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Roche vs Illumina – Round 2. Last week, Roche released a plan to take over Illumina’s Board.

Roche vs Illumina – Round 2

Roche announced that it has provided notice to Illumina, Inc. that it will nominate a slate of highly qualified, independent candidates for election to Illumina’s Board of Directors and propose certain other matters for the consideration of Illumina’s shareholders at Illumina’s 2012 annual meeting, which, if adopted, would result in Roche-nominated directors comprising a majority of the Illumina board.

Roche also named five alternate nominees for election to Illumina’s board. (see the Roche release…) Tuesday, Illumina’s board unanimously rejected Roche’s $5.7 billion bid to take over the maker of gene-mapping tools as “grossly inadequate.” “The timing of the offer is blatantly opportunistic and does not reflect Illumina’s strong platform of new products and pipeline,” Chairman William Rastetter and Chief Executive Officer Jay Flatley said yesterday in a letter to shareholders.

Looking at micro could mend broken hearts. Ribonucleic acid (RNA) could hold the key to treating heart disease.

Looking at micro could mend broken hearts

The breakthrough could lead to the development of targeted therapeutic treatments for heart disease. Professor Thomas Preiss and Dr Jennifer Clancy and their team commenced the research at Sydney’s Victor Chang Cardiac Research Institute in 2008 and completed it at The John Curtin School of Medical Research at ANU. They used the latest sequencing technology to capture and identify thousands of microRNAs found in the cells of the heart. MicroRNAs are short ribonucleic acid molecules, which in turn are one of three building blocks of all life. Even though they are tiny molecules, microRNAs are abundant in cells and act like an army of ants – individually making small changes to the expression of many genes, but in combination resulting in large changes to the cell.

“A number of these therapies are already in pre-clinical development. “That’s why we conducted this survey. Last Month’s RNA-Seq Industry Press. Feb 01, 2012 – DNA Sequencing – Technologies, Markets and Companies Applications of Sequencing in Healthcare 121 Introduction 121 Applications of sequencing in molecular diagnostics 121 Next generation sequencing for detection of solid organ transplant rejection 122 Applications of sequencing in oncology 122 A project to assess sequencing technologies for tumor DNA 123 Amplicon sequencing in…(read more) Feb 01, 2012 – Almac Announce Launch of Next Generation Sequencing (NGS) Data Analysis Services These latest enhancements to Almac’s service portfolio include a comprehensive range of NGS solutions from professional study design to sample processing and expert data analysis for DNA and RNA samples.

Last Month’s RNA-Seq Industry Press

Uniquely, the services are highly customizable and are available on a standalone basis or in combination with Almac’s established bioinformatics offerings…(read more) Jan 1, 2012 – {*style:<b>*}Appistry Opens New Corporate Headquarters in St. New methods for quantifying differential expression with RNA-Seq. A Bayesian method of calling differential expression (BM-DE) from RNA-Seq data Lee J, Ji Y, Liang S, Cai G, Müller P. (2011) On Differential Gene Expression Using RNA-Seq Data.

New methods for quantifying differential expression with RNA-Seq

Cancer Inform 10, 205-15, [abstract] AVAILABILITY: A public domain R package is available from Allele-specific gene expression by RNA-seq Skelly DA, Johansson M, Madeoy J, Wakefield J, Akey JM. (2011) A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Availability: R code to implement the statistical model described is available at: DEB: A web interface for RNA-seq digital gene expression analysis. Rainbow Trout Transcriptome. Researchers at the USDA have generated and characterized a reference transcriptome for rainbow trout that represents multiple tissues responding to multiple stressors common to aquaculture production environments.

Rainbow Trout Transcriptome

This resource compliments existing public transcriptome data and will facilitate approaches aiming to evaluate gene expression associated with stress in this species. Sequencing of a pooled normalized transcriptome library created from gill, brain, liver, spleen, kidney and muscle RNA of control and stressedfish produced 3,160,306 expressed sequence tags which were assembled and annotated. SNP discovery resulted in identification of ~58,000 putative single nucleotide polymorphisms including 24,479 which were predicted to fall within exons.

C Sanchez CC, Weber GM, Gao G, Cleveland BM, Yao J, Rexroad CE. (2011) Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors. BMC Genomics 12, 626. RNA-Seq a hot topic at Plant & Animal Genomes Conference. Sequencing Competition Heats Up! Illumina and Ion Torrent are two of the front runners in development of next-gen sequencing technology and it seems clear that both players believe there is only room for one top dog on this playground.

Sequencing Competition Heats Up!

Back in the middle of 2011, Ion Torrent released an application note “The Ion PGM™ sequencer exhibits superior long-read accuracy” that, not only claimed better performance, but also seemed to stick it to Illumina by claiming they had accomplished in months what had taken Illumina years to accomplish. They also went as far as producing a humorous video, in the vein of Apple vs PC, attacking the Illumina MiSeq instrument.

