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

Health System Performance for the High-Need Patient: A Look at Access to Care and Patient Care Experiences

Achieving a high-performing health system will require improving outcomes and reducing costs for high-need, high-cost patients—those who use the most health care services and account for a disproportionately large share of health care spending. Goal: To compare the health care experiences of adults with high needs—those with three or more chronic diseases and a functional limitation in the ability to care for themselves or perform routine daily tasks—to all adults and to those with multiple chronic diseases but no functional limitations. Methods: Analysis of data from the 2009–2011 Medical Expenditure Panel Survey. Key findings: High-need adults were more likely to report having an unmet medical need and less likely to report having good patient–provider communication. High-need adults reported roughly similar ease of obtaining specialist referrals as other adults and greater likelihood of having a medical home. While adults with private health insurance reported the fewest unmet needs overall, privately insured highneed adults reported the greatest difficulties having their needs met. Conclusion: The health care system needs to work better for the highest-need, most-complex patients. This study's findings highlight the importance of tailoring interventions to address their need

Early Life Stress as an Influence on Limbic Epilepsy: An Hypothesis Whose Time has Come?

The pathogenesis of mesial temporal lobe epilepsy (MTLE), the most prevalent form of refractory focal epilepsy in adults, is thought to begin in early life, even though seizures may not commence until adolescence or adulthood. Amongst the range of early life factors implicated in MTLE causation (febrile seizures, traumatic brain injury, etc.), stress may be one important contributor. Early life stress is an a priori agent deserving study because of the large amount of neuroscientific data showing enduring effects on structure and function in hippocampus and amygdala, the key structures involved in MTLE. An emerging body of evidence directly tests hypotheses concerning early life stress and limbic epilepsy: early life stressors, such as maternal separation, have been shown to aggravate epileptogenesis in both status epilepticus and kindling models of limbic epilepsy. In addition to elucidating its influence on limbic epileptogenesis itself, the study of early life stress has the potential to shed light on the psychiatric disorder that accompanies MTLE. For many years, psychiatric comorbidity was viewed as an effect of epilepsy, mediated psychologically and/or neurobiologically. An alternative – or complementary – perspective is that of shared causation. Early life stress, implicated in the pathogenesis of several psychiatric disorders, may be one such causal factor. This paper aims to critically review the body of experimental evidence linking early life stress and epilepsy; to discuss the direct studies examining early life stress effects in current models of limbic seizures/epilepsy; and to suggest priorities for future research

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

Hawkeye: An interactive visual analytics tool for genome assemblies

Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye. © 2007 Schatz et al.; licensee BioMed Central Ltd

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