Evaluating a Novel Summary Visualization for Clinical Trial Reports: A Usability Study.

Contributions of clinical trials are captured in published reports that are unstructured and often require extensive manual review to gain a deeper understanding of the study itself. Our goal is to increase comprehension and decrease the time necessary to understand these reports through the use of visualization tools. In this paper, we specify and evaluate the visualization of a previously developed representation as well as gain insight from user input for further development.

A formal representation for numerical data presented in published clinical trial reports.

Assessing the quality of and integrating clinical trial reports are necessary to practice evidence-based medicine. In particular, the numerical data is essential to understanding the strength and quality of the clinical trial study. In this paper, we present a formal representation for standardizing numerical data in published clinical trial reports, and our efforts towards developing computational tools to capture and visualize this representation.

Improving the accuracy of therapy descriptions in clinical trials using a bottom-up approach.

Randomized clinical trial (RCT) reports commonly have complicated therapy descriptions that are written in free-text. Drug therapy is difficult to describe due to the dynamic nature of how protocols change and the many ways drugs can be administered. Details regarding protocol changes and drug administration must be explained clearly for reproducibility and reliability.

Tissue-specific alternative splicing of TCF7L2.

Common variants in the transcription factor 7-like 2 (TCF7L2) gene have been identified as the strongest genetic risk factors for type 2 diabetes (T2D). However, the mechanisms by which these non-coding variants increase risk for T2D are not well-established. We used 13 expression assays to survey mRNA expression of multiple TCF7L2 splicing forms in up to 380 samples from eight types of human tissue (pancreas, pancreatic islets, colon, liver, monocytes, skeletal muscle, subcutaneous adipose tissue and lymphoblastoid cell lines) and observed a tissue-specific pattern of alternative splicing.

Comprehensive association study of type 2 diabetes and related quantitative traits with 222 candidate genes.

Objective: Type 2 diabetes is a common complex disorder with environmental and genetic components. We used a candidate gene-based approach to identify single nucleotide polymorphism (SNP) variants in 222 candidate genes that influence susceptibility to type 2 diabetes.

Research Design And Methods: In a case-control study of 1,161 type 2 diabetic subjects and 1,174 control Finns who are normal glucose tolerant, we genotyped 3,531 tagSNPs and annotation-based SNPs and imputed an additional 7,498 SNPs, providing 99.

Genomewide clonal analysis of lethal mutations in the Drosophila melanogaster eye: comparison of the X chromosome and autosomes.

Using a large consortium of undergraduate students in an organized program at the University of California, Los Angeles (UCLA), we have undertaken a functional genomic screen in the Drosophila eye. In addition to the educational value of discovery-based learning, this article presents the first comprehensive genomewide analysis of essential genes involved in eye development. The data reveal the surprising result that the X chromosome has almost twice the frequency of essential genes involved in eye development as that found on the autosomes.

A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.

Identifying the genetic variants that increase the risk of type 2 diabetes (T2D) in humans has been a formidable challenge. Adopting a genome-wide association strategy, we genotyped 1161 Finnish T2D cases and 1174 Finnish normal glucose-tolerant (NGT) controls with >315,000 single-nucleotide polymorphisms (SNPs) and imputed genotypes for an additional >2 million autosomal SNPs. We carried out association analysis with these SNPs to identify genetic variants that predispose to T2D, compared our T2D association results with the results of two similar studies, and genotyped 80 SNPs in an additional 1215 Finnish T2D cases and 1258 Finnish NGT controls.

Screening of 134 single nucleotide polymorphisms (SNPs) previously associated with type 2 diabetes replicates association with 12 SNPs in nine genes.

More than 120 published reports have described associations between single nucleotide polymorphisms (SNPs) and type 2 diabetes. However, multiple studies of the same variant have often been discordant. From a literature search, we identified previously reported type 2 diabetes-associated SNPs.

Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers.

How can you combine professional-quality research with discovery-based undergraduate education? The UCLA Undergraduate Consortium for Functional Genomics provides the answer