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Cancer precision medicine

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https://www.readbyqxmd.com/read/27933468/conditional-screening-for-ultra-high-dimensional-covariates-with-survival-outcomes
#1
Hyokyoung G Hong, Jian Kang, Yi Li
Identifying important biomarkers that are predictive for cancer patients' prognosis is key in gaining better insights into the biological influences on the disease and has become a critical component of precision medicine. The emergence of large-scale biomedical survival studies, which typically involve excessive number of biomarkers, has brought high demand in designing efficient screening tools for selecting predictive biomarkers. The vast amount of biomarkers defies any existing variable selection methods via regularization...
December 8, 2016: Lifetime Data Analysis
https://www.readbyqxmd.com/read/27933214/integrating-next-generation-sequencing-into-clinical-oncology-strategies-promises-and-pitfalls
#2
REVIEW
Peter Horak, Stefan Fröhling, Hanno Glimm
We live in an era of genomic medicine. The past five years brought about many significant achievements in the field of cancer genetics, driven by rapidly evolving technologies and plummeting costs of next-generation sequencing (NGS). The official completion of the Cancer Genome Project in 2014 led many to envision the clinical implementation of cancer genomic data as the next logical step in cancer therapy. Stemming from this vision, the term 'precision oncology' was coined to illustrate the novelty of this individualised approach...
2016: ESMO Open
https://www.readbyqxmd.com/read/27930095/multi-omics-data-integration-and-mapping-of-altered-kinases-to-pathways-reveal-gonadotropin-hormone-signaling-in-glioblastoma
#3
Savita Jayaram, Manoj Kumar Gupta, Rajesh Raju, Poonam Gautam, Ravi Sirdeshmukh
Glioblastoma multiforme (GBM) is one of the most lethal brain tumors with an inadequately understood pathophysiology. Biomarkers that guide accurate diagnosis and treatment decisions would greatly support precision medicine for GBM. Previous studies of GBM have focused on signaling pathways such as epidermal growth factor receptor (EGFR), platelet-derived growth factor receptors (PDGFRs), notch, wnt, and others, identified with single omics technology platforms (genomics, transcriptomics, or proteomics), but not with their integrated use...
December 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27928466/metabolic-positron-emission-tomography-imaging-of-cancer-pairing-lipid-metabolism-with-glycolysis
#4
EDITORIAL
Sandi A Kwee, John Lim
The limitations of fluorine-18 fluorodeoxy-D-glucose (FDG) in detecting some cancers has prompted a longstanding search for other positron emission tomography (PET) tracers to complement the imaging of glycolysis in oncology, with much attention paid to lipogenesis based on observations that the production of various lipid and lipid-containing compounds is increased in most cancers. Radiolabeled analogs of choline and acetate have now been used as oncologic PET probes for over a decade, showing convincingly improved detection sensitivity over FDG for certain cancers...
November 28, 2016: World Journal of Radiology
https://www.readbyqxmd.com/read/27924064/toward-the-use-of-precision-medicine-for-the-treatment-of-head-and-neck-squamous-cell-carcinoma
#5
REVIEW
Wang Gong, Yandi Xiao, Zihao Wei, Yao Yuan, Min Qiu, Chongkui Sun, Xin Zeng, Xinhua Liang, Mingye Feng, Qianming Chen
Precision medicine is a new strategy that aims at preventing and treating human diseases by focusing on individual variations in people's genes, environment and lifestyle. Precision medicine has been used for cancer diagnosis and treatment and shows evident clinical efficacy. Rapid developments in molecular biology, genetics and sequencing technologies, as well as computational technology, has enabled the establishment of "big data", such as the Human Genome Project, which provides a basis for precision medicine...
