21 research outputs found

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

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    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

    Health Care Disparity in Pain

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    Disparity in the treatment of chronic pain has become increasingly pertinent in health care, given the large burden of disease and its economic costs to society. That disease burden is disproportionally carried by minorities and those of lower socioeconomic status for a host of historical and systemic reasons. Only by understanding the cause of such disparities, collecting accurate and thorough data that illuminate all contributing factors, and diversifying the health care workforce, can we achieve more equitable treatment and reduce the burden of chronic pain

    Association of prolonged symptom duration with poor outcomes in lumbar spine surgery: a Michigan Spine Surgery Improvement Collaborative study

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    OBJECTIVE: There is a scarcity of large multicenter data on how preoperative lumbar symptom duration relates to postoperative patient-reported outcomes (PROs). The objective of this study was to determine the effect of preoperative and baseline symptom duration on PROs at 90 days, 1 year, and 2 years after lumbar spine surgery. METHODS: The Michigan Spine Surgery Improvement Collaborative registry was queried for all lumbar spine operations between January 1, 2017, to December 31, 2021, with a follow-up of 2 years. Patients were stratified into three subgroups based on symptom duration: \u3c 3 months, 3 months to \u3c 1 year, and ≥ 1 year. The primary outcomes were reaching the minimal clinically important difference (MCID) for the PROs (i.e., leg pain, Patient-Reported Outcomes Measurement Information System Physical Function (PROMIS PF), EQ-5D, North American Spine Society satisfaction, and return to work). The EQ-5D score was also analyzed as a continuous variable to calculate quality-adjusted life years. Multivariable Poisson generalized estimating equation models were used to report adjusted risk ratios, with the \u3c 3-month cohort used as the reference. RESULTS: There were 37,223 patients (4670 with \u3c 3-month duration, 9356 with 3-month to \u3c 1-year duration, and 23,197 with ≥ 1-year duration) available for analysis. Compared with patients with a symptom duration of \u3c 1 year, patients with a symptom duration of ≥ 1 year were significantly less likely to achieve an MCID in PROMIS PF, EQ-5D, back pain relief, and leg pain relief at 90 days, 1 year, and 2 years postoperatively. Similar trends were observed for patient satisfaction and return to work. With the EQ-5D score as a continuous variable, a symptom duration of ≥ 1 year was associated with 0.04, 0.05, and 0.03 (p \u3c 0.001) decreases in EQ-5D score at 90 days, 1 year, and 2 years after surgery, respectively. CONCLUSIONS: A symptom duration of ≥ 1 year was associated with poorer outcomes on several outcome metrics. This suggests that timely referral and surgery for degenerative lumbar pathology may optimize patient outcome

    Constructing the Islamic state : analysing the interplay between media and policy frames in the aftermath of the November 13th 2015 Paris attacks

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    This article analyses the imagined threat posed by the Islamic State in the aftermath of the November 13th Paris attacks and during the build-up to the December 2nd 2015 House of Commons vote to extend U.K. airstrikes to Syria. Combining Political Communications and International Relations approaches to framing analysis, and focusing on Britain’s three main television news providers (BBC, ITV and Channel 4), it seeks to question (1) how the Islamic State is framed, (2) who shapes those frames, and (3) what consequences arise from adopting certain ways of seeing and speaking over others? The analysis identifies three competing frames (labelled here as the “(Para)Military”, the “Elusive” and the “Extremist” frames), and their main advocates, and shows how, ultimately, U.K. news media tend to support an “elite”-centred understanding of the threat, thus legitimising calls for extending airstrikes into Syria. In so doing, the article provides two contributions to knowledge: first, empirical, by generating substantive new insight into the way the Islamic State was portrayed in the days and weeks following the Paris attacks, and in particular who shapes those portrayals; and, second, conceptual, via its blending of Political Communications and International Relations approaches to framing and their consequences

    A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.

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    High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (pVAAST), a disease-gene identification tool designed for high-throughput sequence data in pedigrees. pVAAST uses a sequence-based model to perform variant and gene-based linkage analysis. Linkage information is then combined with functional prediction and rare variant case-control association information in a unified statistical framework. pVAAST outperformed linkage and rare-variant association tests in simulations and identified disease-causing genes from whole-genome sequence data in three human pedigrees with dominant, recessive and de novo inheritance patterns. The approach is robust to incomplete penetrance and locus heterogeneity and is applicable to a wide variety of genetic traits. pVAAST maintains high power across studies of monogenic, high-penetrance phenotypes in a single pedigree to highly polygenic, common phenotypes involving hundreds of pedigrees
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