Tangent normalization for somatic copy-number inference in cancer genome analysis.

Motivation: Somatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant challenge to the inference of SCNAs for cancer genome analyses. As part of The Cancer Genome Atlas, the Broad Institute Genome Characterization Center developed the Tangent normalization method to generate copy-number profiles using data from single-nucleotide polymorphism (SNP) arrays and whole-exome sequencing (WES) technologies for over 10 000 pairs of tumors and matched normal samples.

Joint Design with Providers of Clinical Decision Support for Value-Based Advanced Shoulder Imaging.

Background: Provider orders for inappropriate advanced imaging, while rarely altering patient management, contribute enough to the strain on available health care resources, and therefore the United States Congress established the Appropriate Use Criteria Program.

Objectives: To examine whether co-designing clinical decision support (CDS) with referring providers will reduce barriers to adoption and facilitate more appropriate shoulder ultrasound (US) over magnetic resonance imaging (MRI) in diagnosing Veteran shoulder pain, given similar efficacies and only 5% MRI follow-up rate after shoulder US.

Methods: We used a theory-driven, convergent parallel mixed-methods approach to prospectively (1) determine medical providers' reasons for selecting MRI over US in diagnosing shoulder pain and identify barriers to ordering US, (2) co-design CDS, informed by provider interviews, to prompt appropriate US use, and (3) assess CDS impact on shoulder imaging use.

The GenePattern Notebook Environment.

Interactive analysis notebook environments promise to streamline genomics research through interleaving text, multimedia, and executable code into unified, sharable, reproducible "research narratives." However, current notebook systems require programming knowledge, limiting their wider adoption by the research community. We have developed the GenePattern Notebook environment (http://www.

GenePattern flow cytometry suite.

Background: Traditional flow cytometry data analysis is largely based on interactive and time consuming analysis of series two dimensional representations of up to 20 dimensional data. Recent technological advances have increased the amount of data generated by the technology and outpaced the development of data analysis approaches. While there are advanced tools available, including many R/BioConductor packages, these are only accessible programmatically and therefore out of reach for most experimentalists.

Evaluating community-based public health leadership training.

Context: Addressing the nation's increasingly complex public health challenges will require more effective multisector collaboration and stronger public health leadership. In 2005, the Healthy Wisconsin Leadership Institute launched an annual, year-long intensive "community teams" program. The goal of this program is to develop collaborative leadership and public health skills among Wisconsin-based multisectoral teams mobilizing their communities to improve public health.

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.

We describe methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, we improve the estimation of background rates for each category. We additionally describe a probabilistic method for defining the boundaries of selected-for SCNA regions with user-defined confidence.