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ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients
Springer Science and Business Media LLC - Tập 7 - Trang 1-15 - 2015
Vinay Varadan, Salendra Singh, Arman Nosrati, Lakshmeswari Ravi, James Lutterbaugh, Jill S. Barnholtz-Sloan, Sanford D. Markowitz, Joseph E. Willis, Kishore Guda
Reliable detection of somatic copy-number alterations (sCNAs) in tumors using whole-exome sequencing (WES) remains challenging owing to technical (inherent noise) and sample-associated variability in WES data. We present a novel computational framework, ENVE, which models inherent noise in any WES dataset, enabling robust detection of sCNAs across WES platforms. ENVE achieved high concordance with...... hiện toàn bộ
The public health utility of genome-wide association study results for smoking behavior
Springer Science and Business Media LLC - Tập 2 - Trang 1-3 - 2010
Helena Furberg, Jamie Ostroff, Caryn Lerman, Patrick F Sullivan
New approaches to improve smoking cessation rates are needed. In recent years, substantial progress has been made in understanding the genetics of smoking behavior, and this knowledge may eventually be used to personalize treatment for smokers. Although there are highly significant and reproducible genetic associations, none are yet ready for clinical applications. We suggest that translational re...... hiện toàn bộ
De novo and rare mutations in the HSPA1L heat shock gene associated with inflammatory bowel disease
Springer Science and Business Media LLC - Tập 9 - Trang 1-11 - 2017
Shinichi Takahashi, Gaia Andreoletti, Rui Chen, Yoichi Munehira, Akshay Batra, Nadeem A. Afzal, R. Mark Beattie, Jonathan A. Bernstein, Sarah Ennis, Michael Snyder
Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disease of the gastrointestinal tract which includes ulcerative colitis and Crohn's disease. Genetic risk factors for IBD are not well understood. We performed a family-based whole exome sequencing (WES) analysis on a core family (Family A) to identify potential causal mutations and then analyzed exome data from a Caucasian pedi...... hiện toàn bộ
Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes
Springer Science and Business Media LLC - Tập 9 Số 1 - Trang 1-19 - 2017
Rahman, Mumtahena, MacNeil, Shelley M., Jenkins, David F., Shrestha, Gajendra, Wyatt, Sydney R., McQuerry, Jasmine A., Piccolo, Stephen R., Heiser, Laura M., Gray, Joe W., Johnson, W. Evan, Bild, Andrea H.
The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components, or pathways, and the inability to study complex signaling networks in patient tumors. Here, pathway-specific genomic signatures were used to interrogate GFRN activity in breast tumors and th...... hiện toàn bộ
From GWAS to the clinic: risk factors for intracranial aneurysms
Springer Science and Business Media LLC - - 2010
Ynte M. Ruigrok, Gabriël J.E. Rinkel
Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing
Springer Science and Business Media LLC - Tập 15 - Trang 1-25 - 2023
Junjie Hu, Lele Zhang, Haoran Xia, Yilv Yan, Xinsheng Zhu, Fenghuan Sun, Liangdong Sun, Shuangyi Li, Dianke Li, Jin Wang, Ya Han, Jing Zhang, Dongliang Bian, Huansha Yu, Yan Chen, Pengyu Fan, Qiang Ma, Gening Jiang, Chenfei Wang, Peng Zhang
Immunotherapy has revolutionized cancer treatment, but most patients are refractory to immunotherapy or acquire resistance, with the underlying mechanisms remaining to be explored. We characterized the transcriptomes of ~92,000 single cells from 3 pre-treatment and 12 post-treatment patients with non-small cell lung cancer (NSCLC) who received neoadjuvant PD-1 blockade combined with chemotherapy. ...... hiện toàn bộ
Multiple PIK3CA mutation clonality correlates with outcomes in taselisib + fulvestrant-treated ER+/HER2–, PIK3CA-mutated breast cancers
Springer Science and Business Media LLC - Tập 15 - Trang 1-14 - 2023
Katherine E. Hutchinson, Jessica W. Chen, Heidi M. Savage, Thomas J. Stout, Frauke Schimmoller, Javier Cortés, Susan Dent, Nadia Harbeck, William Jacot, Ian Krop, Sally E. Trabucco, Smruthy Sivakumar, Ethan S. Sokol, Timothy R. Wilson
Mutations in the p110α catalytic subunit of phosphatidylinositol 3-kinase (PI3K), encoded by the PIK3CA gene, cause dysregulation of the PI3K pathway in 35–40% of patients with HR+/HER2– breast cancer. Preclinically, cancer cells harboring double or multiple PIK3CA mutations (mut) elicit hyperactivation of the PI3K pathway leading to enhanced sensitivity to p110α inhibitors. To understand the role...... hiện toàn bộ
De novo variants in exomes of congenital heart disease patients identify risk genes and pathways
Springer Science and Business Media LLC - Tập 12 - Trang 1-18 - 2020
Cigdem Sevim Bayrak, Peng Zhang, Martin Tristani-Firouzi, Bruce D. Gelb, Yuval Itan
Congenital heart disease (CHD) affects ~ 1% of live births and is the most common birth defect. Although the genetic contribution to the CHD has been long suspected, it has only been well established recently. De novo variants are estimated to contribute to approximately 8% of sporadic CHD. CHD is genetically heterogeneous, making pathway enrichment analysis an effective approach to explore and st...... hiện toàn bộ
Concentration of endogenous estrogens and estrogen metabolites in the NCI-60 human tumor cell lines
Springer Science and Business Media LLC - Tập 4 Số 4 - Trang 31 - 2012
Xia Xu, Timothy D. Veenstra
Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types
Springer Science and Business Media LLC - Tập 8 - Trang 1-12 - 2016
Abel Gonzalez-Perez
Large tumor genome sequencing projects have now uncovered a few hundred genes involved in the onset of tumorigenesis, or drivers, in some two dozen malignancies. One of the main challenges emerging from this catalog of drivers is how to make sense of their heterogeneity in most cancer types. This is key not only to understand how carcinogenesis appears and develops in these malignancies to be able...... hiện toàn bộ
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