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Oncogenomics

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https://www.readbyqxmd.com/read/29610397/the-era-of-precision-oncogenomics
#1
John C Carpten, Elaine R Mardis
No abstract text is available yet for this article.
April 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29610396/precision-oncogenomics-in-pediatrics-a-personal-reflection
#2
Cindy Campbell, Jeffrey P Greenfield
Cindy Campbell, a bereaved parent who lost her son to a rare pediatric brain tumor, shares her experience and frustration over the lack of treatment options and minimal research funding in pediatric oncology. She invites Dr. Jeffrey P. Greenfield to reflect on the situation and share his professional experiences pertaining to advances in oncogenomics and pediatric brain tumors. They share a passion for making this technology available to all pediatric brain tumor patients in the future and using data to inform treatment protocols and improve outcomes...
April 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29610395/the-future-of-cancer-treatment-using-precision-oncogenomics
#3
Lukas D Wartman
Clinicians should soon have the opportunity to use precision oncogenomics to tailor the optimal cancer treatment to a specific patient. Precision oncogenomics will incorporate different sequencing platforms depending on the goal of the sequencing result. For example, the sequencing strategy used in immuno-oncology for the design of a tumor-specific vaccine may be different than that used by oncologists following a patient for clearance of mutations from circulating tumor DNA in the peripheral blood. I will provide a broad overview of several of the ways that precision oncogenomics is likely to influence the field of oncology over the next several years building off the experience at the Genomics Tumor Board at Washington University in St...
April 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29610392/personalized-oncogenomic-analysis-of-metastatic-adenoid-cystic-carcinoma-using-whole-genome-sequencing-to-inform-clinical-decision-making
#4
Manik Chahal, Erin Pleasance, Jasleen Grewal, Eric Zhao, Tony Ng, Erin Chapman, Martin R Jones, Yaoqing Shen, Karen L Mungall, Melika Bonakdar, Gregory A Taylor, Yussanne Ma, Andrew J Mungall, Richard A Moore, Howard Lim, Daniel Renouf, Stephen Yip, Steven J M Jones, Marco A Marra, Janessa Laskin
Metastatic adenoid cystic carcinomas (ACCs) can cause significant morbidity and mortality. Because of their slow growth and relative rarity, there is limited evidence for systemic therapy regimens. Recently, molecular profiling studies have begun to reveal the genetic landscape of these poorly understood cancers, and new treatment possibilities are beginning to emerge. The objective is to use whole-genome and transcriptome sequencing and analysis to better understand the genetic alterations underlying the pathology of metastatic and rare ACCs and determine potentially actionable therapeutic targets...
April 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29581789/integrated-oncogenomic-profiling-of-copy-numbers-and-gene-expression-in-lung-adenocarcinomas-without-egfr-mutations-or-alk-fusion
#5
Yanzhuo Luo, Bingjin Li, Guangxin Zhang, Yuxiao He, Jeeyoo Hope Bae, Fengping Hu, Ranji Cui, Runhua Liu, Zhou Wang, Lizhong Wang
Targeted therapies based on EGFR mutations or on the ALK fusion oncogene have become the standard treatment for certain patients with lung adenocarcinoma (LUAD). However, most LUAD patients have no EGFR mutation or ALK fusion, and their oncogenetic alterations remain to be characterized. Here we conducted an integrated analysis of public datasets to assess the genomic alterations of 23 highly lung cancer-associated genes. The copy numbers of these genes were measured in ten micro-dissected, paired tumors and normal lung tissues of LUAD patients without EGFR mutations or ALK fusion...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29564830/chromothripsis-detection-and-characterization-using-the-ctlpscanner-web-server
#6
Jian Yang, Bo Liu, Haoyang Cai
Accurate detection of chromothripsis event is important to study the mechanisms underlying this phenomenon. CTLPScanner ( http://cgma.scu.edu.cn/CTLPScanner/ ) is a web-based tool for identification and annotation of chromothripsis-like pattern (CTLP) in genomic array data. In this chapter, we illustrate the utility of CTLPScanner for screening chromosome pulverization regions and give interpretation of the results. The web interface offers a set of parameters and thresholds for customized screening. We also provide practical recommendations for effective chromothripsis detection...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29535424/comprehensive-genomic-profiling-of-neuroendocrine-bladder-cancer-pinpoints-molecular-origin-and-potential-therapeutics
#7
Peiye Shen, Ying Jing, Ruiyun Zhang, Mei-Chun Cai, Pengfei Ma, Haige Chen, Guanglei Zhuang
Neuroendocrine bladder cancer is a relatively rare but often lethal malignancy, with cell of origin, oncogenomic architecture and standard treatment poorly defined. Here we performed comprehensive whole-genome and transcriptome sequencing on a unique cohort of genitourinary neuroendocrine neoplasms, mainly small cell carcinomas of the urinary bladder. The mutational landscape and signatures of neuroendocrine bladder cancer strikingly resembled those in conventional urothelial carcinoma, along with typically mixed histologies, supporting a common cellular origin...
