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Big data cancer

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https://www.readbyqxmd.com/read/28425345/surrogate-marker-analysis-in-cancer-clinical-trials-through-time-to-event-mediation-techniques
#1
Sjouke Vandenberghe, Luc Duchateau, Leen Slaets, Jan Bogaerts, Stijn Vansteelandt
The meta-analytic approach is the gold standard for validation of surrogate markers, but has the drawback of requiring data from several trials. We refine modern mediation analysis techniques for time-to-event endpoints and apply them to investigate whether pathological complete response can be used as a surrogate marker for disease-free survival in the EORTC 10994/BIG 1-00 randomised phase 3 trial in which locally advanced breast cancer patients were randomised to either taxane or anthracycline based neoadjuvant chemotherapy...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28423489/target-of-obstructive-sleep-apnea-syndrome-merge-lung-cancer-based-on-big-data-platform
#2
Lifeng Li, Jingli Lu, Wenhua Xue, Liping Wang, Yunkai Zhai, Zhirui Fan, Ge Wu, Feifei Fan, Jieyao Li, Chaoqi Zhang, Yi Zhang, Jie Zhao
Based on our hospital database, the incidence of lung cancer diagnoses was similar in obstructive sleep apnea Syndrome (OSAS) and hospital general population; among individual with a diagnosis of lung cancer, the presence of OSAS was associated with an increased risk for mortality. In the gene expression and network-level information, we revealed significant alterations of molecules related to HIF1 and metabolic pathways in the hypoxic-conditioned lung cancer cells. We also observed that GBE1 and HK2 are downstream of HIF1 pathway important in hypoxia-conditioned lung cancer cell...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28411841/the-molecular-revolution-in-cutaneous-biology-the-era-of-genome-wide-association-studies-and-statistical-big%C3%A2-data-and-computational-topics
#3
REVIEW
Hima Anbunathan, Anne M Bowcock
The investigation of biological systems involving all organs of the body including the skin is in era of big data. This requires heavy-duty computational tools, and novel statistical methods. Microarrays have allowed the interrogation of thousands of common genetic markers in thousands of individuals from the same population (termed genome wide association studies or GWAS) to reveal common variation associated with disease or phenotype. These markers are usually single nucleotide polymorphisms (SNPs) that are relatively common in the population...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28409847/trends-in-immediate-breast-reconstruction-and-early-complication-rates-among-older-women-a-big-data-analysis
#4
Parisa Kamali, Daniel Curiel, Charlotte L van Veldhuisen, Alexandra E M Bucknor, Bernard T Lee, Hinne A Rakhorst, Samuel J Lin
BACKGROUND: Although approximately 57% of breast cancer (BC) diagnoses are in older patients (>60 years), only 4.1-14% receives breast reconstruction (BR). This has been attributed to physician concerns about operative complications. This paper aims to: 1) analyze the 30-day complication rates in the older patient population undergoing immediate breast reconstruction (IBR); and 2) analyze links between complication type and category of reconstruction. METHODS: Using the ACS-NSQIP database (2005-2014), all women older than 60 years of age diagnosed with BC and DCIS were identified...
April 13, 2017: Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28407145/gepia-a-web-server-for-cancer-and-normal-gene-expression-profiling-and-interactive-analyses
#5
Zefang Tang, Chenwei Li, Boxi Kang, Ge Gao, Cheng Li, Zemin Zhang
Tremendous amount of RNA sequencing data have been produced by large consortium projects such as TCGA and GTEx, creating new opportunities for data mining and deeper understanding of gene functions. While certain existing web servers are valuable and widely used, many expression analysis functions needed by experimental biologists are still not adequately addressed by these tools. We introduce GEPIA (Gene Expression Profiling Interactive Analysis), a web-based tool to deliver fast and customizable functionalities based on TCGA and GTEx data...
