The rapid emergence of next-generation sequencing (NGS) is revolutionizing biological research. Technology that was once only available for major sequencing centers is now available to all, as price for entry and time for implementation continues to drop. Purchasing an NGS platform, however, is still a major decision. How do you maximize the greatest potential for your investment? Reaching this potential requires efficient pipeline workflow strategies, careful experimental design, comprehensive targeted enrichment technologies, data analysis, management, and integration, in addition to maintaining your platform and people management all at maximum production. The central theme of Cambridge Healthtech Institute’s Second Annual Beyond Sequencing: Managing Resources and Maintaining NGS Platforms for Peak Performance is efficient use of your NGS platform. Sessions will focus on common bottlenecks, case studies, real-world experiences and solutions from experienced users. Applications of cancer and metagenomics will showcase the latest results, challenges, and opportunities in deep sequencing.
Tuesday, June 21
7:30 am Main Conference Registration and Morning Coffee
Keynote Session: Sequencing at the Frontlines
8:15 Chairperson’s Opening Remarks
8:25 Personal and Nonpersonal Genomes: Their Analysis and Variation
 Michael Snyder, Ph.D., Professor and Chair of Genetics; Director, Stanford Center for Genomics and Personalized Medicine, Stanford University
We have been characterizing the genomes of humans and yeast using omics technologies. 1) We have mapped structural variation in the human genome using paired end mapping and found nearly 1000 differences between individuals and the reference genome. 2) We have used high throughput sequencing (RNA Seq) to map transcribed regions in eucaryotic genomes. We have found extensive diversity in the 3’ end of mRNAs and many novel transcribed regions. 3) We have mapped binding sites of transcribed factors using ChIP Seq. These studies have been used to develop and analyze regulatory networks and variation among individuals and species.
9:05 Lessons Learned: Sample Preparation Using Multiplex Identification of Microbes
 Ronald W. Davis, Ph.D., Professor, Biochemistry and Genetic; Director, Stanford Genome Technology Center, Stanford University School of Medicine
9:50 Networking Coffee Break in the Exhibit Hall with Poster Viewing
10:30 Sequencing-Based DNA Methylation Analyses: Insights into Monoallelic Gene Regulation
 Joseph Costello, Ph.D., Professor and Chair, Molecular Neuro-Oncology, University of California, San Francisco
Sequencing-based DNA methylation profiling is comprehensive and enables investigation into the relationship between genotype and epigenotype genome-wide. Four leading methods yield concordant DNA methylation profiles, but differ widely in methylome coverage, quantitation of methylation levels and resolution. By mapping the genotype of each sample from the sequence reads of the methylation assay, specific epigenetic states can be assigned to genetic alleles. Cell type-specific and evolutionarily conserved monoallelic methylation will be discussed.
11:10 Preparation of Nucleic Acid Libraries for Next-Generation Sequencers with an Automated Molecular Biology Platform for Unknown Pathogen Detection
 Kamlesh D. Patel, Ph.D., Principal Member, Technical Staff, Biosystems Research Group, Sandia National Laboratories
We are developing a nucleic acid sample preparation platform to interface directly with NGS to detect unknown pathogens by enriching informative nucleic acids sequences and suppressing background DNA to maximize the sensitivity of state-of-the-art NGS. We will present our Automated Molecular Biology (AMB) platform with its unique digital microfluidics (DMF) design to function as a central hub for interfacing multiple lab-on-a-chip sample processing modules for consistent and contamination-free preparation of clinically-derived DNA samples. This AMB platform will carry out a diverse series of benchtop-like steps at a scale adapted to handling small, but precious, samples for DNA manipulations, but with far greater speed and efficiency than at the benchtop.
11:50 NGS Leaders Panel Discussion: When People Share Their Genome on Facebook – The Impact on Science and Society
Moderators: Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World
Eric Glazer, Managing Director, NGS Leaders
Panelists to be Announced
There are countless scientific, ethical, legal and economic implications associated with the emergence of personal genomics and the ability to share personal information by way of social media channels. This has set the stage for what experts are calling “a more dramatic change in our way of life than that caused by the computer.” Our diverse panel of subject-matter experts will address a few of the big questions facing all stakeholders in NGS, businesses, regulators and academia.
