Archive

Through next-generation sequencing, microbial genomic research is accelerating the pace of discovery–rapidly expanding our understanding of microbial function and interactions.

Metagenomic and microbiome studies provide researchers deep insight about the microbes that populate our surroundings, infrastructure, and built environments. In this webinar, Dr. Jack Gilbert will present initial findings from the Hospital Microbiome Project. The goal of this ongoing initiative is to characterize the taxonomic composition of surface, air, water and human-associated communities in a new hospital—starting from the introduction of patients to major surgical procedures. Please join us to see Dr. Gilbert present preliminary data and discuss what his team has discovered from this exciting endeavor.

Methods for global gene expression analysis in individual cells have important applications in biology and medicine. This webinar describes the Smart-Seq protocol for polyA+ RNA analysis, applicable at single-cell levels. Compared to existing methods, the Smart-Seq protocol has improved read coverage across transcripts, significantly enhancing analysis of alternative transcript isoforms and improving SNP identification. The sensitivity and quantitative accuracy of the Smart-Seq method for single-cell transcriptomics have been evaluated with total RNA dilution and spike-in RNAs. This method has been proven using cancer cell lines, circulating tumor cells from melanomas, and early embryonic cells. The Smart-Seq protocol provides a robust method for addressing fundamental biological questions that require transcriptome profiling in rare or single cells.

When an infectious disease outbreak occurs, public health officials attempt to identify where it started and how it spread so that they can initiate appropriate control and prevention strategies. Using a combination of field epidemiology (interviewing cases and controls) and molecular epidemiology (genotyping of bacterial or viral pathogens), they attempt to establish links between cases and develop a putative reconstruction of the outbreak. Unfortunately, the low resolution of molecular epidemiology techniques currently available to most reference microbiology laboratories cannot provide detailed information on the underlying transmission dynamics within an outbreak. However, next-generation sequencing offers exciting new possibilities for tracking disease outbreaks with high resolution. Over the course of an outbreak, a small amount of genetic variation accrues in a pathogen's genome as a result of mutations. By tracking the presence or absence of these mutations in all pathogen genomes from a given outbreak, it is possible to identify where particular variants arose and trace person-to-person transmission events. This webinar will provide an introduction to this emerging field of genomic epidemiology, highlighting the application of this approach to reconstruct outbreaks of tuberculosis in British Columbia, Canada.

The HiSeq 2500 System delivers incredible accuracy, throughput, and total workflow turnaround time for high-throughput applications. The simple whole-genome sequencing workflow allows you to quickly go from DNA to annotated variants for interpretation and decision-making. This webinar will highlight the latest system advances:
• New library preparation kits that enable low amounts of DNA input, including FFPE samples
• Improved sequencer performance
• The latest alignment/annotation and interpretation software

RNA-Seq is a powerful tool for studying various aspects of RNA biology, including expression levels, alternative splicing, RNA editing, and gene discovery. Though RNA-Seq has long been in use, robust and easy methods for generating strand-specific libraries and libraries from total RNA samples have not been commercially available. The new Illumina Tru-Seq Strand-specific Total RNA-Seq kits facilitate the generation of high quality libraries via a simple, rapid, and familiar workflow. I will present modENCODE data generated using these new kits and compare the results to those generated from libraries prepared using previous Illumina RNA-Seq kits and the same RNA samples. Specifically, I will discuss the degree of strandedness, evenness of coverage, and discovery of transcribed regions not identified using poly(A)-selected RNA-Seq libraries.

Avadis NGS is an integrated platform that provides analysis, management, and visualization tools for next-generation sequencing data. It supports extensive workflows for RNA-Seq, small RNA-Seq, DNA-Seq, and ChIP-Seq experiments. The typical analysis workflow in Avadis is composed of four parts:

1. Data Import: supports seamless data importing from the MiSeq run folder, importing of FASTQ files and alignment using the COBWeb algorithm, or direct importing of SAM/BAM files.

2. Quality Control: generates various quality control plots and filter steps to ensure the quality of reads for analysis.

3. Analysis: provides core analysis steps specific to each workflow, along with intuitive organization and visualizations.

4. Biological Contextualization: enables investigation of interesting genes for GO enrichment, GSEA, network and pathway analysis.

See how expert bioinformaticians have used in-house and open-source tools to re-analyze and further interrogate IGN data. The presentation will describe the computational requirements, walk you through a reanalysis pipeline, and highlight the benefits of working with universal, industry-standard file formats.

