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  • Articles  (35)
  • Massively Parallel (Deep) Sequencing  (18)
  • Regulation  (17)
  • Oxford University Press  (35)
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  • 1
    Publication Date: 2013-04-02
    Description: As researchers begin probing deep coverage sequencing data for increasingly rare mutations and subclonal events, the fidelity of next generation sequencing (NGS) laboratory methods will become increasingly critical. Although error rates for sequencing and polymerase chain reaction (PCR) are well documented, the effects that DNA extraction and other library preparation steps could have on downstream sequence integrity have not been thoroughly evaluated. Here, we describe the discovery of novel C 〉 A/G 〉 T transversion artifacts found at low allelic fractions in targeted capture data. Characteristics such as sequencer read orientation and presence in both tumor and normal samples strongly indicated a non-biological mechanism. We identified the source as oxidation of DNA during acoustic shearing in samples containing reactive contaminants from the extraction process. We show generation of 8-oxoguanine (8-oxoG) lesions during DNA shearing, present analysis tools to detect oxidation in sequencing data and suggest methods to reduce DNA oxidation through the introduction of antioxidants. Further, informatics methods are presented to confidently filter these artifacts from sequencing data sets. Though only seen in a low percentage of reads in affected samples, such artifacts could have profoundly deleterious effects on the ability to confidently call rare mutations, and eliminating other possible sources of artifacts should become a priority for the research community.
    Keywords: Massively Parallel (Deep) Sequencing
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 2
    Publication Date: 2014-12-03
    Keywords: C91 - Laboratory, Individual Behavior, I18 - Government Policy ; Regulation ; Public Health
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 3
    Publication Date: 2012-09-13
    Description: Recent advances in RNA sequencing technology (RNA-Seq) enables comprehensive profiling of RNAs by producing millions of short sequence reads from size-fractionated RNA libraries. Although conventional tools for detecting and distinguishing non-coding RNAs (ncRNAs) from reference-genome data can be applied to sequence data, ncRNA detection can be improved by harnessing the full information content provided by this new technology. Here we present N orah D esk , the first unbiased and universally applicable method for small ncRNAs detection from RNA-Seq data. N orah D esk utilizes the coverage-distribution of small RNA sequence data as well as thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes. Using publicly available mouse sequence data from brain, skeletal muscle, testis and ovary, we evaluated our method with an emphasis on the performance for microRNAs (miRNAs) and piwi-interacting small RNA (piRNA). We compared our method with D ario and mir D eep 2 and found that N orah D esk produces longer transcripts with higher read coverage. This feature makes it the first method particularly suitable for the prediction of both known and novel piRNAs.
    Keywords: Massively Parallel (Deep) Sequencing
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  • 4
    Publication Date: 2012-06-06
    Description: Non-coding RNAs (ncRNA) account for a large portion of the transcribed genomic output. This diverse family of untranslated RNA molecules play a crucial role in cellular function. The use of ‘deep sequencing’ technology (also known as ‘next generation sequencing’) to infer transcript expression levels in general, and ncRNA specifically, is becoming increasingly common in molecular and clinical laboratories. We developed a software termed ‘RandA’ (which stands for ncRNA Read-and-Analyze) that performs comprehensive ncRNA profiling and differential expression analysis on deep sequencing generated data through a graphical user interface running on a local personal computer. Using RandA, we reveal the complexity of the ncRNA repertoire in a given cell population. We further demonstrate the relevance of such an extensive ncRNA analysis by elucidating a multitude of characterizing features in pathogen infected mammalian cells. RandA is available for download at http://ibis.tau.ac.il/RandA .
    Keywords: Massively Parallel (Deep) Sequencing
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  • 5
    Publication Date: 2011-11-24
    Description: In this paper, a modelling approach is developed for the treatment of ‘don't know’(DK) responses, within choice experiments (CEs). A DK option is motivated by the need to allow respondents the opportunity to express uncertainty. Our model explains a DK using an entropy measure of the similarity between options given to respondents within the CE. We illustrate our model by applying it to a CE examining consumer preferences for nutrient contents in food. We find that similarity between options in a given choice set does explain the tendency for respondents to report DK.
