Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis

Studies of DNA methylation in Arabidopsis have rapidly advanced from the analysis of a single reference accession to investigations of large populations. The goal of emerging population studies is to detect differentially methylated regions (DMRs) at the genome-wide scale, and to relate this variation to gene expression and phenotypic diversity.Whole-genome bisulfite sequencing (WGBS-seq) has established itself as a gold standard in DNA methylation analysis due to its high accuracy and single cytosine measurement resolution. However, scaling up the use of this technology for large population studies is currently not only cost prohibitive but also poses nontrivial bioinformatic challenges. If the end-point of the study is to detect DMRs at the level of several hundred base pairs rather than at the level of single cytosines, low-resolution array-based methods, such as MeDIP-chip, may be entirely sufficient. However, the trade-off between measurement accuracy and experimental/analytical practicality needs to be weighted carefully. To help make such experimental choices, we conducted a side-by-side comparison between the popular dual-channel MeDIP-chip Nimblegen technology and Illumina WGBS-seq in two independent Arabidopsis lines.Our analysis shows that MeDIP-chip performs reasonably well in detecting DNA methylation at probe-level resolution, yielding a genome-wide combined false-positive and false-negative rate of about 0.21. However, detection can be susceptible to strong signal distortions resulting from a combination of dye bias and the CG content of effectively unmethylated genomic regions. We show that these issues can be easily bypassed by taking appropriate data preparation steps and applying suitable analysis tools.We conclude that MeDIP-chip is a reasonable alternative to WGBS-seq in emerging Arabidopsis population epigenetic studies.

Applications of second generation sequencing technologies in complex disorders

Second generation sequencing (2ndGS) technologies generate unprecedented amounts of sequence data very rapidly and at relatively limited costs, allowing the sequence of a human genome to be completed in a few weeks. The principle is on the basis of generating millions of relatively short reads from amplified single DNA fragments using iterative cycles of nucleotide extensions. However, the data generated on this scale present new challenges in interpretation, data analysis and data management. 2ndGS technologies are becoming widespread and are profoundly impacting biomedical research. Common applications include whole-genome sequencing, target resequencing, characterization of structural and copy number variation, profiling epigenetic modifications, transcriptome sequencing and identification of infectious agents. New methodologies and instruments that will enable to sequence the complete human genome in less than a day at a cost of less than $1,000 are currently in development.

Microfluidic DNA fragmentation for on-chip genomic analysis

We report a high-throughput clog-free microfluidic deoxyribonucleic acid (DNA) fragmentation chip that is based on hydrodynamic shearing. Salmon sperm DNA has been reproducibly fragmented down to ∼ 5k bp fragment lengths by applying low hydraulic pressures (≤1 bar) across micromachined constrictions positioned in larger microfluidic channels that create point-sink flow with large velocity gradients near the constriction entrance. Long constrictions (100 µm) produce shorter fragment lengths compared to shorter constrictions (10 µm), while increasing the hydrodynamic pressure requirement. Sample recirculation (10 ×) in short constrictions reduces the mean fragment length and fragment length variation, and improves yield compared to single-pass experiments without increasing the hydrodynamic pressure.

The Littorina sequence database (LSD)--an online resource for genomic data

We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147,491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26,537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt annotations, blast output, protein family domains (PFAM) and Gene Ontology. The database will allow users to search for genetic markers and identifying candidate genes or genes for expression analyses. It is open for additional deposition of sequence information for L. saxatilis and other species of the genus Littorina. The LSD is available at http://mbio-serv2.mbioekol.lu.se/Littorina/.

[Next-generation sequencing technologies and the application in microbiology--a review]

Since its invention in 1970s, nucleic acid sequencing technology has contributed tremendously to the genomics advances. The next-generation sequencing technologies, represented by HiSeq 2000 from Illumina, SOLiD from Applied Biosystems and 454 from Roche, re-energized the application of genomics. In this review, we first introduced the next-generation sequencing technologies, then, described their potential applications in the field of microbiology.

Chinese bioscience: The sequence factory

The bold ambitions of one institute could make China the world leader in genome sequencing. David Cyranoski asks if its science will survive the industrial ramp-up.

The twin spot generator for differential Drosophila lineage analysis

In Drosophila melanogaster, widely used mitotic recombination-based strategies generate mosaic flies with positive readout for only one daughter cell after division. To differentially label both daughter cells, we developed the twin spot generator (TSG) technique, which through mitotic recombination generates green and red twin spots that are detectable after the first cell division as single cells. We propose wide applications of TSG to lineage and genetic mosaic studies.

