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MIK Bachelor Seminars 2012: From DNA to Patient Care Teachers
Module: Bachelor project medische informatiekunde (3de jaar bachelor MIK)

Coordinator:
Prof. Dr. Antoine van Kampen
Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, J1b-208
Tel. +31 (0)20-5667096
Email: a.h.vankampen@amc.uva.nl
wiki.bioinformaticslaboratory.nl

Aim

Overall aim: Next Generation Sequencing (NGS) technologies allow the determination of DNA sequences from normal individuals and patients. The determination of whole-genome sequences is almost done routinely. This opens the possibility to identify mutations that cause disorders, which may lead to a further understanding of the disease, guidance of treatment selection, improved diagnostics and eventually the development of new drugs. In this seminar series you will be provided with a brief introduction to DNA sequencing and how this is applied in practice. Moreover, you will analyse sequence data obtained from Nicolaides Baraitser patients to identify the mutation that causes this disease. As part of this we will point out potential difficulties in the analysis of this data. Finally, due to the very large amounts of sequence data that are being produced by NGS technologies there is an increasing need for state-of-the-art e-infrastructures that provide access to the necessary compute power. In these seminars you will get acquainted with these e-infrastructures and will learn how to get access to them and use them.

This topic is highly relevant for medical informatics. For example, the recently established Dutch Center for Genome Diagnostics is an initiative in which all UMCs participate and which aims to make mutation detection in DNA sequence part of patient care, e.g., diagnostics. This implies an increasing need to integrate results from sequence analysis and the interpretation thereof in clinical information systems to allow medical doctors and/or clinical geneticist to use such information in daily practice. Therefore, it is of importance that medical informatics professionals are aware of such developments and become actively engaged in this field.

Course description

Schedule

Seminar 1. From DNA to diagnostics: setting the context

Goal
In this seminar your will be introduced to Next Generation Sequencing (NGS) and, in particular, exome sequencing. These introductions will provide you with some basic understanding of these technologies and their applications.

Schedule
  • 10.00 – 10.30. Lecture. Introduction to the module (Antoine van Kampen)
  • 10.30 -11.00. Lecture. Recap of biology basics powerpoint (pptx) (Antoine van Kampen)
    • Basic biology to understand DNA sequencing and analysis, e.g., DNA, exons, SNPs, basic genetics
    • OMICS
  • 11.00 -11.15. Break.
  • 11.15 – 11.45. Lecture. Sequencing in practice: the technology powerpoint (ppt) (Aldo Jongejan)
    • The Solid sequencer: principles
    • The data
    • Color space, fastq, bam, sam
    • Introduction some basic tooling bwa, samtools
  • 11.45 – 12.15 Lab visit. Sequencing facility (Frank Baas)

  • 12.15 – 13.15 Lunch

  • 13.15 – 13.45 Lecture. Genome / exome sequencing in patient care powerpoint (pptx) (Antoine van Kampen)
    • Genome and exome sequencing
    • The story of Nicholas Volker (video)
    • Human Genome Projects
    • Genome of the Netherlands, 1k, 10k genome projects
  • 13.45 – 14.45. Computer practicum: sequence databases and online visualization/analysis tools (Antoine van Kampen)

Seminar 2. Bioinformatics@work 1: Identification of the gene mutation that causes Nicolaides Baraitser syndrome

Goal
In this seminar you will analyse exome data obtained from a Nicolaides Baraitser patient. To make this feasible, we will only use a subset of the data.