    Keywords: C35 - Discrete Regression and Qualitative Choice Models, I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 6
    Publication Date: 2014-01-22
    Description: Using the 2007 National Survey of Children's Health data, we find a statistically and economically significant effect of neighborhood parks and playgrounds on childhood obesity based on covariate matching estimators. The park/playground effect depends on gender, age, race, household income, neighborhood safety, and other neighborhood amenities. The results suggest that adding a neighborhood park/playground may reduce the obesity rate and make children more fit, but relevant interventions must consider socioeconomic status of the targeted children as well as other neighborhood amenities.
    Keywords: I18 - Government Policy ; Regulation ; Public Health, I38 - Government Policy ; Provision and Effects of Welfare Programs, R53 - Public Facility Location Analysis ; Public Investment and Capital Stock
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 7
    Publication Date: 2014-03-21
    Description: The economic theory of regulatory capture predicts that industry groups will attempt to influence their regulators (for example, by lobbying for rules that exclude competition). It has been suggested that the same logic applies to any powerful institution with the ability to affect industry profits. When the aim of industry is to alter the public’s perception of its product (for example, by disseminating favorable messages to the news media or via an advertising campaign, or by funding industry-friendly scientific research), the end result has been dubbed deep capture. We develop a formal model of deep capture, in which consumers have imperfect information about product quality, and a dominant producer is able to increase his profits by altering the parameters of the consumer’s search problem. We demonstrate the empirical relevance of the phenomenon with a discussion of the food industry response to the obesity epidemic.
    Keywords: D18 - Consumer Protection, D83 - Search ; Learning ; Information and Knowledge ; Communication ; Belief, I18 - Government Policy ; Regulation ; Public Health, L15 - Information and Product Quality ; Standardization and Compatibility, L51 - Economics of Regulation
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 8
    Publication Date: 2014-04-05
    Description: A substantial share of U.S. hog producers incorporate antimicrobial drugs into their livestock's feed or water at sub-therapeutic levels to promote feed efficiency and weight gain. Recently, in response to concerns that the overuse of antibiotics in livestock could promote the development of antimicrobial drug-resistant bacteria, the U.S. Food and Drug Administration adopted a strategy to phase out the use of antibiotics for production purposes. This study uses a stochastic frontier model and data from the 2009 USDA Agricultural Resource Management Survey of feeder-to-finish hog producers to estimate the potential effects on hog output and output variability resulting from a ban on antibiotics used for growth promotion. We use propensity score nearest neighbor matching to create a balanced sample of sub-therapeutic antibiotic (STA) users and nonusers. We estimate the frontier model for the pooled sample and separately for users and non-users—which allows for a flexible interaction between STA use and the production technology. Point estimates for the matched sample indicate that STA use has a small positive effect on productivity and production risk, increasing output by 1.0–1.3% and reducing the standard deviation of unexplained output by 1.4%. The results indicate that improvements in productivity resulted exclusively from technological improvement rather than from an increase in technical efficiency.
    Keywords: D24 - Production ; Cost ; Capital and Total Factor Productivity ; Capacity, I18 - Government Policy ; Regulation ; Public Health, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
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    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 9
    Publication Date: 2012-02-17
    Description: Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization. Sequencing reads that pass through the junction of the two joined ends of a 3–5-kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly. Longer read lengths increase the possibility that a read will cross the junction. To solve this problem, we developed a mate-paired protocol for use with Illumina sequencing technology that uses Cre-Lox recombination instead of blunt end circularization. In this method, a LoxP sequence is incorporated at the junction site. This sequence allows screening reads for junctions without using a reference genome. Junction reads can be trimmed or split at the junction. Moreover, the location of the LoxP sequence in the reads distinguishes mate-paired reads from spurious paired-end reads. We tested this new method by preparing and sequencing a mate-paired library with an insert size of 3 kb from Saccharomyces cerevisiae . We present an analysis of the library quality statistics and a new bio-informatics tool called DeLoxer that can be used to analyze an IlluminaCre-Lox mate-paired data set. We also demonstrate how the resulting data significantly improves a de novo assembly of the S. cerevisiae genome.