December 4, 2016: Oncotarget
https://www.readbyqxmd.com/read/27920501/three-generations-of-epidermal-growth-factor-receptor-tyrosine-kinase-inhibitors-developed-to-revolutionize-the-therapy-of-lung-cancer
#6
REVIEW
Haijun Zhang
Lung cancer, ~80%-85% of which is non-small-cell lung cancer (NSCLC), is the leading cause of cancer-related mortality worldwide. Sensitizing mutations in epidermal growth factor receptor (EGFR) gene (EGFRm(+)), such as exon 19 deletions and exon 21 L858R point mutations, are the most important drivers in NSCLC patients. In this respect, small-molecule EGFR tyrosine kinase inhibitors (TKIs) have been designed and developed, which launched the era of targeted, personalized and precise medicine for lung cancer...
2016: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/27915475/how-precisely-can-prostate-cancer-be-managed
#7
REVIEW
Liyan Zhuang, Matthew T Johnson
Progress has been made in applying genetic information to disease management in the postgenomic era, and precision medicine is emerging in prostate cancer management. The prostate health index, the 4-kallikrein (4K) score, and the PCA3, TMPRSS2- ERG, and Prostarix tests have potential for refining prostate cancer screening in conjunction with traditional prostate-specific antigen testing. The Confirm MDx and PCA3 tests have shown promise in identifying men who need be rebiopsied after a primary negative biopsy...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27913529/ph-like-acute-lymphoblastic-leukemia
#8
Thai Hoa Tran, Mignon L Loh
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a newly identified high-risk (HR) B-lineage ALL subtype, accounting for ∼15% of children with National Cancer Institute-defined HR B-ALL. It occurs more frequently in adolescents and adults, having been reported in as much as 27% of young adults with ALL between 21 and 39 years of age. It exhibits adverse clinical features, confers a poor prognosis, and harbors a diverse range of genetic alterations that activate cytokine receptor genes and kinase signaling pathways, making it amenable to treatment with tyrosine kinase inhibitor (TKI) therapy...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27913204/the-selective-bcl-2-inhibitor-venetoclax-a-bh3-mimetic-does-not-dysregulate-intracellular-ca-2-signaling
#9
Tamara Vervloessem, Hristina Ivanova, Tomas Luyten, Jan B Parys, Geert Bultynck
Anti-apoptotic B cell-lymphoma-2 (Bcl-2) proteins are emerging as therapeutic targets in a variety of cancers for precision medicines, like the BH3-mimetic drug venetoclax (ABT-199), which antagonizes the hydrophobic cleft of Bcl-2. However, the impact of venetoclax on intracellular Ca(2+) homeostasis and dynamics in cell systems has not been characterized in detail. Here, we show that venetoclax did not affect Ca(2+)-transport systems from the endoplasmic reticulum (ER) in permeabilized cell systems. Venetoclax (1μM) did neither trigger Ca(2+) release by itself nor affect agonist-induced Ca(2+) release in a variety of intact cell models...
November 30, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27903712/the-myeloma-stem-cell-concept-revisited-from-phenomenology-to-operational-terms
#10
REVIEW
Hans Erik Johnsen, Martin Bøgsted, Alexander Schmitz, Julie Støve Bødker, Tarec Christoffer El-Galaly, Preben Johansen, Peter Valent, Niklas Zojer, Els Van Valckenborgh, Karin Vanderkerken, Mark van Duin, Pieter Sonneveld, Martin Perez-Andres, Alberto Orfao, Karen Dybkær
The concept of the myeloma stem cell may have important therapeutic implications, yet its demonstration has been hampered by a lack of consistency in terms and definitions. Here, we summarize the current documentation and propose single-cell in vitro studies for future translational studies. By the classical approach, a CD19(-)/CD45(low/-)/CD38(high)/CD138(+) malignant plasma cell, but not the CD19(+)/CD38(low/-) memory B cell compartment, is enriched for tumorigenic cells that initiate myeloma in xenografted immunodeficient mice, supporting that myeloma stem cells are present in the malignant PC compartment...
