PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (45)
 

Clipboard (0)
None

Select a Filter Below

Year of Publication
more »
1.  Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies 
Briefings in Bioinformatics  2011;14(2):213-224.
Since its launch in 2004, the open-source AMOS project has released several innovative DNA sequence analysis applications including: Hawkeye, a visual analytics tool for inspecting the structure of genome assemblies; the Assembly Forensics and FRCurve pipelines for systematically evaluating the quality of a genome assembly; and AMOScmp, the first comparative genome assembler. These applications have been used to assemble and analyze dozens of genomes ranging in complexity from simple microbial species through mammalian genomes. Recent efforts have been focused on enhancing support for new data characteristics brought on by second- and now third-generation sequencing. This review describes the major components of AMOS in light of these challenges, with an emphasis on methods for assessing assembly quality and the visual analytics capabilities of Hawkeye. These interactive graphical aspects are essential for navigating and understanding the complexities of a genome assembly, from the overall genome structure down to individual bases. Hawkeye and AMOS are available open source at http://amos.sourceforge.net.
doi:10.1093/bib/bbr074
PMCID: PMC3603210  PMID: 22199379
DNA Sequencing; genome assembly; assembly forensics; visual analytics
2.  Computational thinking in the era of big data biology 
Genome Biology  2012;13(11):177.
doi:10.1186/gb-2012-13-11-177
PMCID: PMC3580488  PMID: 23194371
3.  Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i 
PLoS ONE  2013;8(10):e76376.
The ancestor of Gloeobacter violaceus PCC 7421T is believed to have diverged from that of all known cyanobacteria before the evolution of thylakoid membranes and plant plastids. The long and largely independent evolutionary history of G. violaceus presents an organism retaining ancestral features of early oxygenic photoautotrophs, and in whom cyanobacteria evolution can be investigated. No other Gloeobacter species has been described since the genus was established in 1974 (Rippka et al., Arch Microbiol 100:435). Gloeobacter affiliated ribosomal gene sequences have been reported in environmental DNA libraries, but only the type strain's genome has been sequenced. However, we report here the cultivation of a new Gloeobacter species, G. kilaueensis JS1T, from an epilithic biofilm in a lava cave in Kīlauea Caldera, Hawai'i. The strain's genome was sequenced from an enriched culture resembling a low-complexity metagenomic sample, using 9 kb paired-end 454 pyrosequences and 400 bp paired-end Illumina reads. The JS1T and G. violaceus PCC 7421T genomes have little gene synteny despite sharing 2842 orthologous genes; comparing the genomes shows they do not belong to the same species. Our results support establishing a new species to accommodate JS1T, for which we propose the name Gloeobacter kilaueensis sp. nov. Strain JS1T has been deposited in the American Type Culture Collection (BAA-2537), the Scottish Marine Institute's Culture Collection of Algae and Protozoa (CCAP 1431/1), and the Belgian Coordinated Collections of Microorganisms (ULC0316). The G. kilaueensis holotype has been deposited in the Algal Collection of the US National Herbarium (US# 217948). The JS1T genome sequence has been deposited in GenBank under accession number CP003587. The G+C content of the genome is 60.54 mol%. The complete genome sequence of G. kilaueensis JS1T may further understanding of cyanobacteria evolution, and the shift from anoxygenic to oxygenic photosynthesis.
doi:10.1371/journal.pone.0076376
PMCID: PMC3806779  PMID: 24194836
4.  Genotyping in the Cloud with Crossbow 
Crossbow is a scalable, portable, and automatic cloud computing tool for identifying SNPs from high coverage short read resequencing data. It is built on Apache Hadoop, an implementation of the MapReduce software framework. Hadoop allows Crossbow to distribute read alignment and SNP calling subtasks over a cluster of commodity computers. Two robust tools, Bowtie and SOAPsnp, implement the fundamental alignment and variant calling operations respectively, and have demonstrated capabilities within Crossbow of analyzing approximately one billion short reads per hour on a commodity Hadoop cluster with 320 cores. Through protocol examples, this unit will demonstrate the use of Crossbow for identifying variations in three different operating modes: on a Hadoop cluster, on a single computer, and on the Amazon Elastic MapReduce cloud computing service.
doi:10.1002/0471250953.bi1503s39
PMCID: PMC3465669  PMID: 22948728
short reads; read alignment; SNP calling; cloud computing; hadoop; software package
5.  Hybrid error correction and de novo assembly of single-molecule sequencing reads 
Nature biotechnology  2012;30(7):693-700.
