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Big data cancer

Shaoyu Yang, Xueqin Chen, Yuelong Pan, Jiekai Yu, Xin Li, Shenglin Ma
The present study aimed to identify potential serum biomarkers for predicting the clinical outcomes of patients with advanced non-small cell lung cancer (NSCLC) treated with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR‑TKIs). A total of 61 samples were collected and analyzed using the integrated approach of magnetic bead‑based weak cation exchange chromatography and matrix‑assisted laser desorption/ionization‑time of flight‑mass spectrometry. The Zhejiang University Protein Chip Data Analysis system was used to identify the protein spectra of patients that are resistant and sensitive to EGFR‑TKIs...
October 11, 2016: Molecular Medicine Reports
Priyakshi Kalita-de Croft, Fares Al-Ejeh, Amy E McCart Reed, Jodi M Saunus, Sunil R Lakhani
Our understanding of the natural history of breast cancer has evolved alongside technologies to study its genomic, transcriptomic, proteomic, and metabolomics landscapes. These technologies have helped decipher multiple molecular pathways dysregulated in breast cancer. First-generation 'omics analyses considered each of these dimensions individually, but it is becoming increasingly clear that more holistic, integrative approaches are required to fully understand complex biological systems. The 'omics represent an exciting era of discovery in breast cancer research, although important issues need to be addressed to realize the clinical utility of these data through precision cancer care...
November 2016: Advances in Anatomic Pathology
Tsuyoshi Hamada, NaNa Keum, Reiko Nishihara, Shuji Ogino
Molecular pathological epidemiology (MPE) is an integrative field that utilizes molecular pathology to incorporate interpersonal heterogeneity of a disease process into epidemiology. In each individual, the development and progression of a disease are determined by a unique combination of exogenous and endogenous factors, resulting in different molecular and pathological subtypes of the disease. Based on "the unique disease principle," the primary aim of MPE is to uncover an interactive relationship between a specific environmental exposure and disease subtypes in determining disease incidence and mortality...
October 13, 2016: Journal of Gastroenterology
Zhe Wang
Biology research has entered into big data era. Systems biology approaches therefore become the powerful tools to obtain the whole landscape of how cell separate, grow, and resist the stresses. Fission yeast Schizosaccharomyces pombe is wonderful unicellular eukaryote model, especially studying its division and metabolism can facilitate to understanding the molecular mechanism of cancer and discovering anticancer agents. In this perspective, we discuss the recent advanced fission yeast systems biology tools, mainly focus on metabolomics profiling and metabolic modeling, protein-protein interactome and genetic interaction network, DNA sequencing and applications, and high-throughput phenotypic screening...
October 11, 2016: Current Genetics
F M Carozzi, C Ocello, E Burroni, H Faust, M Zappa, E Paci, A Iossa, P Bonanni, M Confortini, C Sani
BACKGROUND AND OBJECTIVES: A randomized trial was conducted in Tuscany, Italy, to evaluate the effectiveness of HPV vaccination for 25year old (yo) women who attend at the first time cervical cancer screening. The trial also evaluated immune response after vaccination, reductions of cytological abnormalities and the impact of vaccination on screening activity. STUDY DESIGN: During 2010-2011, all 25 yo women who were invited to the Florence cervical cancer screening programme were also asked to participate in the trial...
October 3, 2016: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
Audie A Atienza, Katrina J Serrano, William T Riley, Richard P Moser, William M Klein
The era of "Big Data" presents opportunities to substantively address cancer prevention and control issues by improving health behaviors and refining theoretical models designed to understand and intervene in those behaviors. Yet, the terms "model" and "Big Data" have been used rather loosely, and clarification of these terms is required to advance the science in this area. The objectives of this paper are to discuss conceptual definitions of the terms "model" and "Big Data", as well as examine the promises and challenges of Big Data to advance cancer prevention and control research using behavioral theories...