December 2016: Haematologica
https://www.readbyqxmd.com/read/27903462/radiomic-based-pathological-response-prediction-from-primary-tumors-and-lymph-nodes-in-nsclc
#11
Thibaud P Coroller, Vishesh Agrawal, Elizabeth Huynh, Vivek Narayan, Stephanie W Lee, Raymond H Mak, Hugo J W L Aerts
INTRODUCTION: Non-invasive biomarkers that capture the total tumor burden could provide important complementary information for precision medicine to aid clinical decision-making. We investigated the value of radiomic data, extracted from pre-treatment computed tomography (CT) images of the primary tumor and lymph nodes, in predicting pathological response following neoadjuvant chemoradiation prior to surgery. METHODS: Eighty-five patients with resectable locally-advanced (stage II-III) non-small cell lung cancer (NSCLC) (median age: 60...
November 26, 2016: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/27902695/text-mining-genotype-phenotype-relationships-from-biomedical-literature-for-database-curation-and-precision-medicine
#12
Ayush Singhal, Michael Simmons, Zhiyong Lu
The practice of precision medicine will ultimately require databases of genes and mutations for healthcare providers to reference in order to understand the clinical implications of each patient's genetic makeup. Although the highest quality databases require manual curation, text mining tools can facilitate the curation process, increasing accuracy, coverage, and productivity. However, to date there are no available text mining tools that offer high-accuracy performance for extracting such triplets from biomedical literature...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27901097/sequencing-based-breast-cancer-diagnostics-as-an-alternative-to-routine-biomarkers
#13
Mattias Rantalainen, Daniel Klevebring, Johan Lindberg, Emma Ivansson, Gustaf Rosin, Lorand Kis, Fuat Celebioglu, Irma Fredriksson, Kamila Czene, Jan Frisell, Johan Hartman, Jonas Bergh, Henrik Grönberg
Sequencing-based breast cancer diagnostics have the potential to replace routine biomarkers and provide molecular characterization that enable personalized precision medicine. Here we investigate the concordance between sequencing-based and routine diagnostic biomarkers and to what extent tumor sequencing contributes clinically actionable information. We applied DNA- and RNA-sequencing to characterize tumors from 307 breast cancer patients with replication in up to 739 patients. We developed models to predict status of routine biomarkers (ER, HER2,Ki-67, histological grade) from sequencing data...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899776/-new-classification-for-advanced-colorectal-cancer-using-cancerplex%C3%A2-genomic-tests
#14
Hitoshi Kameyama, Yoshifumi Shimada, Hiroshi Ichikawa, Masayuki Nagahashi, Jun Sakata, Takashi Kobayashi, Hitoshi Nogami, Satoshi Maruyama, Yasumasa Takii, Shujiro Okuda, Yiwei Ling, Hiroshi Izutsu, Keisuke Kodama, Mitsutaka Nakada, Toshifumi Wakai
Recently, targeted drugs have been developed for the treatment of colorectal cancer(CRC). Among targets, it is well known that KRAS mutations are associated with resistance to epidermal growth factor receptor(EGFR)monoclonal antibodies. However, response rates using anti-EGFR monotherapy for CRC were less than 20-30% in previous clinical studies. Thus, because the RAS/MAP2K/MAPK and PI3K/AKT pathways are associated with CRC resistance to chemotherapy, we analyzed gene mutations in Stage IV CRC patients using a genomic test(CancerPlex®)...
November 2016: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/27899774/-a-review-multigene-assays-for-clinical-utility-in-breast-cancer
#15
Kazuhiro Araki, Yoshinori Ito
Multigene assays that simultaneously measure the expression of various breast cancer genes have been developed to guide the use of adjuvant chemotherapy in early breast cancer. The efficacy of adjuvant therapies depends on the recurrence risk for an individual patient. As a result, accurate prediction of the recurrence risk is vital for precise adjuvant chemotherapy in individual breast cancer patients. The recurrence risk as typically assessed by conventional examination of histological data of immuno-histological biomarkers(ER, PR, HER2, and Ki-67)is not sufficient to select subsets of patients...
