Summary

The goal of this two-day meeting is to provide an introduction to state-of-art methods for producing and analyzing omics data by NGS (Next Generation Sequencing, or Deep Sequencing) platforms and contribute to building up a community interested in future biomedical applications. The first day will be devoted to tutorials on sample preparation and bioinformatics methods for “upstream” and “downstream” analysis on the principal sequencing platforms; data, sw and hands-on experience on real examples will be provided in the bioinformatics courses. The objective of the second day is to foster the building up of a community of current or future users of Deep Sequencing methods.

Program at a glance — Tutorials and workshop — Venue — Accommodation info — Organizing committee

How to register

Program at a glance

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PART 1: TUTORIALS

The first tutorial will present the state of the art about the available protocols for sample extraction for genome resequencing, CHIP-seq, RNA-seq, also introducing  elements of NGS study design in the biomedical setting. The second tutorial will offer a complete introduction to open source pipelines for ultra-high throughput alignment and signal processing: the course will cover tools for small RNA-Seq, paired/non paired RNA-Seq and derived SNP calling, including BowTie, TopHat, BWA, SAMTools, Cufflinks. The tutorial will also discuss the efficient use of these pipelines on high performance facilities (e.g. computational clusters). The third tutorial will introduce the newest tools available (and forthcoming) in the R Bioconductor distribution for RNA-Seq “downstream” analysis, such as computational statistics for RNA-Seq quality assessment, analysis of gene expression data, including methods for differential gene/exon expression.

T1. Sample preparation and design study for NGS
Alessandro Quattrone and Roberto Bertorelli (CIBIO, Trento), Alberto Ferrarini (Univ. Verona)

This tutorial will cover the fundamentals of DNA and RNA extraction for NGS applications, with a comparative look at the existing protocols and with an analysis of the differences among the commercially available platforms. It will also introduce to the specific types of experimental designs possible with NGS, especially in terms of sample multiplicity, and to the main applications for biomedical studies.

T2. Computational tools for next generation sequencing: from nucleotides to functional genomics.
Marco Chierici, Marco Roncador (Fondazione Bruno Kessler, Trento)

After a brief overview of current deep sequencing technologies and applications, participants will be introduced to alignment strategies and bioinformatics challenges on such ultra high-throughput data. We will show how to run a complete RNA-Seq analysis pipeline by using efficient tools such as Bowtie, Cufflinks, BWA, SAMTools, BEDTools. Hands-on examples will be given of short read alignment, quantification and visualization of gene or miRNA expression levels, identification of genetic polymorphisms, visualization on genome browsers. Participants will be enabled to apply complete pipelines for single- and paired-end data analyses and visualization. Computational aspects such as use of computing clusters will also be given. Participants will benefit most from this tutorial by installing tools on a Linux or Mac laptop.

T3. RNA-seq data analysis using R and Bioconductor
Gabriella Rustici, Angela Goncalves (European Bioinformatics Institute, Cambridge, UK)

This tutorial will illustrate how to use R and Bioconductor for the analysis of gene expression data obtained from high-throughput sequencing (HTS) assays. A short lecture will introduce fundamental concepts in the analysis of HTS data, focusing on RNA-seq, and a practical session will allow participants to use several Bioconductor packages to examine this data. Basic knowledge of the R language is required.

For the three tutorials, a maximum of 25 participants will be considered. Software and datasets will be provided. Participants interested in hands-on experience shall use their own laptops; please contact organizers if additional workplaces are required. ECM credits on request (7 credits).

PART 2: WORKSHOP

A keynote by an international leader in Omics technologies and invited talks on challenging studies on clinical data will demonstrate the potentiality of NGS platforms for supporting breakthrough progress. A panel session will review needs and guidelines for reproducible research on high-throughput genomics data and the framework of the FDA regulatory initiatives. A focus group session will be devoted to discuss initiatives for a transition of research groups from standard high-throughput technologies (e.g. microarrays) to NGS technologies.