    Keywords: Massively Parallel (Deep) Sequencing
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  • 10
    Publication Date: 2014-10-10
    Description: The sequencing of libraries containing molecules shorter than the read length, such as in ancient or forensic applications, may result in the production of reads that include the adaptor, and in paired reads that overlap one another. Challenges for the processing of such reads are the accurate identification of the adaptor sequence and accurate reconstruction of the original sequence most likely to have given rise to the observed read(s). We introduce an algorithm that removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. Our algorithm is faster, and provides a more accurate reconstruction of the original sequence for both simulated and ancient DNA data sets, than other approaches. leeHom is released under the GPLv3 and is freely available from: https://bioinf.eva.mpg.de/leehom/
    Keywords: Massively Parallel (Deep) Sequencing
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  • 11
    Publication Date: 2014-07-03
    Description: With the rise of behavioural economics has come the belief that decision-making biases justify paternalistic policies. Such views challenge the notion of consumer sovereignty and the validity of traditional approaches of economic welfare analysis. While behavioural economics might improve the effectiveness of policies that are already justified on some other market-failure grounds, this article argues that the existence of cognitive failures, alone, do not justify government regulation. If one abandons the idea that consumers know what is in their best interest, judging the merits of policies becomes arbitrary and reflects only what a paternalist wants for others. The typical behavioural economic experiment occurs with college students devoid of real-world context. The biases found in such setting may not extrapolate well to conditions where people have more experience and knowledge, and where they can learn from past mistakes. Even when behavioural biases persist in the ‘real world’, consumers face incentives to engage in activities that protect them from the adverse consequences of the biases, and public policies that shield people from such consequences reduce incentives to self-regulate. The article concludes with some ideas for future research and a discussion of the merits of freedom of choice.
    Keywords: D03 - Behavioral Economics ; Underlying Principles, I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 12
    Publication Date: 2014-04-15
    Description: Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity. Pyrosequencing reads containing ambiguous bases (Ns) are generally discarded based on the assumptions of their non-sequence-dependent formation and high error rates. However, taxonomic composition differed by removal of reads with Ns. We determined whether Ns from pyrosequencing occur in a sequence-dependent manner. Our reads and the corresponding flow value data revealed occurrence of sequence-specific N errors with a common sequential pattern (a homopolymer + a few nucleotides with bases other than the homopolymer + N) and revealed that the nucleotide base of the homopolymer is the true base for the following N. Using an algorithm reflecting this sequence-dependent pattern, we corrected the Ns in the 16S (86.54%), bphD (81.37%) and nifH (81.55%) amplicon reads from a mock community with high precisions of 95.4, 96.9 and 100%, respectively. The new N correction method was applicable for determining most of Ns in amplicon reads from a soil sample, resulting in reducing taxonomic biases associated with N errors and in shotgun sequencing reads from public metagenome data. The method improves the accuracy and precision of microbial community analysis and genome sequencing using 454 pyrosequencing.
    Keywords: Massively Parallel (Deep) Sequencing
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  • 13
    Publication Date: 2014-09-02
    Description: In response to low consumption levels of fruits and vegetables by Supplemental Nutrition Assistance Program (SNAP) participants, the USDA Food and Nutrition Service created the Healthy Incentives Pilot (HIP) to test the efficacy of providing a 30% incentive for purchases of targeted fruits and vegetables (TFVs). Four to six months after implementation, mean daily TFV intake for adult HIP participants was 0.22 cup-equivalents higher (24% higher) than for control-group SNAP participants. These impact estimates with a random-assignment research design generally agree with previously published nonexperimental elasticity estimates, which imply that a pure price reduction of 30% would increase fruit and vegetable consumption by about 20%.