Monogenic diseases are frequent causes of neonatal morbidity and mortality. Over 3,500 monogenic diseases have been characterized, many of which feature clinical and genetic heterogeneity. Since disease presentation at birth is often undifferentiated, there is an immense need for molecular diagnosis in infants. Disease progression in newborns is often fast and heterogeneous, so molecular diagnosis must occur rapidly for relevant clinical decision making. Here, we describe 50-hour differential diagnosis of genetic disorders by whole genome sequencing (WGS), featuring substantially automated bioinformatic analysis. This is intended to be a prototype for deployment in neonatal intensive care units.

Get a head start on data analysis and learn guidance on best practices used by the IGN. This presentation will demonstrate how popular open-source tools can be used to perform further analysis of alignment and variant data. For users with some in-house informatics expertise and experience with large data sets, this information will help you expand on what you already know.

Speaker: Abizar Lakdawalla, Ph.D., Illumina, Inc.

This webinar will introduce the latest advances in next-generation sequencing for analyzing microbial genomes and transcriptomes, and will present key studies highlighting this technology.

Sequencing microbial genomes provides a comprehensive understanding that no other method can provide. For example, it is now possible to achieve single base resolution of the bacterial chromosome, and detailed sequence of all extrachromosomal elements, including plasmids and phages. Improvements in next-generation sequencing methods now enable routine whole bacterial genome sequencing in a single day. Assembling the genome from sequencing reads can be easily performed on a desktop computer, allowing high resolution classification of bacterial subtypes. Many important features, including resistance, virulence, and pathogenicity, can be examined simultaneously with high accuracy. In addition to genomic experiments, next-generation sequencing can be used to analyze the complete transcriptome of microbes for interpretation of gene structure and regulation. Sequencing complex microbial populations or metagenomes provides a comprehensive census of species within samples, including those that cannot be cultured or phenotyped. Subtle changes in microbial populations resulting from, or predictive of, changes in the health status of a patient can be assessed easily and accurately with next-generation sequencing.

In this webinar, IGN Informatics partners will describe preconfigured solutions that automate data analysis, allowing you to go directly to biological analysis. You'll hear from three leading IGN partners, Knome, Ingenuity, and Diagnomics, who offer analysis solutions uniquely suited for the needs of IGN customers. Ideal for labs with no in-house informatics expertise, these solutions help facilitate all steps of the downstream analysis, including annotation, filtering, and multi-sample analysis.

Ingenuity
Rapid Identification of Causal NGS Variants using Ingenuity Variant Analysis

• Karen Lavery, Ph.D., Field Application Scientist, Ingenuity
• Brent Applegate (additional panelist)

Knome
Human Whole Genome Interpretation...for Humans

• Nathan Pearson, Ph.D., Director of Research, Knome, Inc.

Diagnomics
Genetic Analysis, Research to Bedside

• Jongsun Park, Ph.D., Senior Scientist & Group Leader, Diagnomics
• Min Seob Lee, Ph.D. (additional panelist)

Dr. Tim Stinear has completed an in depth comparison of the MiSeq and Ion Torrent PGM to determine which technology is best suited to a microbial laboratory. Join Dr. Tim Stinear for a presentation comparing genome sequencing of three reference bacteria of varying DNA composition with the MiSeq personal sequencer using Nextera^® library prep against the latest PGM chemistry and chips. In this webinar, Dr. Stinear will cover:

• Rapid library preparation with Nextera
• High-quality de novo bacterial sequencing with the MiSeq system
• Comparison of data output and quality between MiSeq and Ion Torrent PGM

The genetic basis for many rare, familial conditions has been difficult to elucidate due to the limited numbers of families affected and the small sizes of these families. Whole-exome sequencing provides an opportunity to identify the underlying basis for these diseases, some of which are novel presentations of known diseases and some of which are novel diseases themselves. In this webinar, Dr. Wendy Chung, M.D., Ph.D. will present several examples of how whole-exome sequencing has been successfully used to elucidate the pathogenesis of disease and how it directly affected patient care.

Jon Bell, Product Manager, DNA Sequencing Applications
Illumina
Rob Tarbox, Senior Product Manager
Illumina
Rupert Yip, Ph.D., Senior Product Manager, Bioinformatics
Illumina

In this webinar, the first of a three-part series, explore how the MiSeq system can empower your research. As the only fully integrated personal sequencer, MiSeq delivers a streamlined solution that takes you from rapid sample prep through automated data analysis and storage in the BaseSpace cloud. Sequencing doesn't get any easier than this.

