Technology Driving Precision Medicine

Co-Located with Molecular Med TRI-CON Asia

May 28-31, 2013
Marina Bay Sands, Singapore


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Thursday, May 30

8:00 Morning Coffee


8:40 Chairperson’s Remarks

Bogi Eliasen, Program Director, FarGen, Ministry of Health, Faroe Island


8:50 Next-Gen Sequencing Analysis Using GigaGalaxy

Tin-Lap LeeTin-Lap Lee, Ph.D., Associate Professor, Program in Reproduction, Development and Endocrinology, School of Biomedical Sciences, The Chinese University of Hong Kong

Despite the plummeting costs of sequencing, the downstream processes create financial and bioinformatics challenges for many biomedical scientists. To alleviate this major stumbling block, we have established a Galaxy-based platform (CBIIT-GigaGalaxy) for fast and efficient genomic data analysis. We have implemented the first web-based Short Oligonucleotide Analysis Package (SOAP) for Next-gen sequencing analyses in a simplified drop-down menu format. SOAP aims to provide a full solution to next generation sequencing data analysis, allowing reproducible data analysis.

9:20 Predicting TF-DNA Binding in vivo: NGS Data Brings Us a Few Steps Closer

Shyam PrabhakarShyam Prabhakar, Ph.D., Associate Director, Genome Analytics; Group Leader, Computational and Systems Biology, Genome Institute of Singapore

Accurate bioinformatic prediction of TF-DNA binding in vivo had long been considered impossible, particularly in large genomes. However, thanks to NGS assays and a series of conceptual advances, the outlines of a solution are beginning to emerge. Through unconventional analyses of multiple ChIP-seq and DNase-seq datasets, we have characterized multiple ways in which in vivo TF-DNA binding affinity differs from the predictions of simple models. Quantitative models of these effects, when combined with chromatin accessibility information, could yield the answer to a problem that has vexed bioinformaticians for decades.

9:50 Coffee Break in the Exhibit Hall with Poster Viewing

10:40 From Complete Catalogs to “Actionable” Shortlists: Integrative Analysis for Next-Generation Sequencing Data

Han LiangHan Liang, Ph.D., Assistant Professor, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

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.

11:00 Open Source and Web-Based Analysis of NGS Data Using Galaxy at the Center for Research Informatics University of Chicago

Jorge AndradeJorge Andrade, Ph.D., Director, Bioinformatics, Center for Research Informatics, Biological Sciences Division, University of Chicago

Next Generation Sequencing technologies like Whole Genome Re-Sequencing, Whole Exome, ChIP-Seq and RNA-Seq, are promptly becoming the most popular research strategy for drug discovery and biomedical research. Three important challenges for NGS data analysis will be addressed in my talk: 1. How to handle (transfer/share/manage) in a secure and compliant environment, the huge amounts of data generated by NGS; 2. What kind of algorithms, statistical models and pipelines should constitute a standard bioinformatics analysis of NGS; and 3. How to ensure repeatability (Scientific Integrity) when performing bioinformatics analysis of NGS.

The Center for Research Informatics at the University of Chicago, has developed a set of NGS bioinformatics pipelines for the analysis of Illumina and SOLiD data, this pipelines use the open source Galaxy bioinformatics framework to integrate our High Performance Computing Cluster, Large Scale Computational Storage the most popular analysis tools and algorithms to execute well-defined and production-ready pipelines that can be applied to virtually any sample size of NGS data. This pipeline and computational resources are publically available and should constitute a big contribution from the University of Chicago to the biomedical research community.

11:20 Next-Generation Sequencing – From Data Generation to Data Archival

Lavanya Veeravalli, Bioinformatics Specialist, Genome Institute of Singapore

Several core bioinformatics pipelines in various platforms have been developed in Genome Institute of Singapore to manage and analyze the exponentially increasing high throughput Next Generation Sequencing (NGS) data. We studied and benchmarked the algorithms to compress NGS data in FASTQ format and developed an archival pipeline including the compression algorithm, referred to as “QUIP” into HDF5 archival information package to achieve the best, if not, optimal, way of organizing ever increasing libraries that are being sequenced in GIS.

Illumnia logo11:40 Luncheon Presentation: Sequencing in the Cloud Era with Illumina's BaseSpace Bioinformatics Platform

Michael JanisMichael Janis, Senior Product Manager, BaseSpace, Illumina Inc.

The promise of sequencing data is to provide revolutionary insight into almost all areas of public and human health. Yet  the ability to extract the full value of this data is at risk without the development of new bioinformatics approaches.  Learn how Illumina's BaseSpace has become a valuable platform for bioinformatics developers and how the rapid growth of data within BaseSpace is enabling new types of genomics research.



