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- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: 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.
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| 2. |
- Bianco, L., et al.
(författare)
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Discovery of W-157 and Os-161
- 2010
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 690:1, s. 15-18
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Tidskriftsartikel (refereegranskat)abstract
- The nuclides W-157 and Os-161 have been discovered ill reactions of Ni-58 ion beams with a Cd-106 target. The Os-161 alpha-decay energy and half-life were 6890 +/- 12 keV and 640 +/- 60 mu s. The daughter W-157 nuclei beta-decayed with a half-life of 275 +/- 40 ms, populating both low-lying alpha-decaying states in Ta-157, which is consistent with a 7/2(-) ground state in W-157. Fine structure observed in the alpha decay of Os-161 places the lowest excited state in W-157 with 1(pi) = 9/2(-) at 318 +/- 30 key. The branching ratio of 5.5(-2.2)(+3.1)% indicates that Os-161 also has a 7/2(-) ground state. Shell-model calculations analysing the effects of monopole shifts and a tensor force on the relative energies of 2f(7/2) and 1h(9/2) neutron states in N = 83 isotones are presented. (C) 2010 Elsevier B.V. All rights reserved.
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| 3. |
- Stevenson, Bradley S, et al.
(författare)
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Hoeflea anabaenae sp. nov., an epiphytic symbiont that attaches to the heterocysts of a strain of Anabaena.
- 2011
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 61:10, s. 2439-2444
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Tidskriftsartikel (refereegranskat)abstract
- The heterotrophic, epiphytic symbiotic bacterial strain WH2K(T) was previously isolated from a two-member culture in which it was attached to the heterocysts of a strain of Anabaena (SSM-00). Analysis of its 16S rRNA genes demonstrated that the symbiont was most closely related to the type strain of Hoeflea marina (96.9% similarity), which belongs to the family Phyllobacteriaceae within the order Rhizobiales of the class Alphaproteobacteria. A polyphasic taxonomic study was performed on strain WH2K(T) that consisted of irregular rods (2-5μm long, 0.2μm wide) that appeared to be narrower at one polar end. Optimal growth was obtained in complex media with 15 g l(-1) sea salts, at 18-34 °C (30 °C optimum) and at pH values in the range of 6.0-8.0 (6.5 optimum). Unknown growth requirements were provided by small amounts of yeast extract but not standard vitamin and trace metal solutions. Of the substrates tested, WH2K(T) was only able to utilize acetate, pyruvate, malate, and fumarate. Growth was only observed under aerobic and microaerobic conditions and nitrate was not reduced. No photosynthetic pigments were detected under any of the growth conditions tested. The predominant fatty acids were present in a summed feature that comprises C (18:1) ω7c, / 9t /12t or any combination of these (64.0%) and an unidentified fatty acid of estimated chain length (ECL of C(17.6) (13.5%), The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphoglycolipid, unknown lipids and an unidentified aminolipid. The only respiratory ubiquinone detected was Q-10. The DNA %G+C content of the strain is 58.1%. The organism can form a site-specific attached symbiotic relationship with a species of Anabaena. Based on phylogenetic and phenotypic evidence it is proposed that strain WH2K(T) be classified as a fourth species of the genus Hoeflea, for which the name Hoeflea anabaenae sp. nov. is proposed. The type strain of Hoeflea anabaenae sp. nov. is WH2K(T) (=CCUG 56626(T) =NRRL B-59520(T)).
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