Illumina didn’t think it was funny and fired right back with its presentation, “Analysis of Inaccuracies in Ion Torrent’s Long Read Application Note” disputing the Ion Torrent claims and demonstrating better performance. Most recently, at the J.P. Who will eventually be the winner of this high stake race? Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq. Chinese bayberry (Myrica rubra Sieb. and Zucc.) is an important subtropical fruit crop and an ideal species for fruit quality research due to the rapid and substantial changes that occur during development and ripening, including changes in fruit color and taste.

Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq

RNA-Seq generated 1.92 G raw data, which was then de novo assembled into 41,239 UniGenes with a mean length of 531 bp. Approximately 80% of the UniGenes (32,805) were annotated against public protein databases, and coding sequences (CDS) of 31,665 UniGenes were determined. Over 3,600 UniGenes were differentially expressed during fruit ripening, with 826 up-regulated and 1,407 down-regulated. GO comparisons between the UniGenes of these two types and interactive pathways (Ipath) analysis found that energy-related metabolism was enhanced, and catalytic activity was increased.

All genes involved in anthocyanin biosynthesis were up-regulated during the fruit ripening processes, concurrent with color change. Bioinformatics Seminar – Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification. Time – Tuesday, January 31, 2012 04:30 PM Place – Department of Statistics, Purdue University – in PHYS 223 Speaker – Yu (Michael) Zhu RNA-Seq has emerged as a powerful technique for transcriptome study.

Bioinformatics Seminar – Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification

As much as the improved sensitivity and coverage, RNA-Seq also brings challenges for data analysis. The massive amount of sequence read data, excessive variability, uncertainties, and bias and noises stemming from multiple sources make the analysis of RAN-Seq data difficult. Reference - Ming Hu. Bioinformatics Seminar – Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification.

Effects of Sample Preparation on Transcriptome Sequencing Results. Seq of Cows Milk. Cow milk is a complex bioactive fluid consumed by humans beyond infancy.

Seq of Cows Milk

Even though the chemical and physical properties of cow milk are well characterized, very limited research has been done on characterizing the milk transcriptome. This study performs a comprehensive expression profiling of genes expressed in milk somatic cells of transition (day 15), peak (day 90) and late (day 250) lactation Holstein cows by RNA sequencing. Milk samples were collected from Holstein cows at 15, 90 and 250 days of lactation, and RNA was extracted from the pelleted milk cells.

Gene expression analysis was conducted by Illumina RNA sequencing. Sequence reads were assembled and analyzed in CLC Genomics Workbench. The results revealed that 69% of NCBI Btau 4.0 annotated genes are expressed in bovine milk somatic cells. Wickramasinghe S, Rincon G, Islas-Trejo A, Medrano JF. (2012) Transcriptional profiling of bovine milk using RNA sequencing. Truly Digital RNA-Seq. Researchers at Harvard University have developed a method of truly digital RNA-Seq that does not rely on the counting of individual reads.

Truly Digital RNA-Seq

How is this possible you ask? Following reverse transcription, a large set of barcode sequences is added in excess, and nearly every cDNA molecule is uniquely labeled by random attachment of barcode sequences to both ends. After PCR, paired-end deep sequencing is performed to read the two barcodes and cDNA sequences. Rather than counting the number of reads, RNA abundance is measured based on the number of unique barcode sequences observed for a given cDNA sequence. The barcodes have been optimized to be unambiguously identifiable, even in the presence of multiple sequencing errors. With this method, they have developed a simple strategy for mitigating sequence-dependent bias and inaccuracy at low copy numbers, inherent to standard RNA-Seq library preparation techniques. The Challenge of RNA-Seq. The authors of a recent review1, make some key points about some of the challenges that are general to all RNA-seq experiments: RNA-Seq rules!

– “By comparison to these [other next-gen sequencing] applications, RNA-sequencing (RNA-seq) may be leading the pack in popularity because of its ability to characterize transcriptomes, to assess differential gene expression and to essentially challenge the continued use of microarray technology for studying transcription.” There is no magic to RNA-Seq. – “We are concerned that next-generation technologies will, most likely, remain expensive for a while, and that there may be an inclination to revert to single sample science that is void of any ability to estimate biological and/or technical variation, or to test scientific hypotheses.”

When asked: Do we yet have a firm handle on the most appropriate/accurate pipeline for analysis of RNA-Seq datasets? RNA-Seq Blog readers responded: Transcriptome analysis of Crassostrea gigas with short read RNA-Seq. Researchers at the University of Washington used SOLiD sequencing to examine gene expression patterns in Pacific oyster (Crassostrea gigas) populations exposed to varying degrees of anthropogenic impact. Novel transcripts were identified and RNA-Seq analysis revealed several hundred differentially expressed genes. To evaluate the effectiveness of restricting characterization solely to short-read sequences, mapping and RNA-Seq analysis were also performed using publicly available transcriptome sequence data as a scaffold. This study demonstrates that ultra-short read sequencing technologies can effectively generate novel transcriptome information, identify differentially expressed genes, and will be important for examining environmental physiology of non-model organisms.