Emerging single-molecule sequencing instruments can generate multi-kilobase sequences with the potential to dramatically improve genome and transcriptome assembly. However, the high error rate of single-molecule reads is challenging, and has limited their use to resequencing bacteria. To address this limitation, we introduce a novel correction algorithm and assembly strategy that utilizes shorter, high-identity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on Pacbio RS reads of phage, prokaryotic, and eukaryotic whole genomes, including the novel genome of the parrot Melopsittacus undulatus, as well as for RNA-seq reads of the corn (Zea mays) transcriptome. Our approach achieves over 99.9% read correction accuracy and produces substantially better assemblies than current sequencing strategies: in the best example, quintupling the median contig size relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.
doi:10.1038/nbt.2280
PMCID: PMC3707490  PMID: 22750884
6.  The DNA60IFX contest 
Genome Biology  2013;14(6):124.
doi:10.1186/gb-2013-14-6-124
PMCID: PMC3706964  PMID: 23809492
7.  Allergic Bronchopulmonary Aspergillosis Presenting as Chronic Cough in an Elderly Woman Without Previously Documented Asthma 
The Permanente Journal  2013;17(2):e103-e108.
This is a case report from a specialist point of view that includes a comprehensive review of the clinical course pre- and postconsultation along with a brief but pertinent review of the literature as it relates to this particular unusual and protracted case, which was ultimately successfully diagnosed and treated.
A nonsmoking woman in her mid-70s presents to the allergist for consultation of a chronic cough of almost 3-years’ duration without a specific diagnosis as to etiology in spite of numerous diagnostic tests and therapeutic trials.
This is a case report from a specialist point of view that includes a comprehensive review of her clinical course pre- and postconsultation along with a brief but pertinent review of the literature as it relates to this particular unusual and protracted case, which was ultimately successfully diagnosed and treated.
doi:10.7812/TPP/12-051
PMCID: PMC3662291  PMID: 23704852
8.  Current challenges in de novo plant genome sequencing and assembly 
Genome Biology  2012;13(4):243.
Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community.
doi:10.1186/gb-2012-13-4-243
PMCID: PMC3446297  PMID: 22546054
DNA sequencing; genome assembly; plant genomics
9.  De Novo Gene Disruptions in Children on the Autistic Spectrum 
Neuron  2012;74(2):285-299.
SUMMARY
Exome sequencing of 343 families, each with a single child on the autism spectrum and at least one unaffected sibling, reveal de novo small indels and point substitutions, which come mostly from the paternal line in an age-dependent manner. We do not see significantly greater numbers of de novo missense mutations in affected versus unaffected children, but gene-disrupting mutations (nonsense, splice site, and frame shifts) are twice as frequent, 59 to 28. Based on this differential and the number of recurrent and total targets of gene disruption found in our and similar studies, we estimate between 350 and 400 autism susceptibility genes. Many of the disrupted genes in these studies are associated with the fragile X protein, FMRP, reinforcing links between autism and synaptic plasticity. We find FMRP-associated genes are under greater purifying selection than the remainder of genes and suggest they are especially dosage-sensitive targets of cognitive disorders.
doi:10.1016/j.neuron.2012.04.009
PMCID: PMC3619976  PMID: 22542183
10.  Illuminating the genetics of complex human diseases 
BMC Proceedings  2012;6(Suppl 6):O4.
doi:10.1186/1753-6561-6-S6-O4
PMCID: PMC3467579
11.  The rise of a digital immune system 
GigaScience  2012;1:4.
Driven by million-fold improvements in biotechnology, biology is increasingly shifting towards high-resolution, quantitative approaches to study the molecular dynamics of entire populations. One exciting application enabled by this new era of biology is the “digital immune system”. It would work in much the same way as an adaptive, biological immune system: by observing the microbial landscape, detecting potential threats, and neutralizing them before they spread beyond control. With the potential to have an enormous impact on public health, it is time to integrate the necessary biotechnology, computational, and organizational systems to seed the development of a global, sequencing-based pathogen surveillance system.
doi:10.1186/2047-217X-1-4
PMCID: PMC3617452  PMID: 23587178
12.  Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score 
Bioinformatics  2012;28(16):2097-2105.