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12:45 pm Luncheon Presentation
Integrated NGS Analysis Enables Rapid Biological Interpretation From Raw Reads:Case Study on Prostate Cancer RNAseq Data
Cecilie Boysen, Ph.D., Senior Consulting Manager, Americas, CLC Bio, LLC
Sandeep Sanga, Ph.D., Bioinformatics Product Development Scientist, Computational Biology, Ingenuity Systems, Inc.
High-resolution analysis of altered expression of genes can help pinpoint specific pathways and processes activated in growing tumors. Determining these activated pathways and networks can highlight dysregulated processes, inform treatment options, and suggest potential biomarkers that ultimately improve patient prognosis and treatment.
2:00 Chairperson’s Remarks
2:05 Automated Sample Preparation Technologies for Next-Generation Sequencing Platforms
Nader Pourmand, Ph.D., Assistant Professor, Biomolecular Engineering, University of California, Santa Cruz
Next-generation sequencing platforms provide gigabases of genetic information in a single run. An important prerequisite for these platforms are high-throughput, automated and cost-effective preprocessing approaches for DNA sample library construction. During my talk, I will discuss our fully-automated sample preparation pipeline. This method is capable of preparing dozens of DNA libraries in just a few hours.
2:35 Reduction of Non-Desired Sequence Reads by LNA Oligonucleotide for miRNA/Pre-miRNA Deep Sequencing
Mick Kawano, Ph.D., Research Scientist, RIKEN Omics Science Center
We show a method for constructing small RNA libraries for high-throughput sequencing in which we have made a significant improvement to commonly available standard protocols. We added LNA/DNA oligonucleotides complementary to the adapter-dimer and non-desired products during the reverse transcription reaction to reduce the products which often contaminate standard libraries and reduce the yield. This technique enabled a deep-sequencing for miRNA and pre-miRNA.
3:05 Technology Presentation
3:20 Networking Refreshment Break in the Exhibit Hall with Poster Viewing
4:00 Troubleshooting Next-Generation Sequencing for Rare-Variant Detection
Todd E. Druley, M.D., Ph.D., Assistant Professor, Pediatrics and Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine
There is a greater emphasis in research and clinical medicine to identify highly-penetrant, rare genetic variants that are driving complex phenotypes. However, accurate detection of rare variants in heterogeneous samples requires a careful understanding of the limitations of the various next-generation sequencing platforms, and how these limitations will change as the technology matures. We will discuss our lab’s experience at quantifying and overcoming these limitations through the optimization of sequencing-library creation methods and bioinformatic development.
4:30 Geoseq: Managing Public and Private Deep-Sequencing Datasets for Comparative Analyses
Ravi Sachidanandam, Assistant Professor, Genetics and Genomic Sciences, Mount Sinai School of Medicine
Geoseq currently curates submissions to the SRA collection at NCBI and makes them searchable and accessible. In addition, it allows local datasets to be privately managed, and analyzed in conjunction with public sets. In addition, Geoseq allows other analysis platforms to be used. It facilitates SNP calling, mRNA-seq, small RNA-seq, DNA-seq as well as ChIP-Seq analysis.
5:00 Compressing and Querying the Genome
Vineet Bafna, Ph.D., Professor, Computer Science and Engineering, University of California, San Diego
The development of inexpensive sequencing technologies makes it likely that our genomic information will soon be an integral part of our health record, accessible for querying by researchers and clinicians. We consider the imminent future where individual donor genomic sequences are generated as sub-chromosomal fragments, and most queries involve the analysis of genetic variations between the donor genome and a standard reference. We propose a general vision of layered software for genomics, along with algorithms for compressing and indexing, that allow applications to efficiently query this vast genomic database.
5:30 Networking Refreshment Break in the Exhibit Hall with Poster Viewing
6:30 Close of Day