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SELECTBIO Conferences International Conference on Advances in Next Generation Sequencing

International Conference on Advances in Next Generation Sequencing Agenda

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Thursday, 28 May 2015





Opening Lecture


Ravi SirdeshmukhKeynote Presentation

Proteomics, High Throughput Science and India - Cancer Perspective
Ravi Sirdeshmukh, Distinguished Scientist & Associate Director , Institute of Bioinformatics, India


Coffee Break and Networking Session

SESSION 1: NGS Challenges and Possible Solutions/ Session Chair: Surinder Sahota


B R DasKeynote Presentation

Next Generation Sequencing from Indian Perspective: Opportunities and Challenges
B R Das, Advisor & Mentor- R&D, CoE, Molecular Pathology, SRL Limited, India

This talk will highlight the Opportunities and Challenges faced in Next Generation Sequencing from Indian Perspective. It will discuss about the role of NGS multiple gene panels in diagnostics, prognostics and treatment of diseases. Further, it will discuss the challenges faced in setting up the infrastructure including huge investment along with technical skills required in terms of laboratory experiment and interpretation of the huge data in Indian Labs.


Integrating Bioinformatics Tools and Infrastructure to Enable High-Throughput Biology
Sven Nahnsen, Head, University of Tuebingen, Germany

This talk will present the latest developments towards the integrative analysis of large and complex NGS-based data. Further, it will discuss its Integrated Technology which includes Liferay as a portlet container and gUSE/WS-PGRADE as a workflow engine and finally on openBIS for data management application.


Anthony PapenfussKeynote Presentation

Analysis Challenges and Solutions for Cancer Genomics Data
Anthony Papenfuss, Head, Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Australia

In this talk, some of the Challenges, Solutions and open questions will be discussed. It will cover analysis in clinical cancer genomics and genomics discovery projects and will highlight the progress made in developing tools to support analyses, method validation and reporting. In addition, it will cover single nucleotide variants and copy number analysis. . Further, the talk will introduce several tools that have been developed and will discuss how the data and the questions have influenced the tools developed.



Poster Viewing


Lunch Break and Networking Session

SESSION 2: Applications of NGS-I/ Session Chair: Bibhuranjan Das


Jurg BahlerKeynote Presentation

Genome Regulation in Fission Yeast
Jurg Bahler, Professor, University College London, United Kingdom

This Keynote Presentation will highlight the method used for Quantification of Transcriptome and how this Integrated data set supports quantitative biology and affords unique insights into cell regulation. It will also discuss how Cell-Cycle regulated transcription tunes mRNA numbers to phase-specific requirements. In addition, it will also throw light about analyses of non-coding RNAs, alternative splicing and intronic lariats/ branch points based on RNAs, alternative splicing and intronic lariats/branch points based on RNA- seq data sampled in different physiological conditions and mutant backgrounds.


Hybrid Genome Assembly with Multi-Platform NGS Data
Farhat Habib, Scientist, IISER, India

This talk will illustrate few Hybrid Approaches used for assembling data from multiple sequencing platforms to form Hybrid Genome which allows one to correct for the biases and errors of one platform with information from a complementary platform. Further, it will also discuss the approach taken with the assembly of the Hydra vulgaris genome which is a complex genome with a large repeat content.



Coffee Break and Networking Session

SESSION 3: Applications of NGS-II/ Session Chair: Anthony Papenfuss


De novo Genome Assembly and Annotation of Indica Rice
Malali Gowda, Director, Centre for Cellular and Molecular Platforms, India

This talk will highlight the role of NGS Technologies in generating High Quality rice genome assembly and annotation. Initially, it will present the deep sequence of first indica cultivar, HR12 and assembly of HR12 genome using combination of Illumina’s short reads and PacBio long reads which improves the quality of HR12 assembly and annotation. Finally, it will discuss how HR12 genomic resources (assembly, annotated genes, repeats, variants etc) from this study will accelerate rice improvement programs in India and beyond.


De novo Transcriptome Analysis- Insights from Plant Transcriptome Data
Sriram Parameswaran, Chief Technology officer, Genotypic Technology Pvt Ltd, India

This talk will highlight how De novo transcreiptome sequencing enables to explore rare and non-genetically characterized plants obtained in situ and identify its genetic coding complement. Further, it will also discuss how De novo transcriptome data can be used to assign functional classes, pathway and derive gene interaction that encode novel biochemical activity. This talk will focus on biological insights obtained from de novo transcriptomics of medicinal plants exploring the insights from three cases.