13:40 Chairperson’s Remarks

Melissa J. Fullwood, Ph.D., Assistant Professor, Yale-NUS; Special Fellow, Cancer Science Institute, Singapore

13:50 Ultra-Fast Alignment and Variation Detection Software for Cancer Genome Analysis

Mingyu Yang, Ph.D. Candidate for Bioinformatics, BIOPIC, COllege of Life Sciences, Peking University


14:10 Metabolite Fingerprinting in Response to Drug Treatment for Asian Population

Villoo Morawala-Patell, Ph.D., Founder and CMD, Avesthagen Limited


14:30 Investigating Tumor Heterogeneity Using Next-Gen Tools

Niranjan NagarajanNiranjan Nagarajan, Ph.D., Assistant Director and Senior Research Scientist, Computational and Systems Biology, Genome Institute of Singapore

Tumor heterogeneity is well known to play a role in cancer progression and treatment and recent advances in high-throughput sequencing and single-cell analysis have provided us with the means to study it in exquisite detail. In this talk, I will outline the state-of-the-art in this field with particular emphasis on new computational tools (including the ones developed in our lab) and how they can be used to provide novel insights in the study of tumor evolution and heterogeneity.


14:50 Q&A with Session Speakers

15:00 Refreshment Break in the Exhibit Hall with Poster Viewing

15:40 Cancer from Every Angle: Data Integration of High-Throughput Capture Technologies

Denis BauerDenis C. Bauer, Ph.D., Research Scientist, CSIRO Mathematics, Informatics and Statistics (CMIS), Commonwealth Scientific and Industrial Research Organization, Australia

In order to understand disease states or cancer progression, we need to gain a better insight into the interplay of different regulatory mechanisms in the cell. However, modern high-throughput data generation allows us to only capture a discreet snapshot of cellular regulation, e.g. RNA, DNA, methylation. Our goal is hence to build predictive models from these layers of discrete 'omics data that capture the continuous regulatory interplay to inform medical genomics research. To achieve this, we generated matched genetics, transcriptomics, epigenomics as well as microbiomics data from lean and obese colorectal cancer patients. We employ statistical and machine learning methods that integrate information from the different 'omics data sources at single base resolution to identify regions with functional relevance for cancer development and prognosis.

16:00 3-D Insights into Chromatin and Transcription in Human Cancer Cells

Melissa FullwoodMelissa J. Fullwood, Ph.D., Assistant Professor, Yale-NUS; Special Fellow, Cancer Science Institute, Singapore

Many distal transcription factor binding sites have been observed. Chromatin interactions can connect distal transcription factor binding sites with target gene promoters. In this talk, I will introduce Chromatin Interaction Analysis with Paired-End Tag sequencing (ChIA-PET), a next-generation sequencing-based method for identifying chromatin interactions between transcription factor binding sites on a genome-wide scale which was part of the ENCODE consortium. Our results suggest that chromatin interactions may be a major mechanism by which transcription regulation occurs in human cells.

16:30 Understanding of Genomic Variations in Cancer – Germline Variants versus Somatic Mutations

Axel HillmerAxel Hillmer, Ph.D., Senior Research Scientist, Cancer Therapeutics & Stratified Oncology, Genome Institute of Singapore

Inherited and acquired genomic variants contribute to the development of cancer. We use an in-house developed DNA paired-end tag (DNA-PET) sequencing approach as well as conventional whole exome and whole genome sequencing approaches to compare the genomic landscape of cancer and non-cancer samples. In gastric cancer, we discovered three distinct somatic mutational signatures – against a genome-wide backdrop of oxidative and microsatellite instability-related mutational signatures, we identified the first exome-specific mutational signature. In chronic myeloid leukemia (CML), we identified an Asia-specific structural germline deletion polymorphism in BIM, a pro-apoptotic member of the BCL2 family of proteins. BIM upregulation is required for tyrosine kinase inhibitors (TKIs) to induce apoptosis in kinase-driven cancers. The polymorphism switched BIM splicing from exon 4 to exon 3, encoding for BIM isoforms lacking the pro-apoptotic BCL2-homology domain 3 (BH3). The polymorphism was sufficient to confer intrinsic TKI resistance in CML and EGFR non-small cell lung cancer (NSCLC) cell lines, a resistance that could be overcome with BH3-mimetic drugs. Importantly, individuals with CML and EGFR NSCLC harboring the polymorphism experienced significantly inferior TKI responses.

16:50 The Next Generation Proteomics – Advances, Applications and Challenge

Chanchal KumarChanchal Kumar, Ph.D., Associate Principal Scientist, MSD Translational Medicine Research Centre Singapore

Mass spectrometry(MS)-based proteomics has established itself as a powerful and ubiquitous method for precise and global protein measurements. Radical advances in proteomics in the last decade have opened newer vistas for diverse systems-wide proteomic investigations in biomedical research. Such investigations include comparison of different proteome states and their temporal dynamics, determination of protein structure and their posttranslational modifications, elucidation of protein localization within organelles, and to determine their interactions with other cellular entities. In this talk, I will focus on current state-of-the-art and emerging paradigms in mass spectrometry(MS)-based proteomics, which in combination with innovative experimental strategies, and advances in computational methods is poised to engender profound changes in systems biology and personalized medicine.

17:10 End of NGS Applications

17:10 Dinner Short Course Registration

17:30 – 19:30 Dinner Short Course (Separate Registration Required)

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