    Keywords: I18 - Government Policy ; Regulation ; Public Health, I38 - Government Policy ; Provision and Effects of Welfare Programs
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 14
    Publication Date: 2014-09-17
    Description: Heterogeneity is a ubiquitous feature of biological systems. A complete understanding of such systems requires a method for uniquely identifying and tracking individual components and their interactions with each other. We have developed a novel method of uniquely tagging individual cells in vivo with a genetic ‘barcode’ that can be recovered by DNA sequencing. Our method is a two-component system comprised of a genetic barcode cassette whose fragments are shuffled by Rci , a site-specific DNA invertase. The system is highly scalable, with the potential to generate theoretical diversities in the billions. We demonstrate the feasibility of this technique in Escherichia coli . Currently, this method could be employed to track the dynamics of populations of microbes through various bottlenecks. Advances of this method should prove useful in tracking interactions of cells within a network, and/or heterogeneity within complex biological samples.
    Keywords: Massively Parallel (Deep) Sequencing
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  • 15
    Publication Date: 2014-09-17
    Description: Barcoded vectors are promising tools for investigating clonal diversity and dynamics in hematopoietic gene therapy. Analysis of clones marked with barcoded vectors requires accurate identification of potentially large numbers of individually rare barcodes, when the exact number, sequence identity and abundance are unknown. This is an inherently challenging application, and the feasibility of using contemporary next-generation sequencing technologies is unresolved. To explore this potential application empirically, without prior assumptions, we sequenced barcode libraries of known complexity. Libraries containing 1, 10 and 100 Sanger-sequenced barcodes were sequenced using an Illumina platform, with a 100-barcode library also sequenced using a SOLiD platform. Libraries containing 1 and 10 barcodes were distinguished from false barcodes generated by sequencing error by a several log-fold difference in abundance. In 100-barcode libraries, however, expected and false barcodes overlapped and could not be resolved by bioinformatic filtering and clustering strategies. In independent sequencing runs multiple false-positive barcodes appeared to be represented at higher abundance than known barcodes, despite their confirmed absence from the original library. Such errors, which potentially impact barcoding studies in an application-dependent manner, are consistent with the existence of both stochastic and systematic error, the mechanism of which is yet to be fully resolved.
    Keywords: Massively Parallel (Deep) Sequencing
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  • 16
    Publication Date: 2012-10-30
    Description: The objective of this article is to gain a better understanding of firms' strategies towards nutritional tax policies and to assess their impacts from a public health point of view. We determine how new products that are nutritionally improved can successfully emerge in an asymmetrical context in which firms do not have the same strategic incentives to change the characteristics of their products. The results show that nutritional regulations may induce changes in the product quality choices by firms, but may also affect the competitive game. Under some conditions, the economic distortions are not compensated by increased health benefits.
    Keywords: H23 - Externalities ; Redistributive Effects ; Environmental Taxes and Subsidies, I18 - Government Policy ; Regulation ; Public Health, L15 - Information and Product Quality ; Standardization and Compatibility
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 17
    Publication Date: 2012-10-30
    Description: We quantify the economic and health effects of a fruit and vegetable (F&V) voucher policy designed for increasing F&V consumption among low-income consumers. The analysis combined two models: an economic model which predicts how F&V consumption is affected by a change in policy, and a health model which evaluates the impact of a change in F&V consumption in terms of death avoided and life-years saved. We find that targeted F&V voucher policies can be more cost-effective than non-targeted policies based on tax decreases, but only when the targeted policy is focused narrowly on the lowest income consumers.
    Keywords: D61 - Allocative Efficiency ; Cost-Benefit Analysis, I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 18
    Publication Date: 2013-07-16
    Description: We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling ( Thymallus thymallus ) and Rainbow trout ( Oncorhynchus mykiss ). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in 〈24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim .
    Keywords: Massively Parallel (Deep) Sequencing
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  • 19
    Publication Date: 2013-07-16
    Description: Both 454 and Ion Torrent sequencers are capable of producing large amounts of long high-quality sequencing reads. However, as both methods sequence homopolymers in one cycle, they both suffer from homopolymer uncertainty and incorporation asynchronization. In mapping, such sequencing errors could shift alignments around homopolymers and thus induce incorrect mismatches, which have become a critical barrier against the accurate detection of single nucleotide polymorphisms (SNPs). In this article, we propose a hidden Markov model (HMM) to statistically and explicitly formulate homopolymer sequencing errors by the overcall, undercall, insertion and deletion. We use a hierarchical model to describe the sequencing and base-calling processes, and we estimate parameters of the HMM from resequencing data by an expectation-maximization algorithm. Based on the HMM, we develop a realignment-based SNP-calling program, termed PyroHMMsnp, which realigns read sequences around homopolymers according to the error model and then infers the underlying genotype by using a Bayesian approach. Simulation experiments show that the performance of PyroHMMsnp is exceptional across various sequencing coverages in terms of sensitivity, specificity and F 1 measure, compared with other tools. Analysis of the human resequencing data shows that PyroHMMsnp predicts 12.9% more SNPs than Samtools while achieving a higher specificity. ( http://code.google.com/p/pyrohmmsnp/ ).
    Keywords: Massively Parallel (Deep) Sequencing
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  • 20
    Publication Date: 2013-05-29
    Description: Clustered regularly interspaced short palindromic repeats (CRISPR) constitute a bacterial and archaeal adaptive immune system that protect against bacteriophage (phage). Analysis of CRISPR loci reveals the history of phage infections and provides a direct link between phage and their hosts. All current tools for CRISPR identification have been developed to analyse completed genomes and are not well suited to the analysis of metagenomic data sets, where CRISPR loci are difficult to assemble owing to their repetitive structure and population heterogeneity. Here, we introduce a new algorithm, Crass, which is designed to identify and reconstruct CRISPR loci from raw metagenomic data without the need for assembly or prior knowledge of CRISPR in the data set. CRISPR in assembled data are often fragmented across many contigs/scaffolds and do not fully represent the population heterogeneity of CRISPR loci. Crass identified substantially more CRISPR in metagenomes previously analysed using assembly-based approaches. Using Crass, we were able to detect CRISPR that contained spacers with sequence homology to phage in the system, which would not have been identified using other approaches. The increased sensitivity, specificity and speed of Crass will facilitate comprehensive analysis of CRISPRs in metagenomic data sets, increasing our understanding of phage-host interactions and co-evolution within microbial communities.
    Keywords: Massively Parallel (Deep) Sequencing
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  • 21
    Publication Date: 2013-05-29
    Description: Read alignment is an ongoing challenge for the analysis of data from sequencing technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and-vote, for mapping reads to a reference genome. The new strategy chooses the mapped genomic location for the read directly from the seeds. It uses a relatively large number of short seeds (called subreads) extracted from each read and allows all the seeds to vote on the optimal location. When the read length is 〈160 bp, overlapping subreads are used. More conventional alignment algorithms are then used to fill in detailed mismatch and indel information between the subreads that make up the winning voting block. The strategy is fast because the overall genomic location has already been chosen before the detailed alignment is done. It is sensitive because no individual subread is required to map exactly, nor are individual subreads constrained to map close by other subreads. It is accurate because the final location must be supported by several different subreads. The strategy extends easily to find exon junctions, by locating reads that contain sets of subreads mapping to different exons of the same gene. It scales up efficiently for longer reads.
    Keywords: Massively Parallel (Deep) Sequencing
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  • 22
    Publication Date: 2013-11-22
    Description: We develop a structural econometric model of the vertical contracts between soft drink manufacturers and retailers to assess the impact of taxes or changes in production costs on consumer prices. Using individual data on food purchases from a representative survey of 19,000 French households in 2005, we estimate consumer demand using a random utility approach. Among a set of possible vertical relationships, we select the model that best fits the data. We evaluate the pass-through rate of changes in input costs (sugar) or of taxes and show that the industry over-shifts cost changes or excise taxes to the consumers. This result challenges the belief that firms do not pass on the full extent of cost changes or excise taxes to consumers.