Motivation: Genome resequencing and short read mapping are two of the primary tools of genomics and are used for many important applications. The current state-of-the-art in mapping uses the quality values and mapping quality scores to evaluate the reliability of the mapping. These attributes, however, are assigned to individual reads and do not directly measure the problematic repeats across the genome. Here, we present the Genome Mappability Score (GMS) as a novel measure of the complexity of resequencing a genome. The GMS is a weighted probability that any read could be unambiguously mapped to a given position and thus measures the overall composition of the genome itself.
Results: We have developed the Genome Mappability Analyzer to compute the GMS of every position in a genome. It leverages the parallelism of cloud computing to analyze large genomes, and enabled us to identify the 5–14% of the human, mouse, fly and yeast genomes that are difficult to analyze with short reads. We examined the accuracy of the widely used BWA/SAMtools polymorphism discovery pipeline in the context of the GMS, and found discovery errors are dominated by false negatives, especially in regions with poor GMS. These errors are fundamental to the mapping process and cannot be overcome by increasing coverage. As such, the GMS should be considered in every resequencing project to pinpoint the ‘dark matter’ of the genome, including of known clinically relevant variations in these regions.
Availability: The source code and profiles of several model organisms are available at http://gma-bio.sourceforge.net
Contact: hlee@cshl.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/bts330
PMCID: PMC3413383  PMID: 22668792
13.  Daily or Intermittent Budesonide in Preschool Children with Recurrent Wheezing 
The New England journal of medicine  2011;365(21):1990-2001.
BACKGROUND
Daily inhaled glucocorticoids are recommended for young children at risk for asthma exacerbations, as indicated by a positive value on the modified asthma predictive index (API) and an exacerbation in the preceding year, but concern remains about daily adherence and effects on growth. We compared daily therapy with intermittent therapy.
METHODS
We studied 278 children between the ages of 12 and 53 months who had positive values on the modified API, recurrent wheezing episodes, and at least one exacerbation in the previous year but a low degree of impairment. Children were randomly assigned to receive a budesonide inhalation suspension for 1 year as either an intermittent high-dose regimen (1 mg twice daily for 7 days, starting early during a predefined respiratory tract illness) or a daily low-dose regimen (0.5 mg nightly) with corresponding placebos. The primary outcome was the frequency of exacerbations requiring oral glucocorticoid therapy.
RESULTS
The daily regimen of budesonide did not differ significantly from the intermittent regimen with respect to the frequency of exacerbations, with a rate per patient-year for the daily regimen of 0.97 (95% confidence interval [CI], 0.76 to 1.22) versus a rate of 0.95 (95% CI, 0.75 to 1.20) for the intermittent regimen (relative rate in the intermittent-regimen group, 0.99; 95% CI, 0.71 to 1.35; P=0.60). There were also no significant between-group differences in several other measures of asthma severity, including the time to the first exacerbation, or adverse events. The mean exposure to budesonide was 104 mg less with the intermittent regimen than with the daily regimen.
CONCLUSIONS
A daily low-dose regimen of budesonide was not superior to an intermittent high-dose regimen in reducing asthma exacerbations. Daily administration led to greater exposure to the drug at 1 year.
doi:10.1056/NEJMoa1104647
PMCID: PMC3247621  PMID: 22111718
14.  Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.▿† 
Journal of Bacteriology  2011;193(19):5450-5464.
Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.
doi:10.1128/JB.05262-11
PMCID: PMC3187462  PMID: 21784931
15.  The Relationship of Asthma-Specific Quality of Life During Pregnancy to Subsequent Asthma and Perinatal Morbidity 
Objective
To determine whether asthma-specific quality of life during pregnancy is related to asthma exacerbations and to perinatal outcomes.
Methods
This was a secondary analysis of data from a randomized controlled trial of inhaled beclomethasone versus theophylline in the treatment of moderate asthma during pregnancy. The Juniper Asthma Quality of Life Questionnaire (AQLQ) was administered to patients at enrollment. Exacerbations were defined as asthma symptoms requiring a hospitalization, unscheduled medical visit, or oral corticosteroid course.
