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@article{liu_pam50_2016,
title = {{PAM}50 gene signatures and breast cancer prognosis with adjuvant anthracycline- and taxane-based chemotherapy: correlative analysis of C9741 (Alliance)},
volume = {2},
rights = {2016 Nature Publishing Group},
url = {https://www.nature.com/articles/npjbcancer201523},
doi = {10.1038/npjbcancer.2015.23},
shorttitle = {{PAM}50 gene signatures and breast cancer prognosis with adjuvant anthracycline- and taxane-based chemotherapy},
abstract = {{PAM}50 intrinsic breast cancer subtypes are prognostic independent of standard clinicopathologic factors. {CALGB} 9741 demonstrated improved recurrence-free ({RFS}) and overall survival ({OS}) with 2-weekly dose-dense ({DD}) versus 3-weekly therapy. A significant interaction between intrinsic subtypes and {DD}-therapy benefit was hypothesized. Suitable tumor samples were available from 1,471 (73\%) of 2,005 subjects. Multiplexed gene-expression profiling generated the {PAM}50 subtype call, proliferation score, and risk of recurrence score ({ROR}-{PT}) for the evaluable subset of 1,311 treated patients. The interaction between {DD}-therapy benefit and intrinsic subtype was tested in a Cox proportional hazards model using two-sided alpha=0.05. Additional multivariable Cox models evaluated the proliferation and {ROR}-{PT} scores as continuous measures with selected clinical covariates. Improved outcomes for {DD} therapy in the evaluable subset mirrored results from the complete data set ({RFS}; hazard ratio=1.20; 95\% confidence interval=0.99–1.44) with 12.3-year median follow-up. Intrinsic subtypes were prognostic of {RFS} (P{\textless}0.0001) irrespective of treatment assignment. No subtype-specific treatment effect on {RFS} was identified (interaction P=0.44). Proliferation and {ROR}-{PT} scores were prognostic for {RFS} (both P{\textless}0.0001), but no association with treatment benefit was seen (P=0.14 and 0.59, respectively). Results were similar for {OS}. The prognostic value of {PAM}50 intrinsic subtype was greater than estrogen receptor/{HER}2 immunohistochemistry classification. {PAM}50 gene signatures were highly prognostic but did not predict for improved outcomes with {DD} anthracycline- and taxane-based therapy. Clinical validation studies will assess the ability of {PAM}50 and other gene signatures to stratify patients and individualize treatment based on expected risks of distant recurrence.},
pages = {15023},
journaltitle = {npj Breast Cancer},
author = {Liu, Minetta C. and Pitcher, Brandelyn N. and Mardis, Elaine R. and Davies, Sherri R. and Friedman, Paula N. and Snider, Jacqueline E. and Vickery, Tammi L. and Reed, Jerry P. and {DeSchryver}, Katherine and Singh, Baljit and Gradishar, William J. and Perez, Edith A. and Martino, Silvana and Citron, Marc L. and Norton, Larry and Winer, Eric P. and Hudis, Clifford A. and Carey, Lisa A. and Bernard, Philip S. and Nielsen, Torsten O. and Perou, Charles M. and Ellis, Matthew J. and Barry, William T.},
urldate = {2019-03-28},
date = {2016-01-06},
langid = {english}
}
@article{barrett_ncbi_2013,
title = {{NCBI} {GEO}: archive for functional genomics data sets—update},
volume = {41},
issn = {0305-1048},
url = {https://academic.oup.com/nar/article/41/D1/D991/1067995},
doi = {10.1093/nar/gks1193},
shorttitle = {{NCBI} {GEO}},
abstract = {Abstract. The Gene Expression Omnibus ({GEO}, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-gen},
pages = {D991--D995},
issue = {D1},
journaltitle = {Nucleic Acids Research},
shortjournal = {Nucleic Acids Res},
author = {Barrett, Tanya and Wilhite, Stephen E. and Ledoux, Pierre and Evangelista, Carlos and Kim, Irene F. and Tomashevsky, Maxim and Marshall, Kimberly A. and Phillippy, Katherine H. and Sherman, Patti M. and Holko, Michelle and Yefanov, Andrey and Lee, Hyeseung and Zhang, Naigong and Robertson, Cynthia L. and Serova, Nadezhda and Davis, Sean and Soboleva, Alexandra},
urldate = {2019-03-28},
date = {2013-01-01},
langid = {english}
}
@article{bruce_identification_2015,
title = {Identification of a {microRNA} signature associated with risk of distant metastasis in nasopharyngeal carcinoma},
volume = {6},
issn = {1949-2553},
url = {http://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path[]=3005&pubmed-linkout=1},
doi = {10.18632/oncotarget.3005},
abstract = {Oncotarget {\textbar} https://doi.org/10.18632/oncotarget.3005 Jeff P. Bruce, Angela B.Y. Hui, Wei Shi, Bayardo Perez-Ordonez, Ilan Weinreb, Wei Xu, Benjamin Haibe-Kains, Daryl M. Waggott, Paul C. Boutros, Brian...},
pages = {4537--4550},
number = {6},
journaltitle = {Oncotarget},
author = {Bruce, Jeff P. and Hui, Angela B. Y. and Shi, Wei and Perez-Ordonez, Bayardo and Weinreb, Ilan and Xu, Wei and Haibe-Kains, Benjamin and Waggott, Daryl M. and Boutros, Paul C. and O’Sullivan, Brian and Waldron, John and Huang, Shao Hui and Chen, Eric X. and Gilbert, Ralph and Liu, Fei-Fei},
urldate = {2019-03-28},
date = {2015-02-20}
}
@article{geiss_direct_2008,
title = {Direct multiplexed measurement of gene expression with color-coded probe pairs},
volume = {26},
rights = {2008 Nature Publishing Group},
issn = {1546-1696},
url = {https://www.nature.com/articles/nbt1385},
doi = {10.1038/nbt1385},
abstract = {We describe a technology, the {NanoString} {nCounter} gene expression system, which captures and counts individual {mRNA} transcripts. Advantages over existing platforms include direct measurement of {mRNA} expression levels without enzymatic reactions or bias, sensitivity coupled with high multiplex capability, and digital readout. Experiments performed on 509 human genes yielded a replicate correlation coefficient of 0.999, a detection limit between 0.1 {fM} and 0.5 {fM}, and a linear dynamic range of over 500-fold. Comparison of the {NanoString} {nCounter} gene expression system with microarrays and {TaqMan} {PCR} demonstrated that the {nCounter} system is more sensitive than microarrays and similar in sensitivity to real-time {PCR}. Finally, a comparison of transcript levels for 21 genes across seven samples measured by the {nCounter} system and {SYBR} Green real-time {PCR} demonstrated similar patterns of gene expression at all transcript levels.},
pages = {317--325},
number = {3},
journaltitle = {Nature Biotechnology},
author = {Geiss, Gary K. and Bumgarner, Roger E. and Birditt, Brian and Dahl, Timothy and Dowidar, Naeem and Dunaway, Dwayne L. and Fell, H. Perry and Ferree, Sean and George, Renee D. and Grogan, Tammy and James, Jeffrey J. and Maysuria, Malini and Mitton, Jeffrey D. and Oliveri, Paola and Osborn, Jennifer L. and Peng, Tao and Ratcliffe, Amber L. and Webster, Philippa J. and Davidson, Eric H. and Hood, Leroy and Dimitrov, Krassen},
urldate = {2019-04-15},
date = {2008-03},
langid = {english}
}