In this webinar, you'll take a tour of the MiSeq system to learn about:

• Accomplishments by researchers in your field who are using MiSeq in their labs
• Updates to our growing applications portfolio
• Advancements to sequencing's fastest and easiest workflow
• Recent improvements to our sequencing-by-synthesis chemistry for faster, longer reads, and expanded capability for applications

This is the first of three webinars in this series. More information to come.

Todd Smith, PhD, Scientific Leader
Geospiza, a PerkinElmer Company
Hugh Arnold, PhD, Senior Applications Scientist
Geospiza, a PerkinElmer Company

PerkinElmer has created a complete NGS workflow model that addresses rising genomics costs—allowing the company to provide complete, cost-effective genetic analysis solutions to its customers. As an Illumina Certified Service Provider (CSPro), PerkinElmer uses Illumina technology, its GeneSifter® LIMS and analysis software platforms, DNA sequencing services, and Caliper's SciClone and LabChip®GX instrumentation to make cost-effective genomics-based medicine possible.

In this webinar, PerkinElmer scientists will demonstrate how they provide affordable sequencing and genetic analysis solutions by:

• Automating sample prep
• Tracking, organizing, and processing data from whole genome, exome, RNA, methylation, and verification assays in automation frameworks

Validating systems for regulated environments using a risk-based approach built upon Good Automated Manufacturing Practice (GAMP) standards

Rick Dewey, MD
Stanford Center for Inherited Cardiovascular Disease

Next-generation sequencing (NGS) presents both challenges and opportunities for clinical care. Dr. Dewey will share examples from his experience at Stanford, successful and otherwise, in which NGS has been applied to cases of familial cardiomyopathy, and other inherited conditions. Bring your questions for a Q&A session.

In this webinar, Dr. Dewey will discuss approaches to:

• Data storage and management
• Error identification and reduction
• Disease risk encoded in the reference sequence
• Variant validation

Melissa Kamkar
Applications Scientist - Team Lead, GenoLogics
Christian Haudenschild
Vice President of Product Development, Illumina

In May 2011, the Illumina FastTrack Sequencing Services lab replaced its homegrown sample tracking database with the GenoLogics LIMS, which provides end-to-end information management of samples, tests, and results for next-generation genomics labs. Within a few weeks, the Illumina lab realized significant benefits and operational improvements with the preconfigured LIMS, eliminating bottlenecks and saving time.

In this webinar, we will present:

• Operational and efficiency gains achieved at the Illumina lab after implementing the GenoLogics LIMS
• Ease and speed of the implementation, and how the Illumina lab team was able to quickly adopt the LIMS
• How the preconfigured LIMS is based on industry best practices, and how they affect sample prep, sample flow, QC, status updates, and work management
• A Q&A session with Christian Haudenschild, Associate Director of Services at the Illumina FastTrack lab

Amy Bouck-Knight, Ph.D.
Bioinformatics Support Scientist, Illumina Technical Support

Interested in leveraging the power of Illumina RNA sequencing in your research, but unsure of what data analysis challenges you will encounter? This webinar will provide an overview of:

• Types of research questions that can be addressed with Illumina RNA Sequencing
• Study design considerations
• Bioinformatic tools for RNA Sequencing data analysis

This webinar will highlight examples of recent and innovative applications of Illumina RNA sequencing technology. We will also cover the basics of RNA sequencing study design, including how to decide on sampling depth, read length, and paired end versus single read sequencing. In addition, we will discuss the use of TopHat, Cufflinks and related open-source software for the analysis of Illumina RNA sequencing data.

Leslie G. Biesecker, M.D.
Sr. Investigator and Head, Human Development Section, Laboratory of Genetic Disease Research, NHGRI, NIH
Flavia M. Facio, M.S., CGC
Genetic Counselor, Genetic Disease Research Branch, NHGRI, NIH

Advances in DNA sequencing platforms along with rapid and dramatic reductions in cost have propelled us into an era where we can begin to contemplate a vision of genomic medicine. NextGen sequencing (NGS) technologies can elucidate an enormous amount of variation for a given individual. While most of these variations are benign or of unknown clinical significance, some are associated with a significant increase in risk of disease for the probands and/or their family members. While other genomic technologies focus on common SNP typing, which detects variants associated with small relative risks (typically on the order of 1.2-1.5), the ability to uncover rare variants with high relative risks is a distinct feature of sequencing-based technologies. Additionally, NGS can uncover variants related to conditions for which the proband might not have been considered at high risk a priori based on personal and family medical histories. These distinguishing characteristics of NGS pose new questions and challenges for the practice of medical genetics and genetic counseling.

