Next-Gen Sequencing Agenda

Registration

ChIP-Enrich: Linking Genomic Regions to Biological Gene Sets Through Enrichment Testing
Maureen Sartor, Assistant Professor, University of Michigan, United States of America

We present a novel gene set enrichment testing method for ChIP-Seq or DNA methylation data that empirically corrects for multiple biases. We show the advantages of our method, ChIP-Enrich, compared to current alternatives using several ChIP-Seq datasets with differing properties.

Technology Spotlight:
Automated De Novo Genome Assembly Using DNASTAR Software
Tom Schwei, Vice President/General Manager, Dnastar Inc

DNASTAR software uses an innovative approach to enable researchers to rapidly and easily close de novo bacterial genome assemblies on a standard desktop computer. By using data from a closely related strain to guide the assembly, the assembly process can be dramatically expedited, potentially saving many weeks of work or more.

Coffee and Networking in Exhibiton Hall

Small RNA as Biomarker for Cancer Diagnosis
Harry Gao, Director, City of Hope Beckman Research Institute, United States of America

We were the first to develop the small RNA-deep sequencing in FFPE sample. We have discovered several novel miRNA-like small RNA differentially expressed in Renal Cell Carcinoma. 

Trinity as a Platform for RNA-seq Assembly and Biological Exploration
Brian Haas, Manager, Broad Institute of MIT and Harvard, United States of America

Technology Spotlight:
For Next-generation Sequencing Library Preparation: Long-span, Mate-pair Scaffolding and Methods for Faster Library Creation
Curtis Knox, Vice President, Lucigen

The NxSeq™ 40 kb Mate-Pair Cloning Kit facilitates the creation of scaffolds for de novo genome assembly. Supporting either Illumina or 454 sequencing, the kit produces 40 kb paired-end sequences with greater efficiency than existing long-span, mate-pair systems. In addition, NxSeq DNA Sample Prep Kits can be used to streamline workflow and speed up DNA library preparation for next generation sequencing.  A fully automated system for library preparation will also be discussed.

Lunch and Networking in Exhibition Hall

Poster Viewing Session

STAndardized RNA SEQuencing (STAR-SEQ): PCR-driven Library Preparation in Presence of Internal Standard Mixtures Optimizes Quality Control and Quantification in RNA Sequencing and Reduces Cost
James Willey, Professor, The University of Toledo Health Science, United States of America

PCR-driven library preparation in presence of internal standard mixtures controls for inter-sample variation in interfering substances, inter-laboratory variation in transcript representation, and 1000-fold inter-gene convergence of transcript representation, resulting in 1000-fold reduction in number of reads required for reliable quantification.

Evaluating RNA-Seq for Biomarker Discovery in Peripheral Whole Blood
Scott Tebbutt, Associate Professor, University of British Columbia, Canada

We performed RNA-seq transcriptome analysis of blood leukocyte samples from six healthy individuals (three females and three males).  Using subject-specific samples as well as pooled technical replicates, we have evaluated the benefits and limitations of globin transcript depletion for next-gen biomarker discovery in whole blood.

Coffee and Networking in Exhibiton Hall

Re-sequencing the Human Genome Reference Sequence
Stephan Schuster, Professor, The Pennsylvania State University, United States of America

With new sequencing technology available it has become possible to largely improve the quality and completeness of the human genome reference.

Evaluation of Strand-specific RNA-Seq Protocols
Allison Peak, Lab Technician, Stowers Institute for Medical Research, United States of America

We tested three commercially available kits for strand-specific RNA-Seq construction - Epicentre ScriptSeq v2, Illumina TruSeq Stranded RNA, and NuGen Encore Complete DR. We looked at the individual kits to evaluate their benefits and limitations.

Round Table Discussions in the Exhibition Hall

End of Day One

Computational Analysis of Cancer Epigenome and Transcriptome
Kaifu Chen, Postdoctoral Fellow, Baylor College of Medicine, United States of America

Analysis of Copy Number and Structural Variation in 1000 Cancer Genomes
Peter Park, Associate Professor, Harvard Medical School, United States of America

We have sequenced nearly 1000 cancer genomes at low coverage (4-8X) as part of The Cancer Genome Atlas. I will describe our analysis of copy number and structural variations in these data as well as our methods for estimation of purity and ploidy, algorithms for detection of structural variations, and issues in experimental design.

Coffee and Networking in Exhibiton Hall

Deep Metagenomic Sequencing of Multiple Ruminant Guts Reveals Species-specific Microbiomes
Mick Watson, Head, The University of Edinburgh, United Kingdom

Ruminant species such as cattle, sheep, deer, goats and reindeer represent a fascinating opportunity to study gut function and metagenomics. With a solely vegetarian diet, the gut microbiome of ruminants is perfectly adapted to digest and gain energy from plant material. However, different animals have different diets (e.g. grass vs lichen) which require different microbes to digest. We have deep-sequenced the rumen gut microbiome of several ruminant species using the Illumina HiSeq 2000 system, generating several hundred gigabases of sequence data in the process. Here we describe bioinformatic investigations into these data, including assembly into large contigs, prediction and annotation of genes and taxon assignment. We show that the vast majority of sequence data comes from as-yet uncharacterized bacterial species, representing huge potential for discovery of novel enzymes. Finally, we show that ruminants can be clustered together according to their gut microbiome structure and species abundance.

The Detection of Transcription Errors in Biological Systems
Kelley Thomas, Professor, University of New Hampshire, United States of America

The transmission and expression of genetic information are fundamental and universal processes in biological systems, and the accuracy of these processes is crucial to evolution and survival of all organisms.  Next-generation sequencing has contributed to a significantly expanded knowledge of baseline mutation rates and patterns across prokaryotes and eukaryotes.  However, the errors associated with gene expression during transcription and translation remain elusive and limited to rates derived from artificial constructs.  Here, we report a new approach for the generation of cDNA libraries coupled with next generation sequencing that allows the genome wide detection of errors in natural transcripts.

Lunch and Networking in Exhibition Hall

Poster Viewing Session

From Complete Catalogs to "Actionable" Shortlists: Integrative Analysis of Next-generation Sequencing Data in Cancer Research
Han Liang, Assistant Professor, The University of Texas MD Anderson Cancer Center, United States of America

Next-generation sequencing has become a revolutionary tool for cancer research. However, there is still a big gap between complete catalogs of genomic alternations identified from NGS studies and “actionable” shortlists for further functional investigation. Using our two recent studies  (RNA-seq in gastric cancer and exome-seq in endometrial cancer), I will discuss how to identify “driver” genes underlying the tumorigenesis.

CANCELLED - High-performance Sample Registration and Screening Methods for Robust Population-scale Sequencing on High-performance Sequencing Platforms
Shawn Levy, Faculty Investigator, Hudsonalpha Institute for Biotechnology, United States of America

Advances in DNA sequencing technology have enabled large-scale sequencing projects analyzing thousands of samples to become possible.  This presentation will describe methods and software tools to uniquely code tens of thousands of samples as well as effectively and efficiently screen for sample cross contamination prior to investing large amounts of resources into whole-genome sequencing.

Coffee and Networking in Exhibiton Hall

Close of Conference