Results
Quality of life assessments were provided by 310 of the 385 participants who completed the study. There was more than a 25% decrease in the odds of a subsequent asthma exacerbation for every 1-point increase in AQLQ score for the overall score (odds ratio [OR] 0.73, 95% confidence interval [CI] 0.55–0.96), emotion domain (OR 0.72, 95% CI 0.59–0.88), and symptoms domain (OR 0.73, 95% CI 0.57–0.94). These relationships were not significantly influenced by initial symptom frequency or forced expiratory volume in 1 s (FEV1). No significant relationships were demonstrated between enrollment AQLQ scores and preeclampsia, preterm birth, low birth weight, or small for gestational age.
Conclusion
Asthma-specific quality of life in early pregnancy is related to subsequent asthma morbidity during pregnancy but not to perinatal outcomes.
doi:10.3109/02770900903483758
PMCID: PMC3249656  PMID: 20100020
asthma; exacerbations; perinatal outcomes; pulmonary function; quality of life
16.  A call for action: comparative effectiveness research in asthma 
Comparative effectiveness research (CER) has received considerable research attention in recent months, and efforts to promote CER are part of the newly enacted Patient Protection and Affordable Care Act. In this paper, we define CER, how it complements traditional efficacy research in asthma, and discuss how CER can help provide the basis for rational decision-making about the care of individual patients with asthma and how best to deliver this care in real-world settings. We present information about the challenges and opportunities to conduct CER, including enhanced patient registries for observational CER and effectiveness trials (also called pragmatic trials). We discuss the urgent need to define the appropriate methodologies for CER and to develop and prioritize a research agenda for CER studies in asthma with the help of a diverse group of stakeholders.
doi:10.1016/j.jaci.2010.08.032
PMCID: PMC3017678  PMID: 20855111
Comparative effectiveness research; comparative clinical effectiveness research; observational studies; effectiveness trials; efficacy trials; pragmatic trials; explanatory trials; asthma
17.  The missing graphical user interface for genomics 
Genome Biology  2010;11(8):128.
Abstract
The Galaxy package empowers regular users to perform rich DNA sequence analysis through a much-needed and user-friendly graphical web interface.
See research article http://genomebiology.com/2010/11/8/R86
Research highlight
With the advent of affordable and high-throughput DNA sequencing, sequencing is becoming an essential component in nearly every genetics lab. These data are being generated to probe sequence variations, to understand transcribed, regulated or methylated DNA elements, and to explore a host of other biological features across the tree of life and across a range of environments and conditions. Given this deluge of data, novices and experts alike are facing the daunting challenge of trying to analyze the raw sequence data computationally. With so many tools available and so many assays to analyze, how can one be expected to stay current with the state of the art? How can one be expected to learn to use each tool and construct robust end-to-end analysis pipelines, all while ensuring that input formats, command-line options, sequence databases and program libraries are set correctly? Finally, once the analysis is complete, how does one ensure the results are reproducible and transparent for others to scrutinize and study?
In an article published in Genome Biology, Jeremy Goecks, Anton Nekrutenko, James Taylor and the rest of the Galaxy Team (Goecks et al. [1]) make a great advance towards resolving these critical questions with the latest update to their Galaxy Project. The ambitious goal of Galaxy is to empower regular users to carry out their own computational analysis without having to be an expert in computational biology or computer science. Galaxy adds a desperately needed graphical user interface to genomics research, making data analysis universally accessible in a web browser, and freeing users from the minutiae of archaic command-line parameters, data formats and scripting languages. Data inputs and computational steps are selected from dynamic graphical menus, and the results are displayed in intuitive plots and summaries that encourage interactive workflows and the exploration of hypotheses. The underlying data analysis tools can be almost any piece of software, written in any language, but all their complexity is neatly hidden inside of Galaxy, allowing users to focus on scientific rather than technical questions.
doi:10.1186/gb-2010-11-8-128
PMCID: PMC2945776  PMID: 20804568
19.  Integrated Microbial Survey Analysis of Prokaryotic Communities for the PhyloChip Microarray ▿ †  
Applied and Environmental Microbiology  2010;76(16):5636-5638.