September 2016: Journal of Cancer Prevention
Haozhe Xie, Jie Li, Qiaosheng Zhang, Yadong Wang
Random Projection (RP) technique has been widely applied in many scenarios because it can reduce high-dimensional features into low-dimensional space within short time and meet the need of real-time analysis of massive data. There is an urgent need of dimensionality reduction with fast increase of big genomics data. However, the performance of RP is usually lower. We attempt to improve classification accuracy of RP through combining other reduction dimension methods such as Principle Component Analysis (PCA), Linear Discriminant Analysis (LDA), and Feature Selection (FS)...
September 21, 2016: Computational Biology and Chemistry
Zhan Ye, Ahmad P Tafti, Karen Y He, Kai Wang, Max M He
BACKGROUND: Many new biomedical research articles are published every day, accumulating rich information, such as genetic variants, genes, diseases, and treatments. Rapid yet accurate text mining on large-scale scientific literature can discover novel knowledge to better understand human diseases and to improve the quality of disease diagnosis, prevention, and treatment. RESULTS: In this study, we designed and developed an efficient text mining framework called SparkText on a Big Data infrastructure, which is composed of Apache Spark data streaming and machine learning methods, combined with a Cassandra NoSQL database...
2016: PloS One
Turki Y Alhazzazi, Faisal T Alghamdi
BACKGROUND: Head and neck cancer (HNC) is the ninth most common cancer worldwide, and has a poor 5-year survival rate averaging 50%, which has not changed for decades. A high prevalence of HNC has been reported in the southwestern region of Saudi Arabia, as compared to other areas of the country. However, data in regards to HNC are scattered and not well documented. Thus, the aim of this systematic review was to gather all available and updated important information regarding HNC in Saudi Arabia, and highlight the gaps of knowledge in our country with regard to this disease...
2016: Asian Pacific Journal of Cancer Prevention: APJCP
Daniele Regge, Simone Mazzetti, Valentina Giannini, Christian Bracco, Michele Stasi
Cancer is a complex disease and unfortunately understanding how the components of the cancer system work does not help understand the behavior of the system as a whole. In the words of the Greek philosopher Aristotle "the whole is greater than the sum of parts." To date, thanks to improved information technology infrastructures, it is possible to store data from each single cancer patient, including clinical data, medical images, laboratory tests, and pathological and genomic information. Indeed, medical archive storage constitutes approximately one-third of total global storage demand and a large part of the data are in the form of medical images...
September 13, 2016: La Radiologia Medica
Bertrand Jordan
The recently announced "Cancer moonshot" may be greeted with scepticism: the previous "War on cancer" (1971) was not very successful. However the current plan seems well targeted, with emphasis not only on research investment but also on a strong effort to "break down silos" and ensure wide dissemination and use of clinical and molecular data. One big uncertainty, however, is what will happen to the programme after the 2016 presidential election… ‡.
August 2016: Médecine Sciences: M/S
Junyi Li, Yi-Xue Li, Yuan-Yuan Li
With rapid development of high-throughput techniques and accumulation of big transcriptomic data, plenty of computational methods and algorithms such as differential analysis and network analysis have been proposed to explore genome-wide gene expression characteristics. These efforts are aiming to transform underlying genomic information into valuable knowledges in biological and medical research fields. Recently, tremendous integrative research methods are dedicated to interpret the development and progress of neoplastic diseases, whereas differential regulatory analysis (DRA) based on gene coexpression network (GCN) increasingly plays a robust complement to regular differential expression analysis in revealing regulatory functions of cancer related genes such as evading growth suppressors and resisting cell death...
2016: BioMed Research International
Issam El Naqa
Oncology, with its unique combination of clinical, physical, technological, and biological data provides an ideal case study for applying big data analytics to improve cancer treatment safety and outcomes. An oncology treatment course such as chemoradiotherapy can generate a large pool of information carrying the 5Vs hallmarks of big data. This data is comprised of a heterogeneous mixture of patient demographics, radiation/chemo dosimetry, multimodality imaging features, and biological markers generated over a treatment period that can span few days to several weeks...
