Doctor of Philosophy

dissertationWhole genome sequencing projects have expanded our understanding of evolution, organism development, and human disease. Now advances in secondgeneration technologies are making whole genome sequencing routine even for small laboratories. However, advances in annotation technology have not kept pace with genome sequencing, and annotation has become the major bottleneck for many genome projects (especially those with limited bioinformatics expertise). At the same time, challenges associated with genomics research extend beyond merely annotating genomes, as annotations must be subjected to diverse downstream analyses, the complexities of which can confound smaller research groups. Additionally, with improvements in genome assembly and the wide availability of next generation transcriptome data (mRNA-seq), researchers have the opportunity to re-annotate previously published genomes, which creates new difficulties for data integration and management that are not well addressed by existing tools. In response to the challenges facing second-generation genome projects, I have developed the annotation pipeline MAKER2 together with accessory software for downstream analysis and data management. The MAKER2 annotation pipeline finds repeats within a genome, aligns ESTs and cDNAs, identifies sites of protein homology, and produces database-ready gene annotations in association with supporting evidence. However MAKER2 can go beyond structural annotation to identify and integrate functional annotations. MAKER2 also provides researchers iv with the capability to re-annotate legacy genome datasets and to incorporate mRNAseq. Additionally, MAKER2 supports distributed parallelization on computer clusters, thus providing a scalable solution for datasets of any size. Annotations produced by MAKER2 can be directly loaded into many popular downstream annotation analysis and management tools from the Generic Model Organism Database Project. By using MAKER2 with these tools, research groups can quickly build genome annotations, perform analyses, and distribute their data to the wider scientific community. Here I describe the internal architecture of MAKER2, and document its computational capabilities. I also describe my work to annotate and analyze eight emerging model organism genomes in collaboration with their associated genome projects. Thus, in the course of my thesis work, I have addressed a specific need within the scientific community for easy-to-use annotation and analysis tools while also expanding our understanding of evolution and biology

Reply to The atypical Spitz tumor of uncertain biologic potential

No abstract.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64914/1/24694_ftp.pd

Quantitative measures for the management and comparison of annotated genomes

<p>Abstract</p> <p>Background</p> <p>The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review.</p> <p>Results</p> <p>In response, we have developed a suite of quantitative measures to better characterize changes to a genome's annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases – <it>H. sapiens</it>, <it>M. musculus</it>, <it>D. melanogaster</it>, <it>A. gambiae</it>, and <it>C. elegans</it>.</p> <p>Conclusion</p> <p>Our results provide the first detailed, historical overview of how these genomes' annotations have changed over the years, and demonstrate the usefulness of these measures for genome annotation management.</p

WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.

MotivationCopy number variations (CNVs) are a major source of genomic variability and are especially significant in cancer. Until recently microarray technologies have been used to characterize CNVs in genomes. However, advances in next-generation sequencing technology offer significant opportunities to deduce copy number directly from genome sequencing data. Unfortunately cancer genomes differ from normal genomes in several aspects that make them far less amenable to copy number detection. For example, cancer genomes are often aneuploid and an admixture of diploid/non-tumor cell fractions. Also patient-derived xenograft models can be laden with mouse contamination that strongly affects accurate assignment of copy number. Hence, there is a need to develop analytical tools that can take into account cancer-specific parameters for detecting CNVs directly from genome sequencing data.ResultsWe have developed WaveCNV, a software package to identify copy number alterations by detecting breakpoints of CNVs using translation-invariant discrete wavelet transforms and assign digitized copy numbers to each event using next-generation sequencing data. We also assign alleles specifying the chromosomal ratio following duplication/loss. We verified copy number calls using both microarray (correlation coefficient 0.97) and quantitative polymerase chain reaction (correlation coefficient 0.94) and found them to be highly concordant. We demonstrate its utility in pancreatic primary and xenograft sequencing data.Availability and implementationSource code and executables are available at https://github.com/WaveCNV. The segmentation algorithm is implemented in MATLAB, and copy number assignment is implemented [email protected] informationSupplementary data are available at Bioinformatics online

Local Civic Health: A Guide to Building Community and Bridging Divides

In the same way that doctors conduct an annual check-up to assess our health, we can collect information to assess the civic health of our communities. Civic health includes factors such as how much people trust each other, show up at public meetings, get involved, vote, and help out neighbors. This seven-part guide is designed to help people at the local level collect data to better understand what factors bring people together or push them apart. This information can help communities to thrive and strengthen democracy at the local level. The guide includes exercises around mapping the different populations who live in your community, evaluating how local spaces build or discourage community, building equity into local engagement processes, and collecting and analyzing data about civic health including surveys, dialogues, interviews, and civic photojournalism

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms

Physio4FMD: protocol for a multicentre randomised controlled trial of specialist physiotherapy for functional motor disorder

