Analysis and Integration of Big Data from Next-Generation Genomics, Epigenomics, and Transcriptomics Christopher Benner Salk Institute for Biological Studies Abstract: Advances in next-generation sequencing (NGS) technology have fundamentally changed our approach to modern biomedical research. Although the quest to sequence millions of genomes has garnered most of the headlines, innovations in NGS assay development have expanded our ability to quantify transcription, genome...

Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features. Nikfarjam A, Sarker A, O'Connor K, Ginn R, Gonzalez G. J Am Med Inform Assoc. 2015 Mar 9. pii: ocu041. doi: 10.1093/jamia/ocu041. [Epub ahead of print] Azadeh Nikfarjam Arizona State University, Department of Biomedical Informatics Social media is becoming increasingly popular as a platform for sharing personal health-related information. This...

Privacy issues when looking for a needle in a genomic haystack Amalio Telenti Human Longevity Inc. Abstract: Very rare single nucleotide variants are the most prevalent form of genetic diversity in the human population. Such variants are generally refered to as Variants of Unknown Significance (VUS). It is expected that VUS will attract increasing attention of the medical services as possibly associated with clinical disease or disease predisposition. The considerations above call...

Objective: Develop and evaluate a foundational oncology-specific standard for communication and coordination of care throughout the cancer journey, with early-stage breast cancer as the use case. Materials and Methods: Due to broad uptake of the HL7 Consolidated Clinical Document Architecture (C-CDA) by health information exchanges and large provider organizations, we developed an implementation guide (IG) in congruence with C-CDA. The resultant product was balloted through the HL7 process...

Tracking Disease Outbreaks and Health Disparities using Big Data, Social Media, Social Network Analysis, and GIS Ming-Hsiang Tsou San Diego State University Abstract: Real time public health data capture using Big Data and social media are now at the forefront of behavioral measurement, disease surveillance, and health promotion in many public health research activities. Public health research community is now rapidly reexamining the role of dynamic environmental-behavioral...

Innovative information visualization of electronic health record data: a systematic review Link: http://jamia.oxfordjournals.org/content/early/2014/11/07/amiajnl-2014-00... West VL, Borland D, Hammond WE. J Am Med Inform Assoc. 2014 Oct 21. pii: amiajnl-2014-002955. doi: 10.1136/amiajnl-2014-002955 Vivian West, PhD, MBA, RN Duke University, Duke Center for Health Informatics This study investigates the use of visualization techniques reported between 1996 and 2013 and evaluates...

ARX - A Comprehensive Tool for Anonymizing Biomedical Data Florian Kohlmayer and Fabian Prasser Technische Universität München Abstract: Collaboration and data sharing have become core elements of biomedical research. Especially when sensitive data from distributed sources are linked, privacy threats have to be considered. Statistical disclosure control allows the protection of sensitive data by introducing fuzziness. Reduction of data quality, however, needs to be balanced...

Generating Practice-based Evidence from Electronic Health Records Nigam Shah Stanford University Abstract: In the era of Electronic Health Records, it is possible to examine the outcomes of decisions made by doctors during clinical practice to identify patterns of care—generating evidence from the collective experience of patients. We will discuss methods that transform unstructured patient notes into a de-identified, temporally ordered, patient-feature matrix. We will then review...

Challenges and remediation for Patient Safety Indicators in the transition to ICD-10-CM. Link: http://www.ncbi.nlm.nih.gov/pubmed/25186492 Boyd AD, Yang YM, Li J, Kenost C, Burton MD, Becker B, Lussier YA. J Am Med Inform Assoc. 2014 Sep 3. pii: amiajnl-2013-002491. doi: 10.1136/amiajnl-2013-002491 Yves Lussier University of Arizona Reporting of hospital adverse events relies on Patient Safety Indicators (PSIs) using International Classification of Diseases, Ninth Edition,...

Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality Hua Xu, Melinda C Aldrich, Qingxia Chen, Hongfang Liu, Neeraja B Peterson, Qi Dai, Mia Levy, Anushi Shah, Xue Han, Xiaoyang Ruan, Min Jiang, Ying Li, Jamii St Julien, Jeremy Warner, Carol Friedman, Dan M Roden, Joshua C Denny J Am Med Inform Assoc Published Online First: 22 July 201 doi:10.1136/amiajnl-2014-002649 Hua Xu The University of Texas...