April 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28388297/cancer-transcriptome-dataset-analysis-comparing-methods-of-pathway-and-gene-regulatory-network-based-cluster-identification
#6
Seungyoon Nam
Cancer transcriptome analysis is one of the leading areas of Big Data science, biomarker, and pharmaceutical discovery, not to forget personalized medicine. Yet, cancer transcriptomics and postgenomic medicine require innovation in bioinformatics as well as comparison of the performance of available algorithms. In this data analytics context, the value of network generation and algorithms has been widely underscored for addressing the salient questions in cancer pathogenesis. Analysis of cancer trancriptome often results in complicated networks where identification of network modularity remains critical, for example, in delineating the "druggable" molecular targets...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28381877/the-genomic-dynamics-during-progression-of-lung-adenocarcinomas
#7
Bin Yang, Longhai Luo, Wen Luo, Yong Zhou, Chao Yang, Teng Xiong, Xiangchun Li, Xuan Meng, Lin Li, Xiaopin Zhang, Zhe Wang, Zhixin Wang
Intra-tumor heterogeneity is a big barrier to precision medicine. To explore the underlying clonal diversity in lung adenocarcinomas, we selected nine individuals with whole-genome sequencing data from primary and matched metastatic tumors as a cohort for study. Similar global pattern of arm-level copy number changes and large variations of somatic single-nucleotide variant between the primary and metastasis are observed in the majority of cases. Importantly, we found breakage-fusion-bridge (BFB) cycles acting as an important mechanism for underlying cancer gene amplification, such as amplification of CDK4, CDKN3 and FGFR1 in early stage...
April 6, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28373898/evaluation-of-in-vivo-mutagenesis-for-assessing-the-health-risk-of-air-pollutants
#8
REVIEW
Yasunobu Aoki
Various kind of chemical substances, including man-made chemical products and unintended products, are emitted to ambient air. Some of these substances have been shown to be mutagenic and therefore to act as a carcinogen in humans. National pollutant inventories (e.g., Pollutant Release and Transfer Registration in Japan) have estimated release amounts of man-made chemical products, but a major concern is the release of suspended particulate matter containing potent mutagens, for example, polycyclic aromatic hydrocarbons and related compounds generated by the combustion of fossil fuel, which are not estimated by PRTR system...
2017: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
https://www.readbyqxmd.com/read/28373602/data-analysis-of-electronic-nose-technology-in-lung-cancer-generating-prediction-models-by-means-of-aethena
#9
Sharina Kort, Marjolein Brusse-Keizer, Jan-Willem Gerritsen, Job van der Palen
INTRODUCTION: Only 15% of lung cancer cases present with potentially curable disease. Therefore, there is large interest in a fast, non-invasive tool to detect lung cancer earlier. Exhaled breath analysis by electronic nose technology measures volatile organic compounds (VOC's) in exhaled breath which are associated with lung cancer. METHODS: The diagnostic accuracy of the Aeonose™ is currently being studied in a multi-centre, prospective study in 210 subjects suspected for lung cancer, where approximately half will have a confirmed diagnosis and the other half will have a rejected diagnosis of lung cancer...
April 4, 2017: Journal of Breath Research
https://www.readbyqxmd.com/read/28372569/cancer-metastasis-issues-and-challenges
#10
EDITORIAL
Chao-Nan Qian, Yan Mei, Jian Zhang
Metastasis is the major cause of treatment failure in cancer patients and of cancer-related deaths. This editorial discusses how cancer metastasis may be better perceived and controlled. Based on big-data analyses, a collection of 150 important pro-metastatic genes was studied. Using The Cancer Genome Atlas datasets to re-analyze the effect of some previously reported metastatic genes-e.g., JAM2, PPARGC1A, SIK2, and TRAF6-on overall survival of patients with renal and liver cancers, we found that these genes are actually protective factors for patients with cancer...