This session will begin with Dr. Leslie Biesecker providing an overview of the application of NGS technologies for clinical research purposes in the context of an NIH intramural study called ClinSeq™. He will review the scale and the nature of genetic results generated by NGS, and the current challenges of annotating variants detected by NGS for return to research participants or patients. Ms. Flavia Facio will then present data on the motivations and expectations of ClinSeq™ research participants, who represent early adopters of NGS, to pursue their genomic information. We will encourage audience participation through a Q&A period at the end of the session.

Rob Tarbox
Sr. Product Manager, Illumina

MiSeq is the latest example of Illumina innovation, combining our proven sequencing technology and a revolutionary workflow to create a cost-effective, highly accurate system for a wide range of next-generation sequencing applications. This presentation will cover these features including: the MiSeq interactive design that supports a "load and go" workflow; on-board data analysis for base calling, quality values, and variant reporting; and the accuracy of Illumina SBS sequencing technology that's been cited in more than 1,400 published papers. In addition to small genome sequencing (fast ChIP-Seq), the MiSeq offers a robust applications roadmap, from amplicon, plasmid, and bacterial genome sequencing, to large genome sequencing, large genome library QC, and structural variation analysis. Supported by Illumina Nextera and TruSeq sample preparation technologies, these applications enable MiSeq to be a flexible next-generation sequencing system for every laboratory.

Patrick Schnable, Ph.D.
Director, Center for Plant Genomics, Iowa State University
Managing Partner, Data2Bio™

Next Generation Sequencing (NGS) technologies are revolutionizing biology. During this webinar Dr. Schnable of Data2Bio will describe ways in which NGS technology can help you more quickly and efficiently answer biological questions, how to design and analyze NGS-based experiments, and the types of results you can expect from NGS experiments. Data2Bio helps biologists design and analyze NGS experiments. The Data2Bio team includes staff who were early adopters of NGS technologies and who have expertise in computer science, bioinformatics, statistics, genomic technologies, and genetics/biology. A key differentiating feature about Data2Bio's data analysis reports is that they are prepared in a style that is highly accessible to biologists. In addition, these reports include visualization tools that allow biologists to explore their data/results on their own desktop computers.

David Williamson, Ph.D.
Bioinformatics Scientist 2, Illumina

Providing unique multi-sample enrichment in a single reaction, Illumina’s new TruSeq Exome Enrichment kit offers the most comprehensive and economical targeted enrichment method for exome resequencing. Optimized to integrate seamlessly with the TruSeq DNA Sample Prep solution, TruSeq Exome kit provides unique multi-sample enrichment in a single reaction that dramatically reduces hands-on time and cost per sample. Please join Illumina Scientists to learn more about:

• Assay biochemistry and workflow
• Probe design features
• Content selection and optimization
• Currently available analysis tools

Alex Helm
Product Manager, Illumina

Learn how to achieve high quality genotype calls from degraded FFPE samples with the new Infinium HD FFPE solution from Illumina.

The problem:

• Today, there is an enormous amount of valuable genetic data locked in paraffin blocks
• Experts estimate there are 200 million to 400 million of these samples worldwide
• Many consist of rare tumor and matched normal tissue and some are very well annotated
• These samples hold tremendous promise for genotyping studies
• Attempts to genotype FFPE samples in the past have been unsuccessful due to the damage these samples sustain during the FFPE process

A solution:

• Using the NEW Infinium HD FFPE solution, researchers can restore damaged FFPE samples and achieve high-quality genotyping calls
• Now, FFPE samples can provide informative, usable data

Jay Shendure, MD, Ph.D.
Assistant Professor, Department of Genome Sciences, University of Washington

To selectively isolate complex, megabase-scale subsets of a mammalian genome, we are developing aqueous-phase and solid-phase protocols for the multiplex capture of complex, arbitrary genomic subsets. Coupling of these capture methods to second-generation sequencing platforms enables the sensitive and specific discovery of genetic variation within targeted regions. We are particularly interested in resequencing of aggregate ~30 megabases that collectively comprise the “protein-coding genome”, or “exome”. In collaboration with other research groups at the University of Washington, we recently demonstrated a novel strategy to identify the genetic basis of a Mendelian disorder by exome sequencing of a few affected individuals. We have applied this approach to solve several Mendelian disorders, including Miller syndrome and Kabuki syndrome. We are now applying exome sequencing to additional Mendelian diseases as well as to complex traits.