Identification of Immunity-Related Genes in the Burying Beetle Nicrophorus vespilloides by Suppression Subtractive Hybridization
Chandan Badapanda, Senior Scientist, Xcelris Genomics, India

In this talk, screening results for immunity related genes in the burying beetle Nicrophorus vespilloides using the suppression subtractive hybridization approach will be discussed. Initially, identification of putative gene objects Nicrophorus cDNA library using ABI 3730 xl automatic DNA sequencer (PE Applied Biosystems), Sequence assembly with Lasergene software package (DNAStar Inc.), enrichment for transcripts will be covered. In addition, In addition, factors involved in mRNA stability determination and central components of the RNA interference machinery identified will be discussed. Further, it will also discuss how it has set up individual searchable databases for the complete sequence dataset and used this to identify the genes.


End of First Day of Conference

Friday, 29 May 2015

SESSION 4: Understanding Cancer using Next Generation Sequencing/ Session Chair: Sven Nahnsen


A 10-year Anthology of Sequencing and it's Role in Understanding Cancer
Sanjay Joshi, CTO, EMC Emerging Technologies Division, United States of America

This talk will present the instrumentation, analytics used for completion of the Human Genome project, ENCODE Phases I and II, RNA-seq, ChIP-seq, and many more landmarks along with its  interpretation. Further, it will discuss the effect of these changes in the understanding of cancer.


Cancer Genome Sequencing and Precision Medicine: What are the Challenges?
Kumar Somasundaram, Professor, Indian Institute of Science, India

This talk will highlight success and difficulties faced in data generation using Next Generation Sequencing with respect to Glioblastoma. In addition, it will also cover various aspects like genetic and epigenetic alterations in glioma, serum biomarkers using high-throughput genomics and proteomics approaches, genome-wide shRNA screening for temozolomide sensitivity and exome sequencing to understand the glioma biology.


Coffee Break and Networking Session

SESSION 5: Next Generation Sequencing in Cancer Research/ Session Chair: Jurg Bahler


Making Sense of Cancer Evolution with Next Generation Sequencing
Anthony Papenfuss, Head, Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Australia

This talk will focus on Investigating Tumour Evolution by Next Generation Sequencing. Initially, this talk will describe sequencing of Primary Melanomas, Multiple Metastases and Several Liposarcomas cell lines. Further, it will discuss how data inference, statistical Inference and Comutational Modelling   helps inferring the order of Mutations in Cancer.


Surinder SahotaKeynote Presentation

Next Generation DNA Sequencing in Probing Tumour Origins and Behaviour in Haematological Malignancy
Surinder Sahota, Reader, University of Southampton, United Kingdom

This Keynote Talk will focus on Haematological Malignancy, particularly B-lymphoid Neoplasms and will describe NGS approaches that allows insights into origins of Human Multiple Myeloma (MM). It will further review key elements of MM genome as emerged from NGS Studies. In addition, profiling of tumour clone in response to therapy using NGS approaches will be highlighted which is essential to provide individualised therapy in cancer patients.


Translating Cancer Genomics to Medicine
Amit Dutt, Principal Investigator, Scientist F, Tata Memorial Centre, India

This talk will highlight newer generation SNP arrays and massively parallel Next Generation DNA sequencing technologies for complete genome characterization of Cancer will helps in advancing Cancer Sciences and leading to discovery of novel molecular subclasses, new therapeutic targets and biomarkers for clinical development. In addition, this talk will discuss  how by using these and conventional technologies will help to the identification of causal alterations in human cancer and discovery of  novel somatic activating alterations at FGFR2, EGFR, AKT, PDGFRA and FGFR1 mutations in endometrial cancer, lung squamous carcinoma and cervical carcinoma. Finally, it will discuss the recent advances in discovery and characterization of  some novel potentially therapeutic target in Indian samples of lung carcinomas and head and neck cancer.


Poster Viewing


Lunch Break and Networking Session

SESSION 6: Advanced Practices in NGS based Genomics and Proteomics/ Session Chair: Ravi Sirdeshmukh


Fast and Accurate Mapping of Short Reads from Next Generation Sequencing Platforms
Debnath Pal, Associate Professor, Indian Institute of Science, India


Integrating Microarray, RNA-seq & Proteomics Data for Biomarker Discovery & Network Analysis
Kshitish Acharya, Faculty Scientist, Institute of Bioinformatics & Applied Biotechnology, India


Coffee Break and Networking Session


David SmithKeynote Presentation

Using Next Generation Sequencing to Study How Human Papillomavirus is responsible for the Development of a Number of Different Cancers
David Smith, Professor, Mayo Clinic, United States of America

This Keynote Talk will discuss the study of whole exome next generation sequencing (NGS) of cervical adenocarcinomas which suggests that HPV is integrated to exonic sequences and plays role in cancer development. Further, it will also discuss the studies with OPSCCs, using both RNA sequencing and mate-pair whole genome sequencing (WGS). Finally, it will demonstrate how NGS could play an important role in the clinical management of HPV-driven cancers, both in terms of defining the best strategies for the clinical management of these cancers and for monitoring each cancers response to clinical treatment.


Poster Award Presentation & Vote of Thanks


End of Conference

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