91 research outputs found

    The Cancer Genomics Resource List 2014

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    Context.— Genomic sequencing for cancer is offered by commercial for-profit laboratories, independent laboratory networks, and laboratories in academic medical centers and integrated health networks. The variability among the tests has created a complex, confusing environment. Objective.— To address the complexity, the Personalized Health Care (PHC) Committee of the College of American Pathologists proposed the development of a cancer genomics resource list (CGRL). The goal of this resource was to assist the laboratory pathology and clinical oncology communities. Design.— The PHC Committee established a working group in 2012 to address this goal. The group consisted of site-specific experts in cancer genetic sequencing. The group identified current next-generation sequencing (NGS)–based cancer tests and compiled them into a usable resource. The genes were annotated by the working group. The annotation process drew on published knowledge, including public databases and the medical literature. Results.— The compiled list includes NGS panels offered by 19 laboratories or vendors, accompanied by annotations. The list has 611 different genes for which NGS-based mutation testing is offered. Surprisingly, of these 611 genes, 0 genes were listed in every panel, 43 genes were listed in 4 panels, and 54 genes were listed in 3 panels. In addition, tests for 393 genes were offered by only 1 or 2 institutions. Table 1 provides an example of gene mutations offered for breast cancer genomic testing with the annotation as it appears in the CGRL 2014. Conclusions.— The final product, referred to as the Cancer Genomics Resource List 2014, is available as supplemental digital content

    Edge localized mode control with an edge resonant magnetic perturbation

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    A low amplitude (ήbr∕BT=1 part in 5000) edge resonantmagnetic field perturbation with toroidalmode number n=3 and poloidal mode numbers between 8 and 15 has been used to suppress most large type I edge localized modes(ELMs) without degrading core plasma confinement. ELMs have been suppressed for periods of up to 8.6 energy confinement times when the edge safety factor q95 is between 3.5 and 4. The large ELMs are replaced by packets of events (possibly type II ELMs) with small amplitude, narrow radial extent, and a higher level of magnetic field and density fluctuations, creating a duty cycle with long “active” intervals of high transport and short “quiet” intervals of low transport. The increased transport associated with these events is less impulsive and slows the recovery of the pedestal profiles to the values reached just before the large ELMs without the n=3 perturbation. Changing the toroidal phase of the perturbation by 60° with respect to the best ELM suppression case reduces the ELM amplitude and frequency by factors of 2–3 in the divertor, produces a more stochastic response in the H-mode pedestal profiles, and displays similar increases in small scale events, although significant numbers of large ELMs survive. In contrast to the best ELM suppression case where the type I ELMs are also suppressed on the outboard midplane, the midplane recycling increases until individual ELMs are no longer discernable. The ELM response depends on the toroidal phase of the applied perturbation because intrinsic error fields make the target plasma nonaxisymmetric, and suggests that at least some of the variation in ELM behavior in a single device or among different devices is due to differences in the intrinsic error fields in these devices. These results indicate that ELMs can be suppressed by small edge resonantmagnetic field perturbations. Extrapolation to next-step burning plasma devices will require extending the regime of operation to lower collisionality and understanding the physical mechanism responsible for the ELM suppression.This work was funded by the U.S. Department of Energy under Grant Nos. DE-FC02-04ER54698, DE-FG02- 04ER54758, DE-FG03-01ER54615, W-7405-ENG-48, DEFG03-96ER54373, DE-FG02-89ER53297, DE-AC05- 00OR22725, and DE-AC04-94AL85000

    Whole-genome phylogenies of the family Bacillaceae and expansion of the sigma factor gene family in the Bacillus cereus species-group

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    <p>Abstract</p> <p>Background</p> <p>The <it>Bacillus cereus </it><it>sensu lato </it>group consists of six species (<it>B. anthracis</it>, <it>B. cereus</it>, <it>B. mycoides</it>, <it>B. pseudomycoides</it>, <it>B. thuringiensis</it>, and <it>B. weihenstephanensis</it>). While classical microbial taxonomy proposed these organisms as distinct species, newer molecular phylogenies and comparative genome sequencing suggests that these organisms should be classified as a single species (thus, we will refer to these organisms collectively as the <it>Bc </it>species-group). How do we account for the underlying similarity of these phenotypically diverse microbes? It has been established for some time that the most rapidly evolving and evolutionarily flexible portions of the bacterial genome are regulatory sequences and transcriptional networks. Other studies have suggested that the sigma factor gene family of these organisms has diverged and expanded significantly relative to their ancestors; sigma factors are those portions of the bacterial transcriptional apparatus that control RNA polymerase recognition for promoter selection. Thus, examining sigma factor divergence in these organisms would concurrently examine both regulatory sequences and transcriptional networks important for divergence. We began this examination by comparison to the sigma factor gene set of <it>B. subtilis</it>.</p> <p>Results</p> <p>Phylogenetic analysis of the <it>Bc </it>species-group utilizing 157 single-copy genes of the family <it>Bacillaceae </it>suggests that several taxonomic revisions of the genus <it>Bacillus </it>should be considered. Within the <it>Bc </it>species-group there is little indication that the currently recognized species form related sub-groupings, suggesting that they are members of the same species. The sigma factor gene family encoded by the <it>Bc </it>species-group appears to be the result of a dynamic gene-duplication and gene-loss process that in previous analyses underestimated the true heterogeneity of the sigma factor content in the <it>Bc </it>species-group.</p> <p>Conclusions</p> <p>Expansion of the sigma factor gene family appears to have preferentially occurred within the extracytoplasmic function (ECF) sigma factor genes, while the primary alternative (PA) sigma factor genes are, in general, highly conserved with those found in <it>B. subtilis</it>. Divergence of the sigma-controlled transcriptional regulons among various members of the <it>Bc </it>species-group likely has a major role in explaining the diversity of phenotypic characteristics seen in members of the <it>Bc </it>species-group.</p
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