038/nrclinonc.2015.123 ID - Arnedos2015 ER - TY - JOUR AU - Harbeck, N. AU - Gnant, M. PY - 2017 DA - 2017// TI - Breast cancer JO - Lancet (London) VL - 389 UR - https://doi.org/10.1016/S0140-6736(16)31891-8 DO - 10.1016/S0140-6736(16)31891-8 ID - Harbeck2017 ER - TY - BOOK PY - 2018 DA - 2018// TI - SEER Stat Fact Sheets: Breast Cancer ID - ref3 ER - TY - JOUR AU - Sayed, R. AU - Jamal, L. AU - Iskandarani, S. AU - Kort, J. AU - Abdel Salam, M. AU - Assi, H. PY - 2019 DA - 2019// TI - Endocrine and targeted therapy for hormone-receptor-positive, HER2-negative advanced breast cancer: insights to sequencing treatment and overcoming resistance based on clinical trials JO - Front Oncol VL - 9 UR - https://doi.org/10.3389/fonc.2019.00510 DO - 10.3389/fonc.2019.00510 ID - Sayed2019 ER - TY - JOUR AU - Rivenbark, A. G. AU - O'Connor, S. M. AU - Coleman, W. B. PY - 2013 DA - 2013// TI - Molecular and cellular heterogeneity in breast cancer: challenges for personalized medicine JO - Am J Pathol VL - 183 UR - https://doi.org/10.1016/j.ajpath.2013.08.002 DO - 10.1016/j.ajpath.2013.08.002 ID - Rivenbark2013 ER - TY - JOUR AU - Ellis, M. J. PY - 2013 DA - 2013// TI - Mutational analysis of breast cancer: guiding personalized treatments JO - Breast (Edinburgh) VL - 22 UR - https://doi.org/10.1016/j.breast.2013.07.003 DO - 10.1016/j.breast.2013.07.003 ID - Ellis2013 ER - TY - JOUR AU - Vasan, N. AU - Yelensky, R. AU - Wang, K. AU - Moulder, S. AU - Dzimitrowicz, H. AU - Avritscher, R. PY - 2014 DA - 2014// TI - A targeted next-generation sequencing assay detects a high frequency of therapeutically targetable alterations in primary and metastatic breast cancers: implications for clinical practice JO - Oncologist VL - 19 UR - https://doi.org/10.1634/theoncologist.2013-0377 DO - 10.1634/theoncologist.2013-0377 ID - Vasan2014 ER - TY - JOUR AU - Yates, L. R. AU - Knappskog, S. AU - Wedge, D. AU - Farmery, J. H. R. AU - Gonzalez, S. AU - Martincorena, I. PY - 2017 DA - 2017// TI - Genomic evolution of breast cancer metastasis and relapse JO - Cancer Cell VL - 32 UR - https://doi.org/10.1016/j.ccell.2017.07.005 DO - 10.1016/j.ccell.2017.07.005 ID - Yates2017 ER - TY - JOUR AU - Basho, R. K. AU - Melllo, D. AU - Ueno, N. T. AU - Wathoo, C. AU - Chen, H. AU - Shariati, M. PY - 2016 DA - 2016// TI - Clinical outcome based on multigene profiling in metastatic breast cancer patients JO - Oncotarget. VL - 7 UR - https://doi.org/10.18632/oncotarget.12987 DO - 10.18632/oncotarget.12987 ID - Basho2016 ER - TY - JOUR AU - Bertucci, F. AU - Ng, C. K. Y. AU - Patsouris, A. AU - Droin, N. AU - Piscuoglio, S. AU - Carbuccia, N. PY - 2019 DA - 2019// TI - Genomic characterization of metastatic breast cancers JO - Nature. VL - 569 UR - https://doi.org/10.1038/s41586-019-1056-z DO - 10.1038/s41586-019-1056-z ID - Bertucci2019 ER - TY - JOUR AU - Lefebvre, C. AU - Bachelot, T. AU - Filleron, T. AU - Pedrero, M. AU - Campone, M. AU - Soria, J. C. PY - 2016 DA - 2016// TI - Mutational profile of metastatic breast cancers: a retrospective analysis JO - PLoS Med VL - 13 UR - https://doi.org/10.1371/journal.pmed.1002201 DO - 10.1371/journal.pmed.1002201 ID - Lefebvre2016 ER - TY - JOUR AU - Salgado, R. AU - Loi, S. PY - 2018 DA - 2018// TI - Tumour infiltrating lymphocytes in breast cancer: increasing clinical relevance JO - Lancet Oncol. VL - 19 UR - https://doi.org/10.1016/S1470-2045(17)30905-1 DO - 10.1016/S1470-2045(17)30905-1 ID - Salgado2018 ER - TY - JOUR AU - Condorelli, R. AU - Mosele, F. AU - Verret, B. AU - Bachelot, T. AU - Bedard, P. L. AU - Cortes, J. PY - 2019 DA - 2019// TI - Genomic alterations in breast cancer: level of evidence for actionability according to ESMO Scale for Clinical Actionability of molecular Targets (ESCAT) JO - Ann Oncol VL - 30 UR - https://doi.org/10.1093/annonc/mdz036 DO - 10.1093/annonc/mdz036 ID - Condorelli2019 ER - TY - JOUR AU - Salgado, R. AU - Denkert, C. AU - Demaria, S. AU - Sirtaine, N. AU - Klauschen, F. AU - Pruneri, G. PY - 2015 DA - 2015// TI - The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014 JO - Ann Oncol VL - 26 UR - https://doi.org/10.1093/annonc/mdu450 DO - 10.1093/annonc/mdu450 ID - Salgado2015 ER - TY - STD TI - Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):3. ID - ref15 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2009 DA - 2009// TI - Fast and accurate short read alignment with Burrows-Wheeler transform JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp324 DO - 10.1093/bioinformatics/btp324 ID - Li2009 ER - TY - JOUR AU - McKenna, A. AU - Hanna, M. AU - Banks, E. AU - Sivachenko, A. AU - Cibulskis, K. AU - Kernytsky, A. PY - 2010 DA - 2010// TI - The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.107524.110 DO - 10.1101/gr.107524.110 ID - McKenna2010 ER - TY - BOOK PY - 2019 DA - 2019// TI - Picard Toolkit.: GitHub Repository ID - ref18 ER - TY - JOUR AU - Lai, Z. AU - Markovets, A. AU - Ahdesmaki, M. AU - Chapman, B. AU - Hofmann, O. AU - McEwen, R. PY - 2016 DA - 2016// TI - VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw227 DO - 10.1093/nar/gkw227 ID - Lai2016 ER - TY - JOUR AU - Wang, K. AU - Li, M. AU - Hakonarson, H. PY - 2010 DA - 2010// TI - ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq603 DO - 10.1093/nar/gkq603 ID - Wang2010 ER - TY - JOUR AU - Kuilman, T. AU - Velds, A. AU - Kemper, K. AU - Ranzani, M. AU - Bombardelli, L. AU - Hoogstraat, M. PY - 2015 DA - 2015// TI - CopywriteR: DNA copy number detection from off-target sequence data JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0617-1 DO - 10.1186/s13059-015-0617-1 ID - Kuilman2015 ER - TY - JOUR AU - Auton, A. AU - Brooks, L. D. AU - Durbin, R. M. AU - Garrison, E. P. AU - Kang, H. M. AU - Korbel, J. O. PY - 2015 DA - 2015// TI - A global reference for human genetic variation JO - Nature. VL - 526 UR - https://doi.org/10.1038/nature15393 DO - 10.1038/nature15393 ID - Auton2015 ER - TY - STD TI - NHLBI GO Exome Sequencing Project (ESP). Exome variant server. Seattle: National Heart, Lung and Blood Institute. Available from: http://evs.gs.washington.edu/EVS/. Accessed 10 Apr 2019. UR - http://evs.gs.washington.edu/EVS/ ID - ref23 ER - TY - JOUR AU - Robinson, J. T. AU - Thorvaldsdottir, H. AU - Winckler, W. AU - Guttman, M. AU - Lander, E. S. AU - Getz, G. PY - 2011 DA - 2011// TI - Integrative genomics viewer JO - Nat Biotechnol VL - 29 UR - https://doi.org/10.1038/nbt.1754 DO - 10.1038/nbt.1754 ID - Robinson2011 ER - TY - JOUR AU - Landrum, M. J. AU - Lee, J. M. AU - Benson, M. AU - Brown, G. R. AU - Chao, C. AU - Chitipiralla, S. PY - 2018 DA - 2018// TI - ClinVar: improving access to variant interpretations and supporting evidence JO - Nucleic Acids Res VL - 46 UR - https://doi.org/10.1093/nar/gkx1153 DO - 10.1093/nar/gkx1153 ID - Landrum2018 ER - TY - JOUR AU - Forbes, S. A. AU - Beare, D. AU - Gunasekaran, P. AU - Leung, K. AU - Bindal, N. AU - Boutselakis, H. PY - 2015 DA - 2015// TI - COSMIC: exploring the world’s knowledge of somatic mutations in human cancer JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1075 DO - 10.1093/nar/gku1075 ID - Forbes2015 ER - TY - STD TI - Chakravarty D, Gao J, Phillips SM, Kundra R, Zhang H, Wang J, et al. OncoKB: a precision oncology knowledge base. JCO Precis Oncol. 