Background Patients with functional motor disorder (FMD) experience persistent and disabling neurological symptoms such as weakness, tremor, dystonia and disordered gait. Physiotherapy is usually considered an important part of treatment; however, sufficiently-powered controlled studies are lacking. Here we present the protocol of a randomised controlled trial (RCT) that aims to evaluate the clinical and cost effectiveness of a specialist physiotherapy programme for FMD. Methods/design The trial is a pragmatic, multicentre, single blind parallel arm randomised controlled trial (RCT). 264 Adults with a clinically definite diagnosis of FMD will be recruited from neurology clinics and randomised to receive either the trial intervention (a specialist physiotherapy protocol) or treatment as usual control (referral to a community physiotherapy service suitable for people with neurological symptoms). Participants will be followed up at 6 and 12 months. The primary outcome is the Physical Function domain of the Short Form 36 questionnaire at 12 months. Secondary domains of measurement will include participant perception of change, mobility, health-related quality of life, health service utilisation, anxiety and depression. Health economic analysis will evaluate the cost impact of trial and control interventions from a health and social care perspective as well as societal perspective. Discussion This trial will be the first adequately-powered RCT of physical-based rehabilitation for FMD. Trial registration International Standard Randomised Controlled Trials Number ISRCTN56136713. Registered 27 March 2018

Uptake and effectiveness of the Children's Fitness Tax Credit in Canada: the rich get richer

<p>Abstract</p> <p>Background</p> <p>The Government of Canada implemented a Children's Fitness Tax Credit (CFTC) in 2007 which allows a non-refundable tax credit of up to $500 to register a child in an eligible physical activity (PA) program. The purposes of this study were to assess whether the awareness, uptake, and perceived effectiveness of this tax credit varied by household income among Canadian parents.</p> <p>Methods</p> <p>An internet-based panel survey was conducted in March 2009 with a representative sample of 2135 Canadians. Of those, parents with children aged 2 to 18 years of age (<it>n </it>= 1004) were asked if their child was involved in organized PA programs (including dance and sports), the associated costs to register their child in these programs, awareness of the CFTC, if they had claimed the CFTC for the tax year 2007, and whether they planned to claim it in the upcoming year. Parents were also asked if they believed the CFTC has lead to their child being more involved in PA programs.</p> <p>Results</p> <p>Among parents, 54.4% stated their child was in organized PA and 55.5% were aware of the CFTC. Parents in the lowest income quartile were significantly less aware and less likely to claim the CFTC than other income groups. Among parents who had claimed the CFTC, few (15.6%) believed it had increased their child's participation in PA programs.</p> <p>Conclusions</p> <p>More than half of Canadian parents with children have claimed the CFTC. However, the tax credit appears to benefit the wealthier families in Canada.</p

Physio4FMD: protocol for a multicentre randomised controlled trial of specialist physiotherapy for functional motor disorder.

BACKGROUND: Patients with functional motor disorder (FMD) experience persistent and disabling neurological symptoms such as weakness, tremor, dystonia and disordered gait. Physiotherapy is usually considered an important part of treatment; however, sufficiently-powered controlled studies are lacking. Here we present the protocol of a randomised controlled trial (RCT) that aims to evaluate the clinical and cost effectiveness of a specialist physiotherapy programme for FMD. // METHODS/DESIGN: The trial is a pragmatic, multicentre, single blind parallel arm randomised controlled trial (RCT). 264 Adults with a clinically definite diagnosis of FMD will be recruited from neurology clinics and randomised to receive either the trial intervention (a specialist physiotherapy protocol) or treatment as usual control (referral to a community physiotherapy service suitable for people with neurological symptoms). Participants will be followed up at 6 and 12 months. The primary outcome is the Physical Function domain of the Short Form 36 questionnaire at 12 months. Secondary domains of measurement will include participant perception of change, mobility, health-related quality of life, health service utilisation, anxiety and depression. Health economic analysis will evaluate the cost impact of trial and control interventions from a health and social care perspective as well as societal perspective. // DISCUSSION: This trial will be the first adequately-powered RCT of physical-based rehabilitation for FMD

Serratia marcescens bacteremia traced to an infused narcotic

BACKGROUND From June 30, 1998, through March 21, 1999, several patients in the surgical intensive care unit of a hospital acquired Serratia marcescens bacteremia. We investigated this outbreak. METHODS A case was defined as the occurrence of S. marcescens bacteremia in any patient in the surgical intensive care unit during the period of the epidemic. To identify risk factors, we compared patients with S. marcescens bacteremia with randomly selected controls. Isolates from patients and from medications were evaluated by pulsed-field gel electrophoresis. The hair of one employee was tested for fentanyl. RESULTS Twenty-six patients with S. marcescens bacteremia were identified; eight (31 percent) had polymicrobial bacteremia, and seven of these had Enterobacter cloacae and S. marcescens in the same culture. According to univariate analysis, patients with S. marcescensbacteremia stayed in the surgical intensive care unit longer than controls (13.5 vs. 4.0 days, PS. marcescens and E. cloacae. The isolates from the case patients and from the fentanyl infusions had similar patterns on pulsed-field gel electrophoresis. After removal of the implicated respiratory therapist, no further cases occurred. Full Text of Results... CONCLUSIONS An outbreak of S. marcescens and E. cloacae bacteremia in a surgical intensive care unit was traced to extrinsic contamination of the parenteral narcotic fentanyl by a health care worker. Our findings underscore the risk of complications in patients that is associated with illicit narcotic use by health care workers