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Special-topic Lecture: Next Generation Sequencing WS 11/12

General Information

Lecturers: Dr. Barbara Hutter, Lars Feuerbach, Fabian Müller

Tutors: Matthias Bieg, Robert Kirsten

Lecture: Block course, March 19 - March 30, 2012

Time:

Lecture: Monday - Friday, 10:00 am - 1:00 pm, E1 3, HS 003

Tutorial: Monday - Thursday, 2:00 pm - 4:00 pm, CIP Pool 003 in E2 1 and CIP Pool 104 in E1 3

Information: This course can be used as a "Spezialvorlesung der Bioinformatik/Special-topic Lecture Bioinformatics"

Note: This course will be presented in English

Requirements: Recommended are

  • basic knowledge of Biology, Genetics, and Biostatistics
  • proficiency in applying Unix command line
  • lectures:
    Bioinformatik I + II
    Softwarewerkzeuge der Bioinformatik

Maximum number of praticipants: 50; registration by email (name, registration number, semester)

Aims/Competences to be developed:

The lecture gives an introduction into modern bioinformatic methods for analyzing high throughput ("Next Generation") sequencing data. It is aimed at advanced students of Bioinformatics (master program) who intend processing such data in their master thesis and/or future working field. The students will get familiar with the basics of modern high throughput sequencing as well as the mathematical and algorithmic background of existing analysis programs. Using examples from up-to-date (tumor) genome research, typical problems and solution approaches will be presented. For deepening understanding of the lecture contents, there will be theoretical and practical exercises. The students will acquire the necessary knowledge and skills to allow independent research and communication with experimental working groups in the currently fast expanding field of high throughput sequencing.


Content:
 
  • Introduction
    What is Next Generation Sequencing, which biological questions are approached with it, which are the bioinformatic challenges?
  • Platforms
    How does second generation sequencing work, which output formats exists, how much data is produced?
  • Alignment
    Why not BLAST? Alternatives: short read mapping with hash-based approaches and Borrows-Wheeler transformation; binary alignment format (BAM); samtools
  • Whole genome sequencing
    1000 Genomes Project, sequencing of tumor genomes in ICGC, integration of viral elements
  • Point mutations
    Finding point mutations in cancer genomes and comparison with normal genome (of the same patient) = discern natural variations from disease-associated ones; genotype likelyhood
  • Annotation
    Effect of mutations in coding exons (conservation MSA, protein structure), noncoding regulatory elements, transcription factor binding sites; pathways and interactions
  • Indels
    Detection and effects of small insertions and deletions in coding exons, noncoding regions; split read mapping
  • Structural variants
    Amplifications, large deletions, rearrangements; overexpression by multiple copies (e.g. MYC), activating and inactivating gene fusions, loss of heterozygosity, copy number profiles
  • Assembly
    New challenges by short sequences; Overlap-layout-consensus and de Bruijn graph, Eulerian path
  • Epigenome
    Defects in epigenetic machinery and their effects on gene expression etc.; amplicon and whole genome bisulfite sequencing, RRBS
  • ChIP-seq
    DNA binding proteins and histone modifications; peak calling
  • RNA-Seq
    Transcriptomes and expression profiles; is the mutated allele expressed at all? Alternative splicing, detection of gene fusions on RNA level
  • Special applications
    microRNA-Seq; RNA-protein interactions with photoactivatable ribonucleosides (PAR-ClIP); alternative sequencing technologies
  • 3rd generation sequencing
    single molecule real time sequencing, nanopores

Literature and web links

Schein/Certification: Autonomous processing of 7 examination sheets that are partially handed out as homework, partially to be solved in practical tutorials.

Admission to the final exam: at least 50% of points from the homework achieved. After failure to pass the final exam there is the possibility to pass an oral exam.

The mark confers to the mark of the final exam.

 

Checklist of example exam problems

Credits: 5 (2 V + 1 Ü)

This course is taught in English.

Lectures:

Day 1, March 19
Introduction_NGS
Platforms
Assignment 1
Day 2, March 20
Alignment

Assignment 2
Day 3, March 21
ChlP-Seq
Annotation
Assignment 3
Day 4, March 22
RNA-Seq

Assignment 4
Day 5, March 23
Whole genome sequencing


Day 6, March 26
Point mutations
Indels
Assignment 5
Day 7, March 27
Genomic rearrangements
Assembly
Assignment 6
Day 8, March 28
Epigenomics

Assignment 7
Day 9, March 29
Special applications


Day 10, March 30
Third generation sequencing



Solutions practical part Day 4-6

 

 

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