March 14, 2018: Oncogene
https://www.readbyqxmd.com/read/29484962/application-and-optimization-of-minimally-invasive-cell-free-dna-techniques-in-oncogenomics
#8
REVIEW
Manish Kumar, Yashmin Choudhury, Sankar Kumar Ghosh, Rosy Mondal
The conventional method of measuring biomarkers in malignant tissue samples has already given subversive growth in cancer diagnosis, prognosis, and therapy selection. However, the regression and heterogeneity associated with tumor tissue biopsy have urged for the development of an alternative approach. Considering the limitations, cell-free DNA has emerged as a surrogate alternative, facilitating preoperative chemoradiotherapy (p < 0.0001) treatment response in rectal cancer and detection of biomarker in lung cancer...
February 2018: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29433521/adopting-clinical-genomics-a-systematic-review-of-genomic-literacy-among-physicians-in-cancer-care
#9
Vu T Dung Ha, Julie Frizzo-Barker, Peter Chow-White
BACKGROUND: This article investigates the genomic knowledge of oncology care physicians in the adoption of clinical genomics. We apply Rogers' knowledge framework from his diffusion of innovation theory to identify three types of knowledge in the process of translation and adoption: awareness, how-to, and principles knowledge. The objectives of this systematic review are to: (1) examine the level of knowledge among physicians in clinical cancer genomics, and (2) identify potential interventions or strategies for development of genomic education for oncology practice...
February 13, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29304224/in-vitro-differentiation-of-human-oocyte-like-cells-from-oogonial-stem-cells-single-cell-isolation-and-molecular-characterization
#10
Erica Silvestris, Paola Cafforio, Stella D'Oronzo, Claudia Felici, Franco Silvestris, Giuseppe Loverro
STUDY QUESTION: Are the large cells derived from cultured DEAD box polypeptide 4 (DDX4)-positive oogonial stem cells (OSCs), isolated from the ovarian cortex of non-menopausal and menopausal women, oocyte-like cells? SUMMARY ANSWER: Under appropriate culture conditions, DDX4-positive OSCs from non-menopausal and menopausal women differentiate into large haploid oocyte-like cells expressing the major oocyte markers growth differentiation factor 9 (GDF-9) and synaptonemal complex protein 3 (SYCP3) and then enter meiosis...
January 3, 2018: Human Reproduction
https://www.readbyqxmd.com/read/29247872/proteomic-analysis-shows-constitutive-secretion-of-mif-and-p53-associated-activity-of-cox-2-lung-fibroblasts
#11
Mandar Dave, Abul B M M K Islam, Roderick V Jensen, Agueda Rostagno, Jorge Ghiso, Ashok R Amin
The differential expression of two closelyassociated cyclooxygenase isozymes, COX-1 and COX-2, exhibited functions beyond eicosanoid metabolism. We hypothesized that COX-1 or COX-2 knockout lung fibroblasts may display altered protein profiles which may allow us to further differentiate the functional roles of these isozymes at the molecular level. Proteomic analysis shows constitutive production of macrophage migration inhibitory factor (MIF) in lung fibroblasts derived from COX-2-/- but not wild-type (WT) or COX-1-/- mice...