The data analysis is carried out in a Linux environment with the help of several applications for sequence analysis. All (Linux) commands to successfully perform the analysis will be provided to you. This will give you an impression about the actual work that needs to be done before you can start with the interpretation of the data (seminar 3) and why e-Biosciences is required for the analysis of next generation sequence data (seminar 4 and 5)

Schedule
  • 10.00 – 11.00. Lecture. Exome sequencing and analysis (Antoine van Kampen)
  • 11.00 – 13.00. Computer practicum. Identification of gene mutations from exome data of Nicolaides-Baraitser (Antoine van Kampen/Perry Moerland)
  • 13.00 - 13.45. Lunch.
  • 13.45 – 14.45. Computer practicum. Continued. (Antoine van Kampen/Perry Moerland)

Background information

The story of Nicholas Volker

Presentation

Computer exercises

Seminar 3. Bioinformatics@work 2: Variant selection and accounting for data bias

Goal
In this seminar you will learn how to prioritize and select variants from exome data. You will also learn how sequencing errors and various biases affect the outcome of an exome sequencing experiment.

The data analysis will continue where you left of yesterday and you will identify the variant that causes Nicolaides-Baraitser. Analyses will be carried out in a Linux environment with the help of several applications for sequence analysis and the statistical programming language R. Most (Linux) commands to successfully perform the analyses will be provided to you, so that you can focus on the interpretation of the results.

Schedule
  • 9.30 – 10.30. Lecture. Variant selection and accounting for data bias (Perry Moerland)
  • 10.45 – 13.00. Computer practicum. Identification of the gene mutation causing Nicolaides-Baraitser using exome data: variant selection and bias (Perry Moerland)
  • 13.00 - 13.45. Lunch.
  • 13.45 – 15.00. Computer practicum. Continued. (Perry Moerland)

Background information

Presentation

Computer exercises

Seminar 4. e-Bioscience@work 1: e-infrastructures

In this seminar we will introduce concepts related to e-Bioscience, with focus on "e-infrastructures” that provide resources that enable large scale data analysis for biomedical research. An overview is presented of the state-of-the-art computing technologies used for data-intensive biomedical research, including grids, scientific workflows, and semantic web. An invited lecture presents the developments on the Dutch scenario. This seminar will also provide the opportunity for hands-on experience with the Dutch e-Science infrastructure.

Schedule

Background information

Seminar 5. e-Bioscience @work 2: DNA Data Analysis on the e-Bioinfra

In this seminar we present how an e-infrastructure can be used for biomedical research to perform DNA data analysis along the lines introduced in previous seminars. The available platform (e-bioinfra, AMC e-infrastructure for biomedical research, which is used in the practice for seminar 4) is described in more detail, exposing its main functions. Examples of large studies that have been performed at the AMC and in The Netherlands will be presented by guest speakers. During the practice the students will perform data analysis for a small genomics study using the e-bioinfra.

Background information

Seminar 6. Wrap-up and borrel

Contents:
  • Presentations by students
  • Evaluation and closing

Final assignment
  • Divided in 4 groups;
  • 2 groups focus on genome/exome sequencing, 2 groups focus on e-Science;
  • The students will prepare (30 minutes) a powerpoint presentation and one student of each group will present (10 minutes, 5 minutes discussion);
  • Given the focus of each group but also their knowledge about (topics in) medical informatics, the students should present their vision about the role of medical informatics in biomedical sciences. Where do you see possibilities for MI in biomedical sciences? How do you see the relation with bioinformatics? What is your role in the management/analysis/integration of biomedical data? Etc.

Dr. Silvia Olabarriaga
Bioinformatics Laboratory, Academic Medical Centre

Dr. ir. Perry Moerland
Bioinformatics Laboratory, Academic Medical Centre

Prof. Dr. Antoine van Kampen
Bioinformatics Laboratory, Academic Medical Centre

Dr. Aldo Jongejan
Bioinformatics Laboratory, Academic Medical Centre

Barbera van Schaik
Bioinformatics Laboratory, Academic Medical Centre

Shayan Shahand
Bioinformatics Laboratory, Academic Medical Centre

Prof. Dr. Frank Baas
Genomics Facility, Academic Medical Centre

Tom Visser
SARA, BiGGrid

Dr. Lia van der Hoek
Virus Discovery Lab, Academic Medical Centre

Topic revision: r27 - 30 Jan 2012, SilviaOlabarriaga
 

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