Dipesh Risal, Ph.D.
Senior Product Manager, Informatics, Illumina, Inc.

Every Illumina sequencer is powered by TruSeq—the technology that delivers the most accurate human genome sequence at any coverage. During this webinar you’ll learn how TruSeq technology delivers:

• The most uniform genomic coverage
• The fewest gaps across genic and non-genic regions
• The highest percentage of error-free reads
• The most bases over Q30

TruSeq reagent chemistry delivers the highest quality data across a broad range of applications. Discover the details for yourself.

Shawn Levy, Ph.D.
Faculty Investigator, Hudson Alpha Institute for Biotechnology

Learn how RNA sequencing data provides:

• Superior data at a lower cost than arrays
• Optimized workflows enabling rapid expression profiling
• Straightforward analysis for data interpretation and comparison

Benjamin F. Voight, Ph.D.
Research Scientist, Medical Population Genetics, The Broad Institute of Harvard and MIT

During this genotyping webinar, Dr. Voight discussed: Benefits of GWAS and candidate gene analysis; Design details and genotyping strategies of the Metabochip; Initial replication efforts of the Diabetes Genome-wide Replication And Meta-analysis (DIAGRAM) Consortium; Highlights of the 1,000 Genomes Project; Overview of Type 2 Diabetes whole genome sequencing project

Cole Trapnell
Postdoctoral Research fellow, Harvard Medical School and the Broad Institute of MIT and Harvard

Learn how RNA sequencing analysis provides: Access to widely adopted, supported, and efficient data analysis tools; The ability to easily perform multiple analyses with the same data set; Familiar format and easy comparison to array data

Tanya Boyaniwsky
Senior Market Manager, Illumina
Jordan Stockton, Ph.D.,
Senior Market Manager, Computational Biology, Illumina

The Illumina Genome Network links researchers interested in conducting large, human whole-genome sequencing projects with leading institutes worldwide that provide highly economical and rapid turnaround sequencing services. Comprised of CSPro® certified organizations with proven expertise in generating high-quality, economical human genome data, the Illumina Genome Network enables individual researchers to complete their genome sequencing projects quickly and confidently.

Christopher E. Mason, Ph.D.,
Assistant Professor, Weill Medical College of Cornell University

Learn how RNA sequencing: offers easy adaptability for any gene expression lab, provides much richer data than gene expression microarrays, enables whole-transcriptome analysis.

Gary Schroth, Ph.D.,
Sr. Director, Gene Expression Applications R&D, Illumina
Shujun Luo,
Sr. Staff Scientist, Illumina

Session will introduce an improved solution for the reduction of abundant transcripts in RNA-Seq experiments, based on an Illumina-optimized protocol utilizing duplex-specific nuclease (DSN) from Evrogen. Illumina scientists will provide a brief overview of DSN, will describe the enhancements made to the DSN workflow to optimize its performance for Illumina RNA-Seq, and will demonstrate its utility in a wide range of applications, including ncRNA discovery and FFPE transcriptome profiling.

Rob Tarbox
Illumina

Next generation sequencing is rapidly changing the landscape of genetics, enabling researchers to obtain a deeper understanding of complex biological systems. This session will explore the applications that have benefited from Illumina sequencing technology, review the simple, industry-leading workflow including both sample prep and data analysis and discuss applications that are well suited to the capabilities that the Illumina Genome Analyzer IIe provides.

Mark Ross, Ph.D.
Illumina
Tina Hambuch, Ph.D.
Illumina

Identification of Somatic Mutations in a Human Melanoma Genome

Making it Personal: Individual Genome Sequencing in the Clinical Lab

Nicholas T. Ingolia, Ph.D.
Postdoctoral fellow, Weissman Laboratory, University of California, San Francisco

