16GT: A fast and sensitive variant caller using a 16-genotype probabilistic model

© The Author 2017. Published by Oxford University Press. 16GT is a variant caller for Illumina whole-genome and whole-exome sequencing data. It uses a new 16-genotype probabilistic model to unify single nucleotide polymorphism and insertion and deletion calling in a single variant calling algorithm. In benchmark comparisons with 5 other widely used variant callers on a modern 36-core server, 16GT demonstrated improved sensitivity in calling single nucleotide polymorphisms, and it provided comparable sensitivity and accuracy for calling insertions and deletions as compared to the GATK HaplotypeCaller. 16GT is available at https://github.com/aquaskyline/16GT.Link_to_subscribed_fulltex

Quake: quality-aware detection and correction of sequencing errors

We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake. Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake

Searching for SNPs with cloud computing

Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three

Group versus individual academic detailing to improve the use of antihypertensive medications in primary care: a cluster-randomized controlled trial

Purpose To compare group versus individual academic detailing to increase diuretic or β-blocker use in hypertension. Methods We conducted a cluster-randomized controlled trial in a large health maintenance organization. Subjects (N=9820) were patients with newly treated hypertension in the year preceding the intervention (N=3692), the 9 months following the intervention (N=3556), and the second year following intervention (N=2572). We randomly allocated 3 practice sites to group detailing (N=227 prescribers), 3 to individual detailing (N=235 prescribers), and 3 to usual care (N=319 prescribers). Individual detailing entailed a physician-educator meeting individually with clinicians to address barriers to prescribing guideline-recommended medications. The group detailing intervention incorporated the same social marketing principles in small groups of clinicians. Results In the first year following the intervention, the rates of diuretic or β-blocker use increased by 13.2% in the group detailing practices, 12.5% in the individual detailing practices, and 6.2% in the usual care practices. As compared with usual care practices, diuretic or β-blocker use was more likely in group detailing practices (adjusted odds ratio (OR), 1.40; 95% confidence interval (CI), 1.11 – 1.76) and individual detailing practices (adjusted OR, 1.30; 95% CI, 0.95 – 1.79). Neither intervention affected blood pressure control. Two years following this single-visit intervention, there was still a trend suggesting a persistent effect of individual (OR, 1.22; 95% CI, 0.92 – 1.62), but not group, detailing (OR, 1.06; 95% CI, 0.80 – 1.39), as compared with usual care. Conclusion Both group and individual academic detailing improved antihypertensive prescribing over and above usual care but may require reinforcement to sustain improvements

COMPANION: development of a patient-centred complexity and casemix classification for adult palliative care patients based on needs and resource use – a protocol for a cross-sectional multi-centre study

BACKGROUND: A casemix classification based on patients’ needs can serve to better describe the patient group in palliative care and thus help to develop adequate future care structures and enable national benchmarking and quality control. However, in Germany, there is no such an evidence-based system to differentiate the complexity of patients’ needs in palliative care. Therefore, the study aims to develop a patient-oriented, nationally applicable complexity and casemix classification for adult palliative care patients in Germany. METHODS: COMPANION is a mixed-methods study with data derived from three subprojects. Subproject 1: Prospective, cross-sectional multi-centre study collecting data on patients’ needs which reflect the complexity of the respective patient situation, as well as data on resources that are required to meet these needs in specialist palliative care units, palliative care advisory teams, and specialist palliative home care. Subproject 2: Qualitative study including the development of a literature-based preliminary list of characteristics, expert interviews, and a focus group to develop a taxonomy for specialist palliative care models. Subproject 3: Multi-centre costing study based on resource data from subproject 1 and data of study centres. Data and results from the three subprojects will inform each other and form the basis for the development of the casemix classification. Ultimately, the casemix classification will be developed by applying Classification and Regression Tree (CART) analyses using patient and complexity data from subproject 1 and patient-related cost data from subproject 3. DISCUSSION: This is the first multi-centre costing study that integrates the structure and process characteristics of different palliative care settings in Germany with individual patient care. The mixed methods design and variety of included data allow for the development of a casemix classification that reflect on the complexity of the research subject. The consecutive inclusion of all patients cared for in participating study centres within the time of data collection allows for a comprehensive description of palliative care patients and their needs. A limiting factor is that data will be collected at least partly during the COVID-19 pandemic and potential impact of the pandemic on health care and the research topic cannot be excluded. TRIAL REGISTRATION: German Register for Clinical Studies trial registration number: DRKS00020517