2017;2017. https://doi.org/10.1200/PO.17.00011. ID - ref27 ER - TY - JOUR AU - Mayakonda, A. AU - Lin, D. C. AU - Assenov, Y. AU - Plass, C. AU - Koeffler, H. P. PY - 2018 DA - 2018// TI - Maftools: efficient and comprehensive analysis of somatic variants in cancer JO - Genome Res VL - 28 UR - https://doi.org/10.1101/gr.239244.118 DO - 10.1101/gr.239244.118 ID - Mayakonda2018 ER - TY - JOUR AU - Dees, N. D. AU - Zhang, Q. AU - Kandoth, C. AU - Wendl, M. C. AU - Schierding, W. AU - Koboldt, D. C. PY - 2012 DA - 2012// TI - MuSiC: identifying mutational significance in cancer genomes JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.134635.111 DO - 10.1101/gr.134635.111 ID - Dees2012 ER - TY - JOUR AU - Leiserson, M. D. AU - Wu, H. T. AU - Vandin, F. AU - Raphael, B. J. PY - 2015 DA - 2015// TI - CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0700-7 DO - 10.1186/s13059-015-0700-7 ID - Leiserson2015 ER - TY - JOUR AU - Sanchez-Vega, F. AU - Mina, M. AU - Armenia, J. AU - Chatila, W. K. AU - Luna, A. AU - La, K. C. PY - 2018 DA - 2018// TI - Oncogenic signaling pathways in The Cancer Genome Atlas JO - Cell VL - 173 UR - https://doi.org/10.1016/j.cell.2018.03.035 DO - 10.1016/j.cell.2018.03.035 ID - Sanchez-Vega2018 ER - TY - JOUR AU - Loi, S. AU - Drubay, D. AU - Adams, S. AU - Pruneri, G. AU - Francis, P. A. AU - Lacroix-Triki, M. PY - 2019 DA - 2019// TI - Tumor-infiltrating lymphocytes and prognosis: a pooled individual patient analysis of early-stage triple-negative breast cancers JO - J Clin Oncol VL - 37 UR - https://doi.org/10.1200/JCO.18.01010 DO - 10.1200/JCO.18.01010 ID - Loi2019 ER - TY - JOUR AU - Luen, S. J. AU - Salgado, R. AU - Fox, S. AU - Savas, P. AU - Eng-Wong, J. AU - Clark, E. PY - 2017 DA - 2017// TI - Tumour-infiltrating lymphocytes in advanced HER2-positive breast cancer treated with pertuzumab or placebo in addition to trastuzumab and docetaxel: a retrospective analysis of the CLEOPATRA study JO - Lancet Oncol VL - 18 UR - https://doi.org/10.1016/S1470-2045(16)30631-3 DO - 10.1016/S1470-2045(16)30631-3 ID - Luen2017 ER - TY - JOUR AU - Zehir, A. AU - Benayed, R. AU - Shah, R. H. AU - Syed, A. AU - Middha, S. AU - Kim, H. R. PY - 2017 DA - 2017// TI - Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients JO - Nat Med VL - 23 UR - https://doi.org/10.1038/nm.4333 DO - 10.1038/nm.4333 ID - Zehir2017 ER - TY - STD TI - Dustin D, Gu G, Fuqua SAW. ESR1 mutations in breast cancer. Cancer. 2019;125:3714–28. ID - ref35 ER - TY - JOUR AU - Zundelevich, A. AU - Dadiani, M. AU - Kahana-Edwin, S. AU - Itay, A. AU - Sella, T. AU - Gadot, M. PY - 2020 DA - 2020// TI - ESR1 mutations are frequent in newly diagnosed metastatic and loco-regional recurrence of endocrine-treated breast cancer and carry worse prognosis JO - Breast cancer Res VL - 22 UR - https://doi.org/10.1186/s13058-020-1246-5 DO - 10.1186/s13058-020-1246-5 ID - Zundelevich2020 ER - TY - JOUR AU - Loibl, S. AU - Turner, N. C. AU - Ro, J. AU - Cristofanilli, M. AU - Iwata, H. AU - Im, S. A. PY - 2017 DA - 2017// TI - Palbociclib combined with fulvestrant in premenopausal women with advanced breast cancer and prior progression on endocrine therapy: PALOMA-3 results JO - Oncologist VL - 22 UR - https://doi.org/10.1634/theoncologist.2017-0072 DO - 10.1634/theoncologist.2017-0072 ID - Loibl2017 ER - TY - JOUR AU - Cristofanilli, M. AU - DeMichele, A. AU - Giorgetti, C. AU - Turner, N. C. AU - Slamon, D. J. AU - Im, S. A. PY - 2018 DA - 2018// TI - Predictors of prolonged benefit from palbociclib plus fulvestrant in women with endocrine-resistant hormone receptor-positive/human epidermal growth factor receptor 2-negative metastatic breast cancer in PALOMA-3 JO - Eur J Cancer VL - 104 UR - https://doi.org/10.1016/j.ejca.2018.08.011 DO - 10.1016/j.ejca.2018.08.011 ID - Cristofanilli2018 ER - TY - JOUR AU - Dieras, V. AU - Rugo, H. S. AU - Schnell, P. AU - Gelmon, K. AU - Cristofanilli, M. AU - Loi, S. PY - 2019 DA - 2019// TI - Long-term pooled safety analysis of palbociclib in combination with endocrine therapy for HR+/HER2- advanced breast cancer JO - J Natl Cancer Inst VL - 111 UR - https://doi.org/10.1093/jnci/djy109 DO - 10.1093/jnci/djy109 ID - Dieras2019 ER - TY - JOUR AU - Mayer, I. A. AU - Abramson, V. G. AU - Formisano, L. AU - Balko, J. M. AU - Estrada, M. V. AU - Sanders, M. E. PY - 2017 DA - 2017// TI - A phase Ib study of alpelisib (BYL719), a PI3Kalpha-specific inhibitor, with letrozole in ER+/HER2- metastatic breast cancer JO - Clin Cancer Res VL - 23 UR - https://doi.org/10.1158/1078-0432.CCR-16-0134 DO - 10.1158/1078-0432.CCR-16-0134 ID - Mayer2017 ER - TY - JOUR AU - Andre, F. AU - Ciruelos, E. AU - Rubovszky, G. AU - Campone, M. AU - Loibl, S. AU - Rugo, H. S. PY - 2019 DA - 2019// TI - Alpelisib for PIK3CA-mutated, hormone receptor-positive advanced breast cancer JO - N Engl J Med VL - 380 UR - https://doi.org/10.1056/NEJMoa1813904 DO - 10.1056/NEJMoa1813904 ID - Andre2019 ER - TY - JOUR AU - Pellegrino, B. AU - Musolino, A. AU - Llop-Guevara, A. AU - Serra, V. AU - Silva, P. AU - Hlavata, Z. PY - 2020 DA - 2020// TI - Homologous recombination repair deficiency and the immune response in breast cancer: a literature review JO - Transl Oncol VL - 13 UR - https://doi.org/10.1016/j.tranon.2019.10.010 DO - 10.1016/j.tranon.2019.10.010 ID - Pellegrino2020 ER - TY - JOUR AU - Shen, H. AU - Yang, E. S. AU - Conry, M. AU - Fiveash, J. AU - Contreras, C. AU - Bonner, J. A. PY - 2019 DA - 2019// TI - Predictive biomarkers for immune checkpoint blockade and opportunities for combination therapies JO - Genes Dis VL - 6 UR - https://doi.org/10.1016/j.gendis.2019.06.006 DO - 10.1016/j.gendis.2019.06.006 ID - Shen2019 ER - TY - JOUR AU - Condorelli, R. AU - Spring, L. AU - O'Shaughnessy, J. AU - Lacroix, L. AU - Bailleux, C. AU - Scott, V. PY - 2018 DA - 2018// TI - Polyclonal RB1 mutations and acquired resistance to CDK 4/6 inhibitors in patients with metastatic breast cancer JO - Ann Oncol VL - 29 UR - https://doi.org/10.1093/annonc/mdx784 DO - 10.1093/annonc/mdx784 ID - Condorelli2018 ER - TY - JOUR AU - O'Leary, B. AU - Cutts, R. J. AU - Liu, Y. AU - Hrebien, S. AU - Huang, X. AU - Fenwick, K. PY - 2018 DA - 2018// TI - The genetic landscape and clonal evolution of breast cancer resistance to palbociclib plus fulvestrant in the PALOMA-3 trial JO - Cancer Discov VL - 8 UR - https://doi.org/10.1158/2159-8290.CD-18-0264 DO - 10.1158/2159-8290.CD-18-0264 ID - O'Leary2018 ER - TY - STD TI - Oliveira KCS, Ramos IB, Silva JMC, Barra WF, Riggins GJ, Palande V, et al. Current perspectives on circulating tumor DNA, precision medicine, and personalized clinical management of cancer. Mol Cancer Res. 2020;18:517-28. ID - ref46 ER -