Gavery MR, Roberts SB. (2011) Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas. Transcriptome analysis of Crassostrea gigas with short read RNA-Seq. Happy New Year! First Anolis carolinensis RNA-Seq data sets released. Simultaneous RNA-seq-based Transcript Inference and Quantification Using Mixed Integer Programming.

Study Finds 454, Illumina Offer Similar Performance for Transcriptome Sequencing-Based SNP Discovery. From GenomeWeb – In Sequence In a head-to-head comparison of the Roche 454 GS FLX and Illumina GAII sequencing platforms, fish population researchers found that the two systems were equally capable of finding SNPs by sequencing the transcriptomes of fish from a species lacking a reference genome, though versions of the Illumina system introduced since the study was conducted appear to have a cost advantage over newer 454… Seminar Tomorrow: RNA-Seq transcriptome analysis. RNA-Seq transcriptome analysis for gene identification, polymorphism detection and transcript profiling in two perennial ryegrass genotypes with divergent vernalization requirement By senior scientist Torben Asp, Department of Molecular Biology and Genetics, Aarhus University Thursday, 15 December 2011 at 10:00-11:00 Center for LIFE Applied Bioinformatics and Department of Plant Biology and Biotechnology hereby invites you to attend the seminar: Meeting room M117-1 + K117-2, Thorvaldsensvej 40, 1.floor (map) 1871 Frederiksberg.

RNA-Seq Data Analysis Online Course. Making Sense of RNA-Seq Data Course Duration Course will run for four weeks from 02.01.2012 to 29.01.2012. Course Material Course material will be delivered online for each week at the start of the week. Register at or write to uday@labindia-gpod.com Registration Send a copy of your biodata along with DD of Rs 5000/- in the name of Labindia Instruments Pvt. Ltd. payable at Thane to Co-ordinator, Labindia-GPOD, Swnand, Jivan Vihar Housing Society, SB Road, Pune or make online payment with debit/credit card using payment gateway. Course Topics Tools for mapping reads to reference genome or transcriptomeDe novo assembly of TranscriptomeFinding isoforms and novel transcriptsSummarising mapped readsNormalization and Differential ExpressionGene set and pathway enrichment. Seq Hands-on Workshop. RNA-Seq Satellite Workshop at ABRF 2012. Seq Blog on Pearltrees. RNA-Seq of the yeast Scheffersomyces stipitis. RNA-Seq Blog Poll Results. Seq used to Trim the Mollusc Family Tree.

Alternative Splicing – RNA-Seq. RNA-Seq of the yeast Scheffersomyces stipitis. Seq Workshop – An introductory course to RNA-Seq. Video Protocol – Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA. Video Protocol – Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA. Another weapon in the war against bias. Flowcell Reverse Transcription Sequencing (FRT-seq) RNA CaptureSeq for targeted RNA sequencing of the human transcriptome.

Seq greatly improves the accuracy of prediction of protein-coding genes. RNA-Seq Blog Poll Results. Seq used to Trim the Mollusc Family Tree. The Transcriptome of the Potato – Solanum tuberosum. Seq greatly improves the accuracy of prediction of protein-coding genes. Transcriptome Sequencing Reveals Two Gene Families Prone to Rearrangement in Breast Cancer. RNA-Seq Satellite Workshop at ABRF 2012. RNA-Seq – Insights into the Active Genome. Integrated RNA-Seq Data Analysis Pipeline – Generating Evidence-Backed Hypotheses in Silico.

New RNA-Seq Chapters – Methods in Molecular Biology. Seq: A practical guide to the analysis of differential gene expression. Alternative Splicing – RNA-Seq. Transcriptome Sequencing of the Oilseed Rape. Advanced RNA-Seq and ChiP-Seq Data Analysis – Hands-on training at EBI. New RNA-Seq Chapters – Methods in Molecular Biology. Human Transcriptome Array Outperforms RNA-Seq. Comprehensive RNA-Seq Data Presentation with Comparison to Microarrays. RNA-PET – Genome Wide Full-Length Transcript Analysis Using 5′ and 3′ Paired-End-Tag RNA-Seq. A reference transcriptome for the cauliflower coral – Pocillopora damicornis. New RNA-Seq template preparation protocol enables detection of imprinted macro ncRNAs. New RNA-Seq template preparation protocol enables detection of imprinted macro ncRNAs. ReCount – A multi-experiment resource of analysis-ready RNA-seq gene count datasets.

RNA CaptureSeq for targeted RNA sequencing of the human transcriptome. Introduction to transcriptome analysis using HighThroughput Sequencing technologies (HTS) Will genome sequencing be routine in cancer care and research? Seq Hands-on Workshop. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.