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MIK Bachelor Seminars 2013: 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
www.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 sequences 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 - 13.15 Lunch

  • 13.15 - 13.45 Lecture. Genome / exome sequencing in patient care powerpoint (pptx) (Barbera van Schaik)
    • 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 an e-science approach is required for the analysis of next generation sequence data (seminars 4 and 5)

Schedule
  • 10.00 - 11.00. Lecture. Exome sequencing and analysis (Barbera van Schaik)
  • 11.00 - 13.00. Computer practicum. Identification of gene mutations from exome data of Nicolaides-Baraitser (Barbera van Schaik)
  • 13.00 - 13.45. Lunch.
  • 13.45 - 14.45. Computer practicum. Continued. (Barbera van Schaik)

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: e-infrastructures

In this seminar we will introduce concepts related to e-bioscience, which is a new approach to carry out large scale and collaborative biomedical research using advanced computing infrastructures (e-infrastructures). After presenting general concepts, the seminar will focus on practical aspects and examples of e-infrastructures in NL and worldwide. During the practice the students will see behind the scenes of cloud and grid computing on the Dutch e-Science infrastructure, and reflect upon the infrastructure needed to support a hypothetical research project.

Schedule (morning lectures in room L0-218-2 and afternoon practice in room L0-230)

Background information
  • Guide to e-Science Next Generation Scientific Research and Discovery, Springer, 2011.
  • see many links in the slides

Seminar 5. e-Bioscience @work: Usage of e-infrastructures

IIn this seminar we will present how e-infrastructures are used in practice based on scientific workflow management technology. The major concepts will be introduced, and we will show these are implemented in practice in the e-science platform used at the AMC (e-bionfra). These concepts will be then illustrated in two manners. Firstly, a guest speaker will present how the e-bioinfra and other Dutch e-infrastructure resources are used in practice for the analysis of sequencing data at the AMC. Secondly, during the practice the students will have hands-on experience with one workflow management system. Additionally, an invited speaker will present how high-performance computing applications (for protein research) can be offered as a service

Schedule (morning lectures in room L0-218-2 and afternoon practice in room L0-227)

Background information

  • e-bioinfra website
  • Olabarriaga SD, Glatard T, de Boer PT. A virtual laboratory for medical image analysis. IEEE Trans Inf Technol Biomed. 2010 Jul;14(4):979-85. Epub 2010 Apr 5. (pubmed)
  • Shahand S, Santcroos M, van Kampen AHC, Olabarriaga SD. A Grid-enabled Gateway for Biomedical Data Analysis. Journal of Grid Computing, December 2012, Volume 10, Issue 4, pp 725-742 (abstract)
  • Barbera D C van Schaik, Mark Santcroos, Vladimir Korkhov, Aldo Jongejan, Marcel Willemsen, Antoine H C van Kampen, Silvia D Olabarriaga (2012) Challenges in DNA sequence analysis on a production grid In: PoS (EGICF12-EMITC2)039 1-19 (pdf)
  • Hunting viruses on a haystack (isgtw)
  • see also many links in the slides

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

Topic revision: r20 - 29 Sep 2014, PerryMoerland
 

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