    Keywords: H32 - Firm, I18 - Government Policy ; Regulation ; Public Health, L13 - Oligopoly and Other Imperfect Markets, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 23
    Publication Date: 2014-05-28
    Description: We propose a methodology to evaluate social projects from the perspective of children's opportunities on the basis of the effects of these projects on the distribution of outcomes. We condition our evaluation on characteristics for which individuals are not responsible; in this case, we use parental education level and indigenous background. The methodology is applied to evaluate the effects on children's health opportunities of Mexico's Oportunidades program, one of the largest conditional cash transfer programs for poor households in the world. The evidence from this program shows that gains in health opportunities for children from indigenous backgrounds are substantial and are situated in crucial parts of the distribution, whereas gains for children from nonindigenous backgrounds are more limited.
    Keywords: D63 - Equity, Justice, Inequality, and Other Normative Criteria and Measurement, I18 - Government Policy ; Regulation ; Public Health, I38 - Government Policy ; Provision and Effects of Welfare Programs
    Print ISSN: 0258-6770
    Electronic ISSN: 1564-698X
    Topics: Economics
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  • 24
    Publication Date: 2013-01-20
    Description: The RNA transcriptome varies in response to cellular differentiation as well as environmental factors, and can be characterized by the diversity and abundance of transcript isoforms. Differential transcription analysis, the detection of differences between the transcriptomes of different cells, may improve understanding of cell differentiation and development and enable the identification of biomarkers that classify disease types. The availability of high-throughput short-read RNA sequencing technologies provides in-depth sampling of the transcriptome, making it possible to accurately detect the differences between transcriptomes. In this article, we present a new method for the detection and visualization of differential transcription. Our approach does not depend on transcript or gene annotations. It also circumvents the need for full transcript inference and quantification, which is a challenging problem because of short read lengths, as well as various sampling biases. Instead, our method takes a divide-and-conquer approach to localize the difference between transcriptomes in the form of alternative splicing modules (ASMs), where transcript isoforms diverge. Our approach starts with the identification of ASMs from the splice graph, constructed directly from the exons and introns predicted from RNA-seq read alignments. The abundance of alternative splicing isoforms residing in each ASM is estimated for each sample and is compared across sample groups. A non-parametric statistical test is applied to each ASM to detect significant differential transcription with a controlled false discovery rate. The sensitivity and specificity of the method have been assessed using simulated data sets and compared with other state-of-the-art approaches. Experimental validation using qRT-PCR confirmed a selected set of genes that are differentially expressed in a lung differentiation study and a breast cancer data set, demonstrating the utility of the approach applied on experimental biological data sets. The software of DiffSplice is available at http://www.netlab.uky.edu/p/bioinfo/DiffSplice .
    Keywords: Massively Parallel (Deep) Sequencing
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  • 25
    Publication Date: 2013-02-02
    Description: Template switching (TS) has been an inherent mechanism of reverse transcriptase, which has been exploited in several transcriptome analysis methods, such as CAGE, RNA-Seq and short RNA sequencing. TS is an attractive option, given the simplicity of the protocol, which does not require an adaptor mediated step and thus minimizes sample loss. As such, it has been used in several studies that deal with limited amounts of RNA, such as in single cell studies. Additionally, TS has also been used to introduce DNA barcodes or indexes into different samples, cells or molecules. This labeling allows one to pool several samples into one sequencing flow cell, increasing the data throughput of sequencing and takes advantage of the increasing throughput of current sequences. Here, we report TS artifacts that form owing to a process called strand invasion. Due to the way in which barcodes/indexes are introduced by TS, strand invasion becomes more problematic by introducing unsystematic biases. We describe a strategy that eliminates these artifacts in silico and propose an experimental solution that suppresses biases from TS.