August 29, 2016: Methods: a Companion to Methods in Enzymology
Ligang Luo, Liping Li, Jiajia Hu, Xiaozhe Wang, Boulin Hou, Tianze Zhang, Lue Ping Zhao
BACKGROUND: Healthcare providers generate a huge amount of biomedical data stored in either legacy system (paper-based) format or electronic medical records (EMR) around the world, which are collectively referred to as big biomedical data (BBD). To realize the promise of BBD for clinical use and research, it is an essential step to extract key data elements from unstructured medical records into patient-centered electronic health records with computable data elements. Our objective is to introduce a novel solution, known as a double-reading/entry system (DRESS), for extracting clinical data from unstructured medical records (MR) and creating a semi-structured electronic health record database, as well as to demonstrate its reproducibility empirically...
2016: BMC Medical Informatics and Decision Making
Santiago Palacios, Andrea Mejía
INTRODUCTION: Today, it is a mandatory practice to prescribe a combination of estrogens and progestogens for menopausal women requiring hormone therapy and with a uterus. The WHI study and its reanalysis demonstrate a big difference in results between the conjugated equin estrogen (CEE) only vs.CEE plus medroxyprogesterone acetate (MPA) arms in relation with breast cancer and cardiovascular risk. The conclusion is that risk is clearly higher in the arm with MPA than in the CEE only arm...
August 22, 2016: Expert Opinion on Drug Safety
Leonard G Gomella
No abstract text is available yet for this article.
August 2016: Canadian Journal of Urology
Erik Hulegårdh, Mari Punab, Erik Holmberg, Katrin Palk, Edward Laane, Hele Everaus, Lovisa Wennström, Dick Stockelberg
This study focuses on the incidence, treatment, and survival of de novo acute leukemia in a 25-year perspective in western Sweden and Estonia. At the beginning of our study, Estonia was a part of the Eastern bloc with planned economy, but since 1991 it is a member of the European Union and transforming into a market economy. Survival rates have steadily increased in both countries. However, a gap between their survival curves remains. Based on our data, it is difficult to explain the big difference in the 5-year relative survival in favor of western Sweden (55 vs...
2016: Acta Haematologica
Sheida Nabavi
BACKGROUND: With advances in technologies, huge amounts of multiple types of high-throughput genomics data are available. These data have tremendous potential to identify new and clinically valuable biomarkers to guide the diagnosis, assessment of prognosis, and treatment of complex diseases, such as cancer. Integrating, analyzing, and interpreting big and noisy genomics data to obtain biologically meaningful results, however, remains highly challenging. Mining genomics datasets by utilizing advanced computational methods can help to address these issues...
2016: BMC Genomics
Seungyoon Nam
Traditionally, biologists have devoted their careers to studying individual biological entities of their own interest, partly due to lack of available data regarding that entity. Now, in the field of cancer, tremendously large, high-throughput data, too complex for conventional processing methods (i.e., "big data"), has accumulated and made freely available in public data repositories. Such challenges urge biologists to inspect their biological entities of interest using novel approaches, firstly including repository data retrieval...
August 8, 2016: BMB Reports
John H Phan, Ryan Hoffman, Sonal Kothari, Po-Yen Wu, May D Wang
The Big Data era in Biomedical research has resulted in large-cohort data repositories such as The Cancer Genome Atlas (TCGA). These repositories routinely contain hundreds of matched patient samples for genomic, proteomic, imaging, and clinical data modalities, enabling holistic and multi-modal integrative analysis of human disease. Using TCGA renal and ovarian cancer data, we conducted a novel investigation of multi-modal data integration by combining histopathological image and RNA-seq data. We compared the performances of two integrative prediction methods: majority vote and stacked generalization...
February 2016: ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics
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