PhyloTrac is an integrated desktop application for analysis of PhyloChip microarray data. PhyloTrac combined with PhyloChip provides turnkey and comprehensive identification and analysis of bacterial and archaeal communities in complex environmental samples. PhyloTrac is free for noncommercial organizations and is available for all major operating systems at http://www.phylotrac.org/.
doi:10.1128/AEM.00303-10
PMCID: PMC2918976  PMID: 20581189
20.  Cloud Computing and the DNA Data Race 
Nature biotechnology  2010;28(7):691-693.
doi:10.1038/nbt0710-691
PMCID: PMC2904649  PMID: 20622843
21.  Quake: quality-aware detection and correction of sequencing errors 
Genome Biology  2010;11(11):R116.
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.
doi:10.1186/gb-2010-11-11-r116
PMCID: PMC3156955  PMID: 21114842
22.  Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera 
BMC Genomics  2010;11:602.
Background
The ectoparasitic mite Varroa destructor has emerged as the primary pest of domestic honey bees (Apis mellifera). Here we present an initial survey of the V. destructor genome carried out to advance our understanding of Varroa biology and to identify new avenues for mite control. This sequence survey provides immediate resources for molecular and population-genetic analyses of Varroa-Apis interactions and defines the challenges ahead for a comprehensive Varroa genome project.
Results
The genome size was estimated by flow cytometry to be 565 Mbp, larger than most sequenced insects but modest relative to some other Acari. Genomic DNA pooled from ~1,000 mites was sequenced to 4.3× coverage with 454 pyrosequencing. The 2.4 Gbp of sequencing reads were assembled into 184,094 contigs with an N50 of 2,262 bp, totaling 294 Mbp of sequence after filtering. Genic sequences with homology to other eukaryotic genomes were identified on 13,031 of these contigs, totaling 31.3 Mbp. Alignment of protein sequence blocks conserved among V. destructor and four other arthropod genomes indicated a higher level of sequence divergence within this mite lineage relative to the tick Ixodes scapularis. A number of microbes potentially associated with V. destructor were identified in the sequence survey, including ~300 Kbp of sequence deriving from one or more bacterial species of the Actinomycetales. The presence of this bacterium was confirmed in individual mites by PCR assay, but varied significantly by age and sex of mites. Fragments of a novel virus related to the Baculoviridae were also identified in the survey. The rate of single nucleotide polymorphisms (SNPs) in the pooled mites was estimated to be 6.2 × 10-5per bp, a low rate consistent with the historical demography and life history of the species.
Conclusions
This survey has provided general tools for the research community and novel directions for investigating the biology and control of Varroa mites. Ongoing development of Varroa genomic resources will be a boon for comparative genomics of under-represented arthropods, and will further enhance the honey bee and its associated pathogens as a model system for studying host-pathogen interactions.
doi:10.1186/1471-2164-11-602
PMCID: PMC3091747  PMID: 20973996
23.  Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment 
Parallel computing  2009;35(8):429-440.
MUMmerGPU uses highly-parallel commodity graphics processing units (GPU) to accelerate the data-intensive computation of aligning next generation DNA sequence data to a reference sequence for use in diverse applications such as disease genotyping and personal genomics. MUMmerGPU 2.0 features a new stackless depth-first-search print kernel and is 13× faster than the serial CPU version of the alignment code and nearly 4× faster in total computation time than MUMmerGPU 1.0. We exhaustively examined 128 GPU data layout configurations to improve register footprint and running time and conclude higher occupancy has greater impact than reduced latency. MUMmerGPU is available open-source at http://mummergpu.sourceforge.net.