Technologies for diabetes genomics

The genetic risk for diabetes largely depends on the type of diabetes and the penetrance and severity of the effect of the contributing genes. This ranges from the high-risk mutations of neonatal diabetes and maturityonset diabetes of the young to the lower, but still significant, risk conferred by common human leukocyte antigen alleles in type 1 diabetes to the still-lower risk conferred by the common variants associated with type 2 diabetes. There are many new molecular technologies, each with their own set of methodological issues, that have been used for genome-wide association studies and that can be used for determining the genetic risk for these various types of diabetes. These technologies include whole genome single nucleotide polymorphism microarrays, high-throughput polymorphism analyzers, next-generation sequencers, and copy-number variant technologies.

Exploring clinical associations using '-omics' based enrichment analyses

Background

The vast amounts of clinical data collected in electronic health records (EHR) is analogous to the data explosion from the “-omics” revolution. In the EHR clinicians often maintain patient-specific problem summary lists which are used to provide a concise overview of significant medical diagnoses. We hypothesized that by tapping into the collective wisdom generated by hundreds of physicians entering problems into the EHR we could detect significant associations among diagnoses that are not described in the literature.

Methodology/Principal Findings

We employed an analytic approach original developed for detecting associations between sets of gene expression data, called Molecular Concept Map (MCM), to find significant associations among the 1.5 million clinical problem summary list entries in 327,000 patients from our institution's EHR. An odds ratio (OR) and p-value was calculated for each association. A subset of the 750,000 associations found were explored using the MCM tool. Expected associations were confirmed and recently reported but poorly known associations were uncovered. Novel associations which may warrant further exploration were also found. Examples of expected associations included non-insulin dependent diabetes mellitus and various diagnoses such as retinopathy, hypertension, and coronary artery disease. A recently reported association included irritable bowel and vulvodynia (OR 2.9, p = 5.6×10⁻⁴). Associations that are currently unknown or very poorly known included those between granuloma annulare and osteoarthritis (OR 4.3, p = 1.1×10⁻⁴) and pyloric stenosis and ventricular septal defect (OR 12.1, p = 2.0×10⁻³).

Conclusions/Significance

Computer programs developed for analyses of “-omic” data can be successfully applied to the area of clinical medicine. The results of the analysis may be useful for hypothesis generation as well as supporting clinical care by reminding clinicians of likely problems associated with a patient's existing problems.

Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon

BACKGROUND

DNA microarrays are a key resource for global analysis of genome content, gene expression and the distribution of transcription factor binding sites. We describe the development and application of versatile high density ink-jet in situ-synthesized DNA arrays for the G+C rich bacterium Streptomyces coelicolor. High G+C content DNA probes often perform poorly on arrays, yielding either weak hybridization or non-specific signals. Thus, more than one million 60-mer oligonucleotide probes were experimentally tested for sensitivity and specificity to enable selection of optimal probe sets for the genome microarrays. The heat-shock HspR regulatory system of S. coelicolor, a well-characterized repressor with a small number of known targets, was exploited to test and validate the arrays for use in global chromatin immunoprecipitation-on-chip (ChIP-chip) and gene expression analysis.

RESULTS

In addition to confirming dnaK, clpB and lon as in vivo targets of HspR, it was revealed, using a novel ChIP-chip data clustering method, that HspR also apparently interacts with ribosomal RNA (rrnD operon) and specific transfer RNA genes (the tRNAGln/tRNAGlu cluster). It is suggested that enhanced synthesis of Glu-tRNAGlu may reflect increased demand for tetrapyrrole biosynthesis following heat-shock. Moreover, it was found that heat-shock-induced genes are significantly enriched for Gln/Glu codons relative to the whole genome, a finding that would be consistent with HspR-mediated control of the tRNA species.

CONCLUSIONS

This study suggests that HspR fulfils a broader, unprecedented role in adaptation to stresses than previously recognized -- influencing expression of key components of the translational apparatus in addition to molecular chaperone and protease-encoding genes. It is envisaged that these experimentally optimized arrays will provide a key resource for systems level studies of Streptomyces biology.

Applications of ultra-high-throughput sequencing

The genomics era has enabled scientists to more readily pose truly global questions regarding mutation, evolution, gene and genome structure, function, and regulation. Just as Sanger sequencing ushered in a paradigm shift that enabled the molecular basis of biological questions to be directly addressed, to an even greater degree, ultra-high-throughput DNA sequencing is poised to dramatically change the nature of biological research. New sequencing technologies have opened the door for novel questions to be addressed at the level of the entire genome in the areas of comparative genomics, systems biology, metagenomics, and genome biology. These new sequencing technologies provide a tremendous amount of DNA sequence data to be collected at an astounding pace, with reduced costs, effort, and time as compared to Sanger sequencing. Applications of ultra-high-throughput sequencing (UHTS) are essentially limited only by the imaginations of researchers, and include genome sequencing/resequencing, small RNA discovery, deep SNP discovery, chromatin immunoprecipitation (ChIP) and RNA immunoprecipitation (RIP) coupled with sequence identification, transcriptome analysis including empirical annotation, discovery and characterization of alternative splicing, and gene expression profiling. This technology will have a profound impact on plant breeding, biotechnology, and our fundamental understanding of plant evolution, development, and environmental responses. In this chapter, we provide an overview of UHTS approaches and their applications. We also describe a protocol we have developed for deep sequencing of plant transcriptomes using the Illumina/Solexa sequencing platform.