    Keywords: Massively Parallel (Deep) Sequencing
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  • 26
    Publication Date: 2013-08-09
    Description: Human leukocyte antigen (HLA) typing at the allelic level can in theory be achieved using whole exome sequencing (exome-seq) data with no added cost but has been hindered by its computational challenge. We developed ATHLATES, a program that applies assembly, allele identification and allelic pair inference to short read sequences, and applied it to data from Illumina platforms. In 15 data sets with adequate coverage for HLA-A, -B, -C, -DRB1 and -DQB1 genes, ATHLATES correctly reported 74 out of 75 allelic pairs with an overall concordance rate of 99% compared with conventional typing. This novel approach should be broadly applicable to research and clinical laboratories.
    Keywords: Massively Parallel (Deep) Sequencing
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  • 27
    Publication Date: 2013-08-09
    Description: In developing B cells, the immunoglobulin heavy chain ( IgH ) locus is thought to move from repressive to permissive chromatin compartments to facilitate its scheduled rearrangement. In mature B cells, maintenance of allelic exclusion has been proposed to involve recruitment of the non-productive IgH allele to pericentromeric heterochromatin. Here, we used an allele-specific chromosome conformation capture combined with sequencing (4C-seq) approach to unambigously follow the individual IgH alleles in mature B lymphocytes. Despite their physical and functional difference, productive and non-productive IgH alleles in B cells and unrearranged IgH alleles in T cells share many chromosomal contacts and largely reside in active chromatin. In brain, however, the locus resides in a different repressive environment. We conclude that IgH adopts a lymphoid-specific nuclear location that is, however, unrelated to maintenance of allelic exclusion. We additionally find that in mature B cells—but not in T cells—the distal V H regions of both IgH alleles position themselves away from active chromatin. This, we speculate, may help to restrict enhancer activity to the productively rearranged V H promoter element.
    Keywords: Massively Parallel (Deep) Sequencing
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 28
    Publication Date: 2013-04-14
    Description: Polymorphisms in the target mRNA sequence can greatly affect the binding affinity of microarray probe sequences, leading to false-positive and false-negative expression quantitative trait locus (QTL) signals with any other polymorphisms in linkage disequilibrium. We provide the most complete solution to this problem, by using the latest genome and exome sequence reference data to identify almost all common polymorphisms (frequency 〉1% in Europeans) in probe sequences for two commonly used microarray panels (the gene-based Illumina Human HT12 array, which uses 50-mer probes, and exon-based Affymetrix Human Exon 1.0 ST array, which uses 25-mer probes). We demonstrate the impact of this problem using cerebellum and frontal cortex tissues from 438 neuropathologically normal individuals. We find that although only a small proportion of the probes contain polymorphisms, they account for a large proportion of apparent expression QTL signals, and therefore result in many false signals being declared as real. We find that the polymorphism-in-probe problem is insufficiently controlled by previous protocols, and illustrate this using some notable false-positive and false-negative examples in MAPT and PRICKLE1 that can be found in many eQTL databases. We recommend that both new and existing eQTL data sets should be carefully checked in order to adequately address this issue.
    Keywords: Massively Parallel (Deep) Sequencing
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 29
    Publication Date: 2013-04-14
    Description: We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2–4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared with exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic data sets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai .
    Keywords: Massively Parallel (Deep) Sequencing
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 30
    Publication Date: 2013-12-24
    Description: Policymakers have suggested the use of taxes to raise the relative cost of buying fast food. Yet, little is known of the structure of demand for food-away-from-home (FAFH) in general. This study provides estimates of the price-elasticity of demand for four different types of FAFH using a new data set from NPD, Inc. and an econometric approach that accounts for the multiple-discrete–continuous nature of FAFH demand. We find that cross-price elasticities of demand are small, so consumers are unwilling to substitute between food-at-home and any type of FAFH or among types of FAFH. Therefore, taxing fast food may be effective in reducing the number of fast food visits and shifting consumption to at-home meals.
    Keywords: C35 - Discrete Regression and Qualitative Choice Models, D12 - Consumer Economics: Empirical Analysis, I18 - Government Policy ; Regulation ; Public Health, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 31
    Publication Date: 2013-12-05
    Description: The availability of alcoholic beverages in grocery stores varies across the United States due to state-level regulations. Recently there have been a number of controversial legislative proposals to expand the distribution of certain alcoholic beverages, most notably wine. Our econometric results show that, holding constant the total quantity of alcohol consumed, a higher share of wine correlates with lower traffic fatality rates, while the opposite is true for beer. These findings suggest that arguments against the wider distribution of wine as an approach to reduce social problems may not be fully justified.