Confirmed Speakers

• KEYNOTE LECTURE: Piero Carninci (RIKEN Omics, Yokohama): "Whole genome transcriptome analysis"
• Massimo Delledonne (Univ. Verona): "Comparative analysis of different NGS platforms"
• Elia Stupka (UCL Cancer Inst. & Queen Mary Univ. London): "Do we understand enough about genomesto build next generation molecular networks of disease?"
• Fabio Macciardi (Univ. of California & Genomics Bioinformatics Platform, Fond. Filarete Univ. of Milano): "Sequencing Schizophrenia: a complete annotation of genomic variants"
• POCEMON: "Poin of care genomics diagnostics"
• Federico Goodsaid (FDA, Silver Spring, MD): "Regulatory Drivers for Biomarker Science in the Quest for Better Drugs"
• Alessandro Guffanti (Genomnia): "Finding the needles in the haystack: bioinformatics explorations of SOLiD small RNA sequencing results"

• Cesare Furlanello (Predictive Models for Biomedicine, FBK, Trento): "Reproducibility and predictive biomarkers from HT Omics data"
• FOCUS GROUP: Alessandro Quattrone (Centre for Integrative Biology, UNITN) & Gian Paolo Tonini (Translational Oncopathology, National Cancer Research Inst. Genova): “DSD - Deep Sequencing for Disease: Building a Community.” with contributions of: Barbara Simionati (BMR Genomics) "Challenges in managing a NGS service" , Aldo Scarpa (ARC-NET: Centre for Applied Research on Cancer UniVr)  "The Italian Contribution to the International Cancer Genome Consortium" and Piero Carninci (RIKEN Omics, Yokohama) "The OMICS Center facility: experiences and challenges".

 

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VENUE

Castel Ivano (Ivano Fracena (TN); http://www.castelivano.it) towers over the eastern part of the Valsugana valley, in Trentino. It is known for an impressive past, numerous legends and an imposing architecture. Surrounded by a spacious park with  more than 400 kinds of flowers, this medieval castle is a true natural paradise. First written documents date the castle back to 1187, but the original core was built in 590. Today the castle is the seat of an important cultural centre called Castel Ivano Incontri  and hosts conferences, exhibitions and international art events.

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ACCOMMODATION INFO

Participants will directly book for accommodation; please indicate that the reservation refers to the Castel Ivano meeting.

Suggested accommodation

 

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HOW TO REGISTER

Costs (in Euros)

• Tutorial day (lunch included)
  • 1 tutorial: students 35, regular 45
  • full tutorial day: students 70, regular 90
    (ECM credits require attendance to at least two tutorials)
• Workshop day (coffee breaks and lunch included)
  • students 80, regular 120
  • dinner: 30

Registration and Payments

Registration and ECM credits will be managed by Castel Ivano Incontri. Online registration

PLEASE NOTE that required steps for registration are:

1. Register to the CastelIvano website (bottom right: “Autenticazione”): you will receive a confirmation mail (check spam mailbox). Click on link or paste it into browser to validate the registration.
2. Login on the “Autenticazione” box with chosen user name and password (also attached at bottom of the confirmation mail). At first login, please fill personal information form (bottom left).
3. Register by choosing available options (“ISCRIVITI” on page “Congressi”). Students status is valid for undergraduate and graduate (PhD) students.
4. A mail will be received (please check spam mail folder) with information for bank transfer or on-site payment. Separate registrations are needed for September 20 (“TOOLS”) and September 21 (“CHALLENGES”), but the payments can be aggregated.

In case of problems,  please contact the Castel Ivano Secretariat by phone or fax. Registration will be refunded only if notified within September 15.

ORGANIZING COMMITTEE

Scientific organizers: C. Furlanello (Fondazione Bruno Kessler, Trento), A. Quattrone (Centre for Integrative Biology - University of Trento), G.P. Tonini (Istituto Nazionale per la Ricerca sul Cancro - Genova)

Local organization: Castel Ivano Incontri

Supported by: POCEMON FP7 Project

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