A single-molecule barcoding system using nanoslits for DNA analysis : nanocoding

Single DNA molecule approaches are playing an increasingly central role in the analytical genomic sciences because single molecule techniques intrinsically provide individualized measurements of selected molecules, free from the constraints of bulk techniques, which blindly average noise and mask the presence of minor analyte components. Accordingly, a principal challenge that must be addressed by all single molecule approaches aimed at genome analysis is how to immobilize and manipulate DNA molecules for measurements that foster construction of large, biologically relevant data sets. For meeting this challenge, this chapter discusses an integrated approach for microfabricated and nanofabricated devices for the manipulation of elongated DNA molecules within nanoscale geometries. Ideally, large DNA coils stretch via nanoconfinement when channel dimensions are within tens of nanometers. Importantly, stretched, often immobilized, DNA molecules spanning hundreds of kilobase pairs are required by all analytical platforms working with large genomic substrates because imaging techniques acquire sequence information from molecules that normally exist in free solution as unrevealing random coils resembling floppy balls of yarn. However, nanoscale devices fabricated with sufficiently small dimensions fostering molecular stretching make these devices impractical because of the requirement of exotic fabrication technologies, costly materials, and poor operational efficiencies. In this chapter, such problems are addressed by discussion of a new approach to DNA presentation and analysis that establishes scaleable nanoconfinement conditions through reduction of ionic strength; stiffening DNA molecules thus enabling their arraying for analysis using easily fabricated devices that can also be mass produced. This new approach to DNA nanoconfinement is complemented by the development of a novel labeling scheme for reliable marking of individual molecules with fluorochrome labels, creating molecular barcodes, which are efficiently read using fluorescence resonance energy transfer techniques for minimizing noise from unincorporated labels. As such, our integrative approach for the realization of genomic analysis through nanoconfinement, named nanocoding, was demonstrated through the barcoding and mapping of bacterial artificial chromosomal molecules, thereby providing the basis for a high-throughput platform competent for whole genome investigations.

Cytokine multiplex analysis

The ability to monitor gene expression in experimental and clinical samples is an essential element of modern molecular biology and cell biology research. However with the advent of a systems biology approach toward understanding cell and cancer biology, analysis of expression of a single gene is no longer desirable. Today, multiplex analysis, where the expression of 8-100 genes can be monitored in one sample, has become a routine aspect of gene expression analysis. In this chapter the various assays systems commercially available for multiplex analysis of both RNA and protein will be discussed.

Applications of ultra-high-throughput sequencing

The genomics era has enabled scientists to more readily pose truly global questions regarding mutation, evolution, gene and genome structure, function, and regulation. Just as Sanger sequencing ushered in a paradigm shift that enabled the molecular basis of biological questions to be directly addressed, to an even greater degree, ultra-high-throughput DNA sequencing is poised to dramatically change the nature of biological research. New sequencing technologies have opened the door for novel questions to be addressed at the level of the entire genome in the areas of comparative genomics, systems biology, metagenomics, and genome biology. These new sequencing technologies provide a tremendous amount of DNA sequence data to be collected at an astounding pace, with reduced costs, effort, and time as compared to Sanger sequencing. Applications of ultra-high-throughput sequencing (UHTS) are essentially limited only by the imaginations of researchers, and include genome sequencing/resequencing, small RNA discovery, deep SNP discovery, chromatin immunoprecipitation (ChIP) and RNA immunoprecipitation (RIP) coupled with sequence identification, transcriptome analysis including empirical annotation, discovery and characterization of alternative splicing, and gene expression profiling. This technology will have a profound impact on plant breeding, biotechnology, and our fundamental understanding of plant evolution, development, and environmental responses. In this chapter, we provide an overview of UHTS approaches and their applications. We also describe a protocol we have developed for deep sequencing of plant transcriptomes using the Illumina/Solexa sequencing platform.