Translation of mRNA into protein is a central step in the expression of protein-coding genes. Protein synthesis is clearly regulated to control gene expression, but translation has historically been harder to measure than mRNA abundance, particularly on a genome-wide scale. Nonetheless, major pathways of translation regulation have been implicated in development and disease.
We have developed a technique, called ribosome profiling, for making genome-wide measurements of translation and protein synthesis. Transcripts occupied by in vivo translating ribosomes are subjected to nuclease digestion in order to produce ribosome-protected mRNA fragments. We then use deep sequencing on the Illumina platform to analyze millions of these ribosome footprints in parallel, providing a comprehensive picture of cellular translation. Ribosome profiling in budding yeast substantially improved the quantitation of gene expression and revealed extensive translational regulation in response to amino acid starvation. The single-nucleotide precision of ribosome footprinting revealed unexpected features of translation, including the existence of distinct early and late phases of translation characterized by changes in ribosome density across protein-coding genes. We were also able to distinguish when ribosomes were occupying upstream open reading frames (uORFs), which are short translated sequences on transcripts that can regulate the expression of downstream genes.
More recently, we have adapted ribosome profiling to mammalian cells, where it shows a similar ability to provide high-resolution, global measurements of translation.

Heather Martinez, Ph.D.
Applications Support Manager, GenVault

In this session, we describe a novel technology for dry-state, ambient temperature storage and transport of nucleic acids. GenTegra™ is an inert chemical matrix which protects DNA and RNA samples from hydrolysis, oxidation and microbial growth. DNA and RNA stored in GenTegra can be recovered, simply by adding water, and used immediately in downstream analysis. Genomic DNA recovered from GenTegra was successfully genotyped on the Illumina 1MDuo platform, while total RNA was analyzed using the Illumina Human-6v2 platform.

Naomi O'Grady,
Product Manager, Molecular Diagnostics, Genotyping

Understanding genetic variability associated with drug response or disposition is a key step toward personalized medicine. Although the gene products involved in metabolizing and transporting drug molecules have been extensively described and studied, the past and ongoing discoveries of polymorphisms in these genes raise a need for molecular tools that will enable rapid, comprehensive and accurate assessment of pharmacogenetic profiles.

In this session we describe a new genotyping assay for analysis of pharmacogenetic variations associated with drug metabolism.

Bert Eussen,
Department of Clinical Genetics, Erasmus MC
Dr. A. de Klein,
Department of Clinical Genetics, Erasmus MC

In the Molecular Cytogenetic research group at Erasmus Medical Center, our focus is on the detection of sub-microscopic mutations and rearrangements.

By using cytogenetic tools such as karyotyping and FISH in combination with DNA tools such as qPCR, MLPA, and arrays we are able to support a wide range of projects.

The diversity of these projects (ranging from individual cases to small cohorts of approximately 500) requires a flexible and reliable laboratory environment. Currently we are using the Illumina platform in combination with GenomeStudio (Illumina) and Nexus Copy Number software (BioDiscovery) as our preferred array analysis system. By addressing our sample workflow and DNA/array QC as well as by showing some rare cases from different studies, performance of both the array platform and data analysis will be demonstrated.

Christopher Maher, Ph.D., Research Fellow,
Chinnaiyan Lab, Michigan Center for Translational Pathology

Characterization of specific genomic aberrations in cancers has led to the identification of several successful therapeutic targets. Therefore, we recently began employing Next Generation transcriptome sequencing technologies to detect recurrent gene fusions in cancer. To accomplish this we developed an integrative approach, which leverages both the Illumina and 454 sequencing platforms, to detect chimeric transcripts. This led to the discovery of a recurrent, prostate-specific, androgen inducible RNA chimera, SLC45A3-ELK4. However, despite our success utilizing an integrated approach, it required substantial overhead which will become more prohibitive for examining larger cohorts.

Therefore, we focused on employing a single platform for establishing a sensitive, high-throughput methodology to comprehensively catalog functional gene fusions in cancer. To accomplish this, we evaluated a paired-end transcriptome sequencing strategy for gene fusion discovery. Not only did a paired-end approach provide a greater dynamic range in comparison with single read based approaches, we found that it successfully distinguished known recurrent gene fusions, such as BCR-ABL1 in chronic myeloid leukemia and TMPRSS2-ERG in prostate cancer, from private non-specific gene fusions. Furthermore, the comprehensiveness of a paired-end approach enabled the discovery of multiple novel gene fusions in chronic myeloid leukemia, prostate, and breast cancer cell lines that eluded previous approaches.

We therefore extended this analysis to successfully identify novel chimeras in prostate tumor samples. In addition to revealing novel chimeras, we found that paired-end transcriptome sequencing can be used for improving existing transcript annotations. Taken together, this study establishes a highly specific and sensitive methodology for comprehensively cataloguing chimeras within a sample using paired-end transcriptome sequencing which can be applied for nominating casual mutations in cancer.