Clinical validation of the Tempus xO assay.

We have developed a clinically validated NGS assay that includes tumor, germline and RNA sequencing. We apply this assay to clinical specimens and cell lines, and we demonstrate a clinical sensitivity of 98.4% and positive predictive value of 100% for the clinically actionable variants measured by the assay. We also demonstrate highly accurate copy number measurements and gene rearrangement identification.

A user-defined data type for the storage of time series data allowing efficient similarity screening.

The volume of the experimentally measured time series data is rapidly growing, while storage solutions offering better data types than simple arrays of numbers or opaque blobs for keeping series data are sorely lacking. A number of indexing methods have been proposed to provide efficient access to time series data, but none has so far been integrated into a tried-and-proven database system. To explore the possibility of such integration, we have developed a data type for time series storage in PostgreSQL, an object-relational database system, and equipped it with an access method based on SAX (Symbolic Aggregate approXimation). This new data type has been successfully tested in a database supporting a large-scale plant gene expression experiment, and it was additionally tested on a very large set of simulated time series data.

Continuous, data-rich appraisal of surgical trainees' operative abilities: a novel approach for measuring performance and providing feedback.

BACKGROUND: We developed a convenient mechanism, Surgical Training and Assessment Tool (STAT), to accomplish detailed, continuous analysis of surgical trainees' operative abilities, and a simple method, Quality Based Surgical Training (QBST) for implementing it. METHODS: Using a web-accessed computer program, attending physicians and trainees independently assessed the trainee's operative performance after every operative (training) case. Global attributes of surgical knowledge, skill, and independence were assessed as well as the key technical maneuvers of each operation. A system of hierarchical, expandable menus specific to each of hundreds of different surgical procedures allowed the assessments to be made as detailed or as general as the users felt were necessary. In addition, freehand, unscripted commentary was recorded via an optional "remarks" box feature. Finally, an independently chosen, "overall" grade scaled F through A+ concluded each assessment. RESULTS: Over a 31 month period, 72 different users (52 trainees, 20 attending physicians) submitted 3849 performance assessments on 2424 cases, including 132 different case types and amassing 68,260 distinct data points. The mean number of data points per trainee was 1313; the median time spent per assessment was 60 seconds. Graphic displays allowed formative review of individual cases in real time, and summative review of long term trends. Appraisals of knowledge, skill, and independence were strongly correlated with and independently predictive of the overall competency grade (model r(2) = 0.68; test of predictive significance p < 0.001 for each rating). Trainee and attending physician scores were highly correlated (> 0.7) with one another. CONCLUSIONS: QBST/STAT achieves detailed, continuous analysis of surgical trainees' operative abilities, and facilitates timely, specific, and thorough feedback regarding their performance in theater. QBST/STAT promotes trainee self-reflection and generation of continuous, transparent, iterative training goals.

Developing performance criteria for the e-Pelvis simulator using visual analysis.

The e-Pelvis is an inanimate simulator for clinical uterine examination. Data from the e-Pelvis has been studied extensively yet the clinical characteristics of palpation remain elusive. We describe our use of visual representation of the data that enabled expert physician/investigators to discover patterns of palpation.