April 3, 2017: Chinese Journal of Cancer
https://www.readbyqxmd.com/read/28335044/semi-automated-de-identification-of-german-content-sensitive-reports-for-big-data-analytics
#11
Hannes Seuss, Peter Dankerl, Matthias Ihle, Andrea Grandjean, Rebecca Hammon, Nicola Kaestle, Peter A Fasching, Christian Maier, Jan Christoph, Martin Sedlmayr, Alexander Cavallaro, Matthias Hammon
Purpose Projects involving collaborations between different institutions require data security via selective de-identification of words or phrases. A semi-automated de-identification tool was developed and evaluated on different types of medical reports natively and after adapting the algorithm to the text structure. Materials and Methods A semi-automated de-identification tool was developed and evaluated for its sensitivity and specificity in detecting sensitive content in written reports. Data from 4671 pathology reports (4105 + 566 in two different formats), 2804 medical reports, 1008 operation reports, and 6223 radiology reports of 1167 patients suffering from breast cancer were de-identified...
March 23, 2017: RöFo: Fortschritte Auf Dem Gebiete der Röntgenstrahlen und der Nuklearmedizin
https://www.readbyqxmd.com/read/28326610/dose-and-temporal-evaluation-of-ethylene-oxide-induced-mutagenicity-in-the-lungs-of-male-big-blue-mice-following-inhalation-exposure-to-carcinogenic-concentrations
#12
Mugimane G Manjanatha, Sharon D Shelton, Ying Chen, Barbara L Parsons, Meagan B Myers, Karen L McKim, B Bhaskar Gollapudi, Nigel P Moore, Lynne T Haber, Bruce Allen, Martha M Moore
Ethylene oxide (EO) is a direct acting alkylating agent; in vitro and in vivo studies indicate that it is both a mutagen and a carcinogen. However, it remains unclear whether the mode of action (MOA) for cancer for EO is a mutagenic MOA, specifically via point mutation. To investigate the MOA for EO-induced mouse lung tumors, male Big Blue (BB) B6C3F1 mice (10/group) were exposed to EO by inhalation, 6 hr/day, 5 days/week for 4 (0, 10, 50, 100, or 200 ppm EO), 8, or 12 weeks (0, 100, or 200 ppm EO). Lung DNA samples were analyzed for cII mutant frequency (MF) at 4, 8 and 12 weeks of exposure; the mutation spectrum was analyzed for mutants from control and 200 ppm EO treatments...
April 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28316892/from-big-data-to-diagnosis-and-prognosis-gene-expression-signatures-in-liver-hepatocellular-carcinoma
#13
Hong Yang, Xin Zhang, Xiao-Yong Cai, Dong-Yue Wen, Zhi-Hua Ye, Liang Liang, Lu Zhang, Han-Lin Wang, Gang Chen, Zhen-Bo Feng
BACKGROUND: Liver hepatocellular carcinoma accounts for the overwhelming majority of primary liver cancers and its belated diagnosis and poor prognosis call for novel biomarkers to be discovered, which, in the era of big data, innovative bioinformatics and computational techniques can prove to be highly helpful in. METHODS: Big data aggregated from The Cancer Genome Atlas and Natural Language Processing were integrated to generate differentially expressed genes...
2017: PeerJ
https://www.readbyqxmd.com/read/28287094/enlightening-discriminative-network-functional-modules-behind-principal-component-analysis-separation-in-differential-omic-science-studies
#14
Sara Ciucci, Yan Ge, Claudio Durán, Alessandra Palladini, Víctor Jiménez-Jiménez, Luisa María Martínez-Sánchez, Yuting Wang, Susanne Sales, Andrej Shevchenko, Steven W Poser, Maik Herbig, Oliver Otto, Andreas Androutsellis-Theotokis, Jochen Guck, Mathias J Gerl, Carlo Vittorio Cannistraci
Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28281147/molecular-tumor-boards-ethical-issues-in-the-new-era-of-data-medicine
#15
Henri-Corto Stoeklé, Marie-France Mamzer-Bruneel, Charles-Henry Frouart, Christophe Le Tourneau, Pierre Laurent-Puig, Guillaume Vogt, Christian Hervé
The practice and development of modern medicine requires large amounts of data, particularly in the domain of cancer. The future of personalized medicine lies neither with "genomic medicine" nor with "precision medicine", but with "data medicine" (DM) (big data, data mining). The establishment of this DM has required far-reaching changes, to establish four essential elements connecting patients and doctors: biobanks, databases, bioinformatic platforms and genomic platforms. The "transformation" of scientific research areas, such as genetics, bioinformatics and biostatistics, into clinical specialties has generated a new vision of care...