December 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29202482/ligand-activated-bmp-signaling-inhibits-cell-differentiation-and-death-to-promote-melanoma
#12
Arvind M Venkatesan, Rajesh Vyas, Alec K Gramann, Karen Dresser, Sharvari Gujja, Sanchita Bhatnagar, Sagar Chhangawala, Camilla Borges Ferreira Gomes, Hualin Simon Xi, Christine G Lian, Yariv Houvras, Yvonne J K Edwards, April Deng, Michael Green, Craig J Ceol
Oncogenomic studies indicate that copy number variation (CNV) alters genes involved in tumor progression; however, identification of specific driver genes affected by CNV has been difficult, as these rearrangements are often contained in large chromosomal intervals among several bystander genes. Here, we addressed this problem and identified a CNV-targeted oncogene by performing comparative oncogenomics of human and zebrafish melanomas. We determined that the gene encoding growth differentiation factor 6 (GDF6), which is the ligand for the BMP family, is recurrently amplified and transcriptionally upregulated in melanoma...
January 2, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29059366/sbcddb-sleeping-beauty-cancer-driver-database-for-gene-discovery-in-mouse-models-of-human-cancers
#13
Justin Y Newberg, Karen M Mann, Michael B Mann, Nancy A Jenkins, Neal G Copeland
Large-scale oncogenomic studies have identified few frequently mutated cancer drivers and hundreds of infrequently mutated drivers. Defining the biological context for rare driving events is fundamentally important to increasing our understanding of the druggable pathways in cancer. Sleeping Beauty (SB) insertional mutagenesis is a powerful gene discovery tool used to model human cancers in mice. Our lab and others have published a number of studies that identify cancer drivers from these models using various statistical and computational approaches...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29023469/the-common-oncogenomic-program-of-notch1-and-notch3-signaling-in-t-cell-acute-lymphoblastic-leukemia
#14
Sung Hee Choi, Eric Severson, Warren S Pear, Xiaole S Liu, Jon C Aster, Stephen C Blacklow
Notch is a major oncogenic driver in T cell acute lymphoblastic leukemia (T-ALL), in part because it binds to an enhancer that increases expression of MYC. Here, we exploit the capacity of activated NOTCH1 and NOTCH3 to induce T-ALL, despite substantial divergence in their intracellular regions, as a means to elucidate a broad, common Notch-dependent oncogenomic program through systematic comparison of the transcriptomes and Notch-bound genomic regulatory elements of NOTCH1- and NOTCH3-dependent T-ALL cells...
2017: PloS One
https://www.readbyqxmd.com/read/28977985/improving-radiotherapy-in-cancer-treatment-promises-and-challenges
#15
REVIEW
Helen H W Chen, Macus Tien Kuo
Effective radiotherapy for cancer has relied on the promise of maximally eradicating tumor cells while minimally killing normal cells. Technological advancement has provided state-of-the-art instrumentation that enables delivery of radiotherapy with great precision to tumor lesions with substantial reduced injury to normal tissues. Moreover, better understanding of radiobiology, particularly the mechanisms of radiation sensitivity and resistance in tumor lesions and toxicity in normal tissues, has improved the treatment efficacy of radiotherapy...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28961038/focused-ultrasound-for-immuno-adjuvant-treatment-of-pancreatic-cancer-an-emerging-clinical-paradigm-in-the-era-of-personalized-oncotherapy
#16
Ezekiel Maloney, Tanya Khokhlova, Venu G Pillarisetty, George R Schade, Elizabeth A Repasky, Yak-Nam Wang, Lorenzo Giuliani, Matteo Primavera, Joo Ha Hwang
Current clinical treatment regimens, including many emergent immune strategies (e.g., checkpoint inhibitors) have done little to affect the devastating course of pancreatic ductal adenocarcinoma (PDA). Clinical trials for PDA often employ multi-modal treatment, and have started to incorporate stromal-targeted therapies, which have shown promising results in early reports. Focused ultrasound (FUS) is one such therapy that is uniquely equipped to address local and systemic limitations of conventional cancer therapies as well as emergent immune therapies for PDA...