    Keywords: I18 - Government Policy ; Regulation ; Public Health, K23 - Regulated Industries and Administrative Law, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 32
    Publication Date: 2013-12-05
    Description: We study how ready or vulnerable each Primary Care Organization (PCO) in England was in 2010 to the National Health Service reforms announced in the Government white paper Equity and Excellence: Liberating the NHS, later enacted by the Health and Social Care Act 2012. We define vulnerability as a combination of latent variables and present a novel methodological approach to measuring organizational and wider impacts of health policy reforms. Areas with higher concentrations of older people were not correlated with vulnerability except where there was also deprivation. This contrasts with wide-spread qualitative and quantitative evidence of sub-optimal care of older people within the health service. This suggests there may be an over-reliance on using activity, which was proportionately higher in the least vulnerable areas, to determine funding and quality markers rather than outcomes. A risk of the reform process could be a negative impact on deprived areas which appear to be financially less secure and more likely to have long-established health inequalities.
    Keywords: C30 - General, H75 - State and Local Government: Health, Education, and Welfare, I18 - Government Policy ; Regulation ; Public Health
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 33
    Publication Date: 2014-02-14
    Description: Many policy interventions that address rising obesity levels in the United States have been designed to provide consumers with more nutrition information, with the goal of encouraging consumers to decrease their caloric intake. We discuss existing information-provision measures and suggest that they are likely to have little-to-modest impact on encouraging lower caloric intake, because making use of such information requires understanding and/or motivation, which many consumers lack, as well as self-control, which is a limited resource. We highlight several phenomena from the behavioral economics literature (present-biased preferences, visceral factors, and status quo bias) and explain how awareness of these behavioral phenomena can inform both more effective information-provision policies and additional policies for regulating restaurants and public school cafeterias that move beyond information to nudge people towards healthier food choices.
    Keywords: D00 - General, I12 - Health Production, I18 - Government Policy ; Regulation ; Public Health, L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, M31 - Marketing, M38 - Government Policy and Regulation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 34
    Publication Date: 2014-02-14
    Description: Using a lab experiment with 258 adult non-student participants, we examined whether unhealthy foods taxes, healthy foods subsidies, anti-obesity advertising, and healthy foods advertising have an impact on changing consumers' choices of lunch items and the nutrient content of their choices for a selected meal. A difference-in-difference regression model was used to determine the efficacy of the various policy treatments. The results indicate that the unhealthy foods tax, healthy foods advertising, and unhealthy foods tax combined with anti-obesity advertising significantly reduced the content of some nutrients of concern, such as calories, calories from fat, carbohydrates, and cholesterol in meal selections. We also find that when combined with healthy foods subsidy, the healthy foods advertising has very little effect on nutrient consumption; the anti-obesity advertising on its own, however, is not efficient at changing dietary behavior. We discuss the policy implications of our findings and venues for future research.
    Keywords: H20 - General, I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 35
    Publication Date: 2014-02-14
    Description: Across health systems, there is increasing interest in applying behavioral economics insights to health policy challenges. Policy decision makers have recently discussed a range of diverse health policy interventions that are commonly brought together under a behavioral umbrella. These include randomized controlled trials, comparison portals, information labels, financial incentives, sin taxes, and nudges. A taxonomy is proposed to classify such behavioral interventions. In the context of risky health behavior, each cluster of policies is then scrutinized under two respects: (i) What are its genuinely behavioral insights? (ii) What evidence exists on its practical effectiveness? The discussion highlights the main challenges in drawing a clear mapping between how much each policy is behaviorally inspired and its effectiveness.
    Keywords: C90 - General, D03 - Behavioral Economics ; Underlying Principles, I10 - General, I18 - Government Policy ; Regulation ; Public Health
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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