March 9, 2017: Science and Engineering Ethics
https://www.readbyqxmd.com/read/28279424/cardio-oncology-the-role-of-big-data
#16
REVIEW
Anant Mandawat, Andrew E Williams, Sanjeev A Francis
Despite its challenges, a "big data" approach offers a unique opportunity within the field of cardio-oncology. A pharmacovigilant approach using large data sets can help characterize cardiovascular toxicities of the rapidly expanding armamentarium of targeted therapies. Creating a broad coalition of data sharing can provide insights into the incidence of cardiotoxicity and stimulate research into the underlying mechanisms. Population health necessitates the use of big data and can help inform public health interventions to prevent both cancer and cardiovascular disease...
April 2017: Heart Failure Clinics
https://www.readbyqxmd.com/read/28273479/systems-biology-of-metabolism-a-driver-for-developing-personalized-and-precision-medicine
#17
REVIEW
Jens Nielsen
Systems biology uses mathematical models to analyze large datasets and simulate system behavior. It enables integrative analysis of different types of data and can thereby provide new insight into complex biological systems. Here will be discussed the challenges of using systems medicine for advancing the development of personalized and precision medicine to treat metabolic diseases like insulin resistance, obesity, NAFLD, NASH, and cancer. It will be illustrated how the concept of genome-scale metabolic models can be used for integrative analysis of big data with the objective of identifying novel biomarkers that are foundational for personalized and precision medicine...
March 7, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28265786/precision-medicine-driven-by-cancer-systems-biology
#18
Fabian V Filipp
Molecular insights from genome and systems biology are influencing how cancer is diagnosed and treated. We critically evaluate big data challenges in precision medicine. The melanoma research community has identified distinct subtypes involving chronic sun-induced damage and the mitogen-activated protein kinase driver pathway. In addition, despite low mutation burden, non-genomic mitogen-activated protein kinase melanoma drivers are found in membrane receptors, metabolism, or epigenetic signaling with the ability to bypass central mitogen-activated protein kinase molecules and activating a similar program of mitogenic effectors...
March 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28255369/prostate-cancer-between-prognosis-and-adequate-proper-therapy
#19
REVIEW
T Grozescu, F Popa
Knowing the indolent, non-invasive nature of most types of prostate cancer, as well as the simple fact that the disease seems more likely to be associated with age rather than with other factors (50% of men at the age of 50 and 80% at the age of 80 have it [1], with or without presenting any symptom), the big challenge of this clinical entity was to determine severity indicators (so far insufficient) to guide the physician towards an adequate attitude in the clinical setting. The risk of over-diagnosing and over-treating many prostate cancer cases (indicated by all the major European and American studies) is real and poses many question marks...
January 2017: Journal of Medicine and Life
https://www.readbyqxmd.com/read/28226351/-significance-and-contemplation-of-clinical-diagnosis-and-therapy-on-the-renewal-of-the-eighth-edition-of-gastric-cancer-tnm-staging-system
#20
Hongqing Xi, Kecheng Zhang, Bo Wei, Lin Chen
TNM staging is essential for clinical decision-making and prognostic prediction for patients with gastric cancer. The 7th TNM staging manual was formulated in 2009 and implemented in 2010. However, it was published that there were some deficiencies of the 7th edition of gastric cancer TNM staging system in clinical application process, and this old staging system could not meet the clinical needs. With the cooperation and promotion of the American Joint Committee on Cancer (AJCC), the International Union for Cancer Control (UICC) and the International Gastric Cancer Association (IGCA), and through the accumulation and analysis of gastric cancer big data, the 8th TNM staging system was published at the end of 2016...
February 25, 2017: Zhonghua Wei Chang Wai Ke za Zhi, Chinese Journal of Gastrointestinal Surgery
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