November 2, 2017: International Reviews of Immunology
https://www.readbyqxmd.com/read/28950338/successful-targeting-of-the-nrg1-pathway-indicates-novel-treatment-strategy-for-metastatic-cancer
#17
M R Jones, H Lim, Y Shen, E Pleasance, C Ch'ng, C Reisle, S Leelakumari, C Zhao, S Yip, J Ho, E Zhong, T Ng, D Ionescu, D F Schaeffer, A J Mungall, K L Mungall, Y Zhao, R A Moore, Y Ma, S Chia, C Ho, D J Renouf, K Gelmon, S J M Jones, M A Marra, J Laskin
Background: NRG1 fusion-positive lung cancers have emerged as potentially actionable events in lung cancer, but clinical support is currently limited and no evidence of efficacy of this approach in cancers beyond lung has been shown. Patients and methods: Here, we describe two patients with advanced cancers refractory to standard therapies. Patient 1 had lung adenocarcinoma and patient 2 cholangiocarcinoma. Whole-genome and transcriptome sequencing were carried out for these cases with select findings validated by fluorescence in situ hybridization...
December 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28862214/respiratory-cancer-database-an-open-access-database-of-respiratory-cancer-gene-and-mirna
#18
Jyotsna Choubey, Jyoti Kant Choudhari, Ashish Patel, Mukesh Kumar Verma
AIMS: Respiratory cancer database (RespCanDB) is a genomic and proteomic database of cancer of respiratory organ. It also includes the information of medicinal plants used for the treatment of various respiratory cancers with structure of its active constituents as well as pharmacological and chemical information of drug associated with various respiratory cancers. MATERIALS AND METHODS: Data in RespCanDB has been manually collected from published research article and from other databases...
July 2017: Journal of Cancer Research and Therapeutics
https://www.readbyqxmd.com/read/28805821/opposing-effects-of-cancer-type-specific-spop-mutants-on-bet-protein-degradation-and-sensitivity-to-bet-inhibitors
#19
Hana Janouskova, Geniver El Tekle, Elisa Bellini, Namrata D Udeshi, Anna Rinaldi, Anna Ulbricht, Tiziano Bernasocchi, Gianluca Civenni, Marco Losa, Tanya Svinkina, Craig M Bielski, Gregory V Kryukov, Luciano Cascione, Sara Napoli, Radoslav I Enchev, David G Mutch, Michael E Carney, Andrew Berchuck, Boris J N Winterhoff, Russell R Broaddus, Peter Schraml, Holger Moch, Francesco Bertoni, Carlo V Catapano, Matthias Peter, Steven A Carr, Levi A Garraway, Peter J Wild, Jean-Philippe P Theurillat
It is generally assumed that recurrent mutations within a given cancer driver gene elicit similar drug responses. Cancer genome studies have identified recurrent but divergent missense mutations affecting the substrate-recognition domain of the ubiquitin ligase adaptor SPOP in endometrial and prostate cancers. The therapeutic implications of these mutations remain incompletely understood. Here we analyzed changes in the ubiquitin landscape induced by endometrial cancer-associated SPOP mutations and identified BRD2, BRD3 and BRD4 proteins (BETs) as SPOP-CUL3 substrates that are preferentially degraded by endometrial cancer-associated SPOP mutants...
September 2017: Nature Medicine
https://www.readbyqxmd.com/read/28754634/an-androgen-regulated-mir-2909-modulates-tgf%C3%AE-signalling-through-ar-mir-2909-axis-in-prostate-cancer
#20
Shiekh Gazalla Ayub, Deepak Kaul, Taha Ayub
In recent years, microRNAs (miRNAs) have emerged as promising biomarkers for PCa diagnosis and prognosis. miR-2909 is a novel miRNA that can regulate immunogenomics and oncogenomics. The present study investigated the role of miR-2909 in the pathogenesis of PCa and the potential signalling pathways through which it operates. We have identified miR-2909 as a novel mediator of androgen/androgen receptor (AR) signalling that enhances the proliferation potential of PCa cells and assists in cancer survival under reduced androgen levels...
October 5, 2017: Gene
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