doi:10.1016/j.parco.2009.05.002
PMCID: PMC2749273  PMID: 20161021
Short read mapping; GPGPU; suffix trees; CUDA
24.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) 
Ming, Ray | Hou, Shaobin | Feng, Yun | Yu, Qingyi | Dionne-Laporte, Alexandre | Saw, Jimmy H. | Senin, Pavel | Wang, Wei | Ly, Benjamin V. | Lewis, Kanako L. T. | Salzberg, Steven L. | Feng, Lu | Jones, Meghan R. | Skelton, Rachel L. | Murray, Jan E. | Chen, Cuixia | Qian, Wubin | Shen, Junguo | Du, Peng | Eustice, Moriah | Tong, Eric | Tang, Haibao | Lyons, Eric | Paull, Robert E. | Michael, Todd P. | Wall, Kerr | Rice, Danny W. | Albert, Henrik | Wang, Ming-Li | Zhu, Yun J. | Schatz, Michael | Nagarajan, Niranjan | Acob, Ricelle A. | Guan, Peizhu | Blas, Andrea | Wai, Ching Man | Ackerman, Christine M. | Ren, Yan | Liu, Chao | Wang, Jianmei | Wang, Jianping | Na, Jong-Kuk | Shakirov, Eugene V. | Haas, Brian | Thimmapuram, Jyothi | Nelson, David | Wang, Xiyin | Bowers, John E. | Gschwend, Andrea R. | Delcher, Arthur L. | Singh, Ratnesh | Suzuki, Jon Y. | Tripathi, Savarni | Neupane, Kabi | Wei, Hairong | Irikura, Beth | Paidi, Maya | Jiang, Ning | Zhang, Wenli | Presting, Gernot | Windsor, Aaron | Navajas-Pérez, Rafael | Torres, Manuel J. | Feltus, F. Alex | Porter, Brad | Li, Yingjun | Burroughs, A. Max | Luo, Ming-Cheng | Liu, Lei | Christopher, David A. | Mount, Stephen M. | Moore, Paul H. | Sugimura, Tak | Jiang, Jiming | Schuler, Mary A. | Friedman, Vikki | Mitchell-Olds, Thomas | Shippen, Dorothy E. | dePamphilis, Claude W. | Palmer, Jeffrey D. | Freeling, Michael | Paterson, Andrew H. | Gonsalves, Dennis | Wang, Lei | Alam, Maqsudul
Nature  2008;452(7190):991-996.
Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3× draft genome sequence of ‘SunUp’ papaya, the first commercial virus-resistant transgenic fruit tree1 to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far2–5, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.
doi:10.1038/nature06856
PMCID: PMC2836516  PMID: 18432245
25.  Impact of Asthma Controller Medications on Clinical, Economic, and Patient-Reported Outcomes 
Mayo Clinic Proceedings  2009;84(8):675-684.
OBJECTIVE: To comprehensively evaluate clinical, economic, and patient-reported outcomes associated with various therapeutic classes of asthma controller medications.
PATIENTS AND METHODS: This observational study, which used administrative claims data from US commercial health plans, included patients with asthma aged 18 through 64 years who filled a prescription for at least 1 asthma controller medication from September 1, 2003, through August 31, 2005. Outcome metrics included the use of short-acting β-agonists (SABAs), the use of oral corticosteroids, inpatient (INP)/emergency department (ED) visits, and asthma-related health care costs. A subset of 5000 patients was randomly selected for a survey using the Mini-Asthma Quality of Life Questionnaire, the Work Productivity and Activity Impairment questionnaire, and the Asthma Therapy Assessment Questionnaire.
RESULTS: Of 56,168 eligible patients, 823 returned completed questionnaires. Compared with inhaled corticosteroids (ICSs), leukotriene modifiers (LMs) were associated with lower odds of INP/ED visits (odds ratio [OR], 0.80; P<.001), lower odds of using 6 or more SABA canisters (OR, 0.81; P<.001), and higher annual cost ($193; P<.001). In the subgroup analysis of adherent patients, LMs were associated with higher odds of INP/ED visits (OR, 1.74; P=.04), lower odds of using 6 or more SABA canisters (OR, 0.46; P<.001), and higher annual cost ($235; P<.001). Inhaled corticosteroids and LMs had a comparable impact on all patient-reported outcomes. For combination therapy, ICS plus a long-acting β-agonist consistently showed at least equivalent or better outcomes in the use of SABAs and oral corticosteroids, the risk of INP/ED visits, cost, asthma control level, quality of life, and impairment in productivity and activity.
CONCLUSION: Inhaled corticosteroids were associated with a lower risk of INP/ED visits, and a lower cost if adherence was achieved. When adherence cannot be achieved, LMs may be a reasonable alternative. Combination therapy with ICS plus a long-acting β-agonist was associated with better or equivalent clinical, economic, and patient-reported outcomes.
Inhaled corticosteroids were associated with a lower risk of inpatient/emergency department visits, and a lower cost if adherence was achieved. When adherence cannot be achieved, leukotriene modifiers may be a reasonable alternative. Combination therapy with inhaled corticosteroids plus a long-acting β-agonist was associated with better or equivalent clinical, economic, and patient-reported outcomes.
PMCID: PMC2719520  PMID: 19648384

Results 1-25 (45)