Development of ChillPeach genomic tools and identification of cold-responsive genes in peach fruit

The ChillPeach database was developed to facilitate identification of genes controlling chilling injury (CI), a global-scale post-harvest physiological disorder in peach. It contained 7,862 high-quality ESTs (comprising 4,468 unigenes) obtained from mesocarp tissues of two full-sib progeny contrasting for CI, about 48 and 13% of which are unique to Prunus and Arabidopsis, respectively. All ESTs are in the Gateway vector to facilitate functional assessment of the genes. The data set contained several putative SNPs and 184 unigenes with high quality SSRs, of which 42% were novel to Prunus. Microarray slides containing 4,261 ChillPeach unigenes were printed and used in a pilot experiment to identify differentially expressed genes in cold-treated compared to control mesocarp tissues, and in vegetative compared to mesocarp tissues. Quantitative RT-PCR (qRT-PCR) confirmed microarray results for all 13 genes tested. The microarray and qRT-PCR analyses indicated that ChillPeach is rich in putative fruit-specific and novel cold-induced genes. A website ( http://bioinfo.ibmcp.upv.es/genomics/ChillPeachDB ) was created holding detailed information on the ChillPeach database.

FlyBase : a database for the Drosophila research community

FlyBase ( http://flybase.org ) is the primary database of integrated genetic and genomic data about the Drosophilidae, of which Drosophila melanogaster is the most extensively studied species. Information in FlyBase originates from a variety of sources ranging from large-scale genome projects to the primary research literature. Data-types include sequence-level gene models, molecular classification of gene product functions, mutant phenotypes, mutant lesions and chromosome aberrations, gene expression patterns, transgene insertions, and anatomical images. Query tools allow interrogation of FlyBase through DNA or protein sequence, by gene or mutant name, or through terms from the several ontologies used to capture functional, phenotypic, and anatomical data. Links between FlyBase and external databases provide extensive opportunity for extending exploration into other model organism databases and resources of biological and molecular information. This review will introduce the FlyBase web server and query tools.

[Pulsed field gel electrophoresis: theory, instruments and applications]

Pulsed Field Gel Electrophoresis (PFGE) is a powerful technique for the fractionation of high molecular weight DNAs ranging from 10 kb to 10 Mb in size. PFGE separates DNA molecules in agarose gel by subjecting them to electric fields that alternate ("pulsate") in two directions. This technology plays a key role in the modern genomics as it allows manipulations of the DNA of whole chromosomes or their large fragments. In this review we discuss: 1) the theory behind PFGE, 2) different instruments based on the principle of pulsed field, their advantages and limitations, 3) factors affecting the mobility of DNA in PFGE gels, 4) practical applications of the technique.

[Technologies of differential gene expression analysis and applications in research of ischemic heart diseases]

In the post-genome era, the emphasis of the human genome project (HGP) is transferred to the study of functional genomics, which has become the hotspots of modern medicine. Studies on mechanism of various diseases could be deepened with the progressing of differential gene expression analysis technique. By taking the study on ischemic heart diseases as an example, the development of differential gene expression analysis technique and its application were reviewed.

Membrane microfilter device for selective capture, electrolysis and genomic analysis of human circulating tumor cells

This paper presents development of a parylene membrane microfilter device for single stage capture and electrolysis of circulating tumor cells (CTCs) in human blood, and the potential of this device to allow genomic analysis. The presence and number of CTCs in blood has recently been demonstrated to provide significant prognostic information for patients with metastatic breast cancer. While finding as few as five CTCs in about 7.5mL of blood (i.e., 10(10) blood cells in) is clinically significant, detection of CTCs is currently difficult and time consuming. CTC enrichment is performed by either gradient centrifugation of CTC based on their buoyant density or magnetic separation of epithelial CTC, both of which are laborious procedures with variable efficiency, and CTC identification is typically done by trained pathologists through visual observation of stained cytokeratin-positive epithelial CTC. These processes may take hours, if not days. Work presented here provides a micro-electro-mechanical system (MEMS)-based option to make this process simpler, faster, better and cheaper. We exploited the size difference between CTCs and human blood cells to achieve the CTC capture on filter with approximately 90% recovery within 10 min, which is superior to current approaches. Following capture, we facilitated polymerase chain reaction (PCR)-based genomic analysis by performing on-membrane electrolysis with embedded electrodes reaching each of the individual 16,000 filtering pores. The biggest advantage for this on-membrane in situ cell lysis is the high efficiency since cells are immobilized, allowing their direct contact with electrodes. As a proof-of-principle, we show beta actin gene PCR, the same technology can be easily extended to real time PCR for CTC-specific transcript to allow molecular identification of CTC and their further characterization.

Cancer genomics: integrating form and function

The sequencing of the human genome has formed the foundation with which to develop technologies and reagents to perform true genome-scale biological studies. In particular, the development and increasing application of these high-throughput genome-scale technologies have fundamentally altered the way one can approach the analysis of cancer. It is now possible to imagine studies that interrogate the structure, expression and function of every gene in a comprehensive, highly parallel fashion, permitting the development of multidimensional, global views of cancer. In this review, we focus on recent advances in the application of genomic strategies to the study of cancer, with an emphasis on functional genomics and the prospects for integrating the knowledge gained from these approaches to further develop our understanding of cancer and design better therapeutic strategies.