NIDDK data repository: a central collection of clinical trial data

BACKGROUND: The National Institute of Diabetes and Digestive and Kidney Diseases have established central repositories for the collection of DNA, biological samples, and clinical data to be catalogued at a single site. Here we present an overview of the site which stores the clinical data and links to biospecimens. DESCRIPTION: The NIDDK Data repository is a web-enabled resource cataloguing clinical trial data and supporting information from NIDDK supported studies. The Data Repository allows for the co-location of multiple electronic datasets that were created as part of clinical investigations. The Data Repository does not serve the role of a Data Coordinating Center, but rather as a warehouse for the clinical findings once the trials have been completed. Because both biological and genetic samples are collected from many of the studies, a data management system for the cataloguing and retrieval of samples was developed. CONCLUSION: The Data Repository provides a unique resource for researchers in the clinical areas supported by NIDDK. In addition to providing a warehouse of data, Data Repository staff work with the users to educate them on the datasets as well as assist them in the acquisition of multiple data sets for cross-study analysis. Unlike the majority of biological databases, the Data Repository acts both as a catalogue for data, biosamples, and genetic materials and as a central processing point for the requests for all biospecimens. Due to regulations on the use of clinical data, the ultimate release of that data is governed under NIDDK data release policies. The Data Repository serves as the conduit for such requests

SNP and Mutation Data on the Web – Hidden Treasures for Uncovering

SNP data has grown exponentially over the last two years, SNP database evolution has matched this growth, as initial development of several independent SNP databases has given way to one central SNP database, dbSNP. Other SNP databases have instead evolved to complement this central database by providing gene specific focus and an increased level of curation and analysis on subsets of data, derived from the central data set. By contrast, human mutation data, which has been collected over many years, is still stored in disparate sources, although moves are afoot to move to a similar central database. These developments are timely, human mutation and polymorphism data both hold complementary keys to a better understanding of how genes function and malfunction in disease. The impending availability of a complete human genome presents us with an ideal framework to integrate both these forms of data, as our understanding of the mechanisms of disease increase, the full genomic context of variation may become increasingly significant

Baseline characteristics predict risk of progression and response to combined medical therapy for benign prostatic hyperplasia (BPH)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110594/1/bju12802.pd

The cancer translational research informatics platform

<p>Abstract</p> <p>Background</p> <p>Despite the pressing need for the creation of applications that facilitate the aggregation of clinical and molecular data, most current applications are proprietary and lack the necessary compliance with standards that would allow for cross-institutional data exchange. In line with its mission of accelerating research discoveries and improving patient outcomes by linking networks of researchers, physicians, and patients focused on cancer research, caBIG (cancer Biomedical Informatics Grid™) has sponsored the creation of the caTRIP (Cancer Translational Research Informatics Platform) tool, with the purpose of aggregating clinical and molecular data in a repository that is user-friendly, easily accessible, as well as compliant with regulatory requirements of privacy and security.</p> <p>Results</p> <p>caTRIP has been developed as an N-tier architecture, with three primary tiers: domain services, the distributed query engine, and the graphical user interface, primarily making use of the caGrid infrastructure to ensure compatibility with other tools currently developed by caBIG. The application interface was designed so that users can construct queries using either the Simple Interface via drop-down menus or the Advanced Interface for more sophisticated searching strategies to using drag-and-drop. Furthermore, the application addresses the security concerns of authentication, authorization, and delegation, as well as an automated honest broker service for deidentifying data.</p> <p>Conclusion</p> <p>Currently being deployed at Duke University and a few other centers, we expect that caTRIP will make a significant contribution to further the development of translational research through the facilitation of its data exchange and storage processes.</p

aGEM: an integrative system for analyzing spatial-temporal gene-expression information

Motivation: The work presented here describes the ‘anatomical Gene-Expression Mapping (aGEM)’ Platform, a development conceived to integrate phenotypic information with the spatial and temporal distributions of genes expressed in the mouse. The aGEM Platform has been built by extending the Distributed Annotation System (DAS) protocol, which was originally designed to share genome annotations over the WWW. DAS is a client-server system in which a single client integrates information from multiple distributed servers

LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes

<p>Abstract</p> <p>Background</p> <p>Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC) software, which often results in short contig lengths (of 3-5 clones before merging) as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs).</p> <p>Results</p> <p>To address these problems, we propose a novel approach that: (i) reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii) obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii) explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv) performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v) uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC) were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize.</p> <p>Conclusions</p> <p>The results show that compared to other methods, LTC enables the construction of highly reliable and longer contigs (5-12 clones before merging), the detection of "weak" connections in contigs and their "repair", and the elongation of contigs obtained by other assembly methods.</p

Reframing social space: an analysis of symbolic places and their transformations over time

reservedL’obiettivo di questa ricerca è quello di trovare i significati che gli individui attribuiscono a luoghi fisici, attraverso un breve introduzione letteraria al "place attachment", in modo da identificare se, e come, sia possibile instaurare legami affettivi nei confronti di determinate aree spaziali, e da cosa siano scaturiti. Un focus ulteriore viene posto sugli effetti causati dalla pandemia COVID-19, con particolare interesse posto nei cambiamenti vissuti dal target di riferimento, ovvero negli studenti universitari della città di Padova, a seguito delle trasformazioni vissute in ambito accademico: l'utilizzo della DAD (didattica a distanza), il mutamento sul territorio di determinati luoghi di riferimento e i rinnovamenti nei percorsi di quotidianità delle tipiche "vite universitarie". Il disegno di ricerca prevede un approccio di tipo partecipativo con l'utilizzo di metodi creativi, prevedendo una prima fase di raccolta dati attraverso un questionario semi strutturato e la presentazione di una mappa di comunità, per l’esposizione di materiale visivo riguardante il territorio padovano.The aim of this research is to find the meanings that individuals ascribe to physical places, by providing a brief literary introduction to the concept of 'place attachment', in order to identify whether and how emoional ties can be established with regard to certain spatial areas, and how they arose. A further focus is placed on the effects caused by the COVID-19 pandemic, with particular interest placed in the changes experienced by the target audience like, in this case, university students in the city of Padua, as a result of the transformations experienced in the academic sphere: the use of DAD (distance learning), the change in the territory of certain places of interest and the renewals in the everyday paths of typical 'university lives'. The research design provides a participatory approach with the use of creative methods, envisaging an initial phase of data collection through a semi-structured questionnaire and the presentation of a community map, for the display of visual material concerning the Padua area