Improving Informed Consent: The Medium Is Not the Message

An important type of research on informed consent involves empirically testing interventions designed to improve the consent process. Here we report on the experience of eight teams that conducted research involving interventions designed primarily to impact one of three categories: decision-making, knowledge, and the therapeutic misconception

A Perspective on Future Research Directions in Information Theory

Information theory is rapidly approaching its 70th birthday. What are promising future directions for research in information theory? Where will information theory be having the most impact in 10-20 years? What new and emerging areas are ripe for the most impact, of the sort that information theory has had on the telecommunications industry over the last 60 years? How should the IEEE Information Theory Society promote high-risk new research directions and broaden the reach of information theory, while continuing to be true to its ideals and insisting on the intellectual rigor that makes its breakthroughs so powerful? These are some of the questions that an ad hoc committee (composed of the present authors) explored over the past two years. We have discussed and debated these questions, and solicited detailed inputs from experts in fields including genomics, biology, economics, and neuroscience. This report is the result of these discussions

Single-cell sequencing of genomic DNA resolves sub-clonal heterogeneity in a melanoma cell line

Abstract: We performed shallow single-cell sequencing of genomic DNA across 1475 cells from a cell-line, COLO829, to resolve overall complexity and clonality. This melanoma tumor-line has been previously characterized by multiple technologies and is a benchmark for evaluating somatic alterations. In some of these studies, COLO829 has shown conflicting and/or indeterminate copy number and, thus, single-cell sequencing provides a tool for gaining insight. Following shallow single-cell sequencing, we first identified at least four major sub-clones by discriminant analysis of principal components of single-cell copy number data. Based on clustering, break-point and loss of heterozygosity analysis of aggregated data from sub-clones, we identified distinct hallmark events that were validated within bulk sequencing and spectral karyotyping. In summary, COLO829 exhibits a classical Dutrillaux’s monosomic/trisomic pattern of karyotype evolution with endoreduplication, where consistent sub-clones emerge from the loss/gain of abnormal chromosomes. Overall, our results demonstrate how shallow copy number profiling can uncover hidden biological insights

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

DARE Newsletter, Vol. 15, No. 4, Fall 2012

Quarterly newsletter of the Dictionary of American Regional EnglishContents: "Words of America: A Field Guide (Part 1)" by Michael Adams; "Volume VI Preview"; "Staff Member Profile: Trini Stickle"; "Funding Update" by Jon E. Sorenso

DARE Newsletter, Vol. 11, No. 4, Fall 2008

Quarterly newsletter of the Dictionary of American Regional EnglishContents: "Using DARE in the Systematic Study of Regional Variation" by Ed Finegan; "Funding Update" by Jon E. Sorenson; "Coming in Volume V"; "Staff Member Profile: Nathan Carlson"; "Where Are They Now?: Erin Meyer"; "DARE Editor Attends Methods XIII Conference

DARE Newsletter, Vol. 11, Nos. 2/3, Spring/Summer 2008

Quarterly newsletter of the Dictionary of American Regional EnglishContents: "Satisfied Customers Have Their Say" by Joan Houston Hall; "Coming in Volume V"; "DARE Editors Part of Wisconsin Englishes Project"; "Funding Update" by Jon E. Sorenson; "DARE Editor Attends Conference"; "Volunteer Profile: Alyssa Severn"; "DARE Staff Changes

DARE Newsletter, Vol. 14, No. 4, Fall 2011

Quarterly newsletter of the Dictionary of American Regional EnglishContents: "DARE: The View from the Letter Z (Part 2)" by Joan Houston Hall; "Funding Update" by Jon E. Sorenson; "The DARE Bibliography: A Preview"; "Staff Member Profile: Esther Hong"; "DARE in Humanities"; "Volume V DARE Quiz"; "Volume V of DARE Available for Pre-Order