November 2016: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/27899773/-a-novel-treatment-strategy-for-pancreatic-cancer-based-on-gene-profiles
#16
Hideyuki Hayashi, Hiroshi Nishihara
Pancreatic cancer has one of the highest rates of mortality among malignancies and the development of promising future therapies is strongly required. Recently, the utility of gene aberrations as biomarkers for determining therapeutic strategies has been demonstrated in several types of cancer. The detection of druggable mutations that aid in the selection of effective molecular targeting drugs is feasible in clinical settings for certain cancers. On the other hand, personalized therapy for pancreatic cancer guided by genomic biomarkers has not yet been realized and suitable molecular targets for the disease have been unclear until now...
November 2016: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/27899772/-lung-cancer
#17
Kazushi Yoshida, Takashi Kono
Personalized lung cancer therapy has progressed by targeting several oncogenic aberrations that drive lung carcinogenesis. Recent advances in gene analysis technologies, including next-generation sequencing that yields large amounts of genomic data, have greatly contributed to this progress. In addition, immune checkpoint blockade therapy has become available in Japan, and extensive searches for biomarkers predictive of therapeutic response have been carried out. "Clinical sequencing" which analyzes aberrations in a set of therapy-related genes in patient cancer specimens, has been actively conducted in Japan and other countries...
November 2016: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/27896996/cerna-search-method-identified-a-met-activated-subgroup-among-egfr-dna-amplified-lung-adenocarcinoma-patients
#18
Halla Kabat, Leo Tunkle, Inhan Lee
Given the diverse molecular pathways involved in tumorigenesis, identifying subgroups among cancer patients is crucial in precision medicine. While most targeted therapies rely on DNA mutation status in tumors, responses to such therapies vary due to the many molecular processes involved in propagating DNA changes to proteins (which constitute the usual drug targets). Though RNA expressions have been extensively used to categorize tumors, identifying clinically important subgroups remains challenging given the difficulty of discerning subgroups within all possible RNA-RNA networks...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896485/biomarkers-for-precision-medicine-in-bladder-cancer
#19
REVIEW
Takahiro Kojima, Koji Kawai, Jun Miyazaki, Hiroyuki Nishiyama
Bladder cancer (BC) is classified as non-muscle-invasive BC (NMIBC) or muscle-invasive BC (MIBC). Because the recurrence and mortality rates of BC are high, suitable biomarkers for early detection, evaluation of prognosis, and surveillance of drug responses are needed. Urinary markers simplify surveillance schedules and improve early detection of tumors, especially in NMIBC. Various markers have been identified at DNA, RNA, and protein levels with different sensitivities and specificities. Several biomarkers show a higher sensitivity than urinary cytology, but they are not accurate enough to replace it...
November 29, 2016: International Journal of Clinical Oncology
https://www.readbyqxmd.com/read/27889782/molecular-pathology-a-requirement-for-precision-medicine-in-cancer
#20
Manfred Dietel
The increasing importance of targeting drugs and check-point inhibitors in the treatment of several tumor entities (breast, colon, lung, malignant melanoma, lymphoma, etc.) and the necessity of a companion diagnostic (HER2, (pan)RAS, EGFR, ALK, BRAF, ROS1, MET, PD-L1, etc.) is leading to new challenges for surgical pathology. Since almost all the biomarkers to be specifically detected are tissue based, a precise and reliable diagnostic is absolutely crucial. To meet this challenge surgical pathology has adapted a number of molecular methods (semi-quantitative immunohistochemistry, fluorescence in situ hybridization, PCR and its multiple variants, (pyro/Sanger) sequencing, next generation sequencing (amplicon, whole exome, whole genome), DNA arrays, methylation analyses, etc...
2016: Oncology Research and Treatment
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