Fate of lesion-related side branches after coronary artery stenting

AbstractObjectives. The aim of this study was to assess the immediate and long-term patency of lesion-associated side branches after coronary artery stenting.Background. The possible adverse effects related to implantation of coronary stents are not completely known. An important potential complication of stenting is side branch occlusion due to mechanical obstruction or thrombosis.Methods. Serial coronary angiography was performed in 153 patients (167 lesions) at baseline, after conventional balloon angioplasty, immediately after Palmaz-Schatz stent placement and at 6 months. The patency of side branches, where present, was analysed at each of these points.Results. Of 167 lesions stented, 57 stent placements spanned 66 side branches with a diameter ≥1 mm. Twenty-seven (41%) of these side branches had ≥50% ostial stenosis before standard balloon angioplasty. Six side branches became occluded after standard balloon angioplasty and remained occluded after stenting. Of the 60 side branches patent after conventional angioplasty, 57 (95%) remained patent immediately after stenting. All three side branches that became occluded after stenting had ≥50% ostial stenosis at baseline. All 60 side branches, including the 3 initially occluded after stenting, were patent at 6-month follow-up.Conclusions. These findings demonstrate that 1) acute side branch occlusion due to coronary stenting occurs infrequently; 2) when side branch occlusion occurs, it is associated with intrinsic ostial disease; and 3) the patency of side branch ostia is well maintained at long-term follow-up

Sixty years of genome biology

Sixty years after Watson and Crick published the double helix model of DNA's structure, thirteen members of Genome Biology's Editorial Board select key advances in the field of genome biology subsequent to that discovery

Vitamin D status in youth with type 1 and type 2 diabetes enrolled in the Pediatric Diabetes Consortium (PDC) is not worse than in youth without diabetes

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134500/1/pedi12340.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134500/2/pedi12340_am.pd

Progress, challenges and opportunities for Red Listing

Despite its recognition as an important global resource for conservation, the International Union for Conservation of Nature's (IUCN) Red List of Threatened Species only provides assessments of extinction risk for a small and biased subset of known biodiversity. A more complete Red List can better support species-level conservation by indicating how quickly we need to act on species deemed to be priorities for conservation action.Vascular plants represent one of the Red List knowledge gaps, with only 7% of species currently on the Red List (including in the Data Deficient and Least Concern categories). Using vascular plants as a case study we highlight how recent developments, such as changes to rules, improvements to data management systems, better assessment tools and training, can support Red List assessment activity. We also identify ongoing challenges, such as the need to support regional and national assessment initiatives, the largely voluntary nature of the Red List community, as well as the need to meet core operating costs for the Red List. Finally, we highlight how new opportunities such as automation and batch uploading can fast-track assessments, and how better monitoring of assessment growth can help assess the impact of new developments. Most of our findings are also applicable to other species-rich groups that are under-represented on the Red List.We examine trends in plant Red Listing and conclude that the rate of new assessments has not increased in line with what would be required to reach goals such as the Barometer of Life. This may result partly from a lag between recent changes and their effects, but further progress can be made by realising the opportunities outlined here and by growing the Red List community and strengthening collaboration with IUCN

Re-Assembly of the Genome of Francisella tularensis Subsp. holarctica OSU18

Francisella tularensis is a highly infectious human intracellular pathogen that is the causative agent of tularemia. It occurs in several major subtypes, including the live vaccine strain holarctica (type B). F. tularensis is classified as category A biodefense agent in part because a relatively small number of organisms can cause severe illness. Three complete genomes of subspecies holarctica have been sequenced and deposited in public archives, of which OSU18 was the first and the only strain for which a scientific publication has appeared [1]. We re-assembled the OSU18 strain using both de novo and comparative assembly techniques, and found that the published sequence has two large inversion mis-assemblies. We generated a corrected assembly of the entire genome along with detailed information on the placement of individual reads within the assembly. This assembly will provide a more accurate basis for future comparative studies of this pathogen