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BIO392 - Bioinformatics of Sequence Variation

One of the fastest growing areas of bioinformatics is in the analysis, warehousing and representation of genomic and protein sequence variants, particularly with view on the use of molecular data in personalised health and biomedical applications in general. This course will engage participants to explore common data formats, online resources and analysis techniques, with a focus on human genome variation data.

Practical Information

  • from 2025 on in each Spring semester (4 weeks in May) instead of Autumn semester
  • UZH Irchel campus, Y-01F-01
  • Course language is English
  • previous BIO392 HS 2023 in the UZH OLAT system
  • compbiozurich/UZH-BIO392 course material Github repository
  • you will need to have / create a Github account (though this is also addressed at the beginning of the course)
  • the course lab is equipped with iMacs - the use your personal machines is discouraged unless you really know what to do...
Location

Course Days

Genomic Data & Privacy - Risks and Opportunities

UZH BIO392 HS22 - Day 12

Michael Baudis

Today we will discuss opportunities and Risks from genomic data collections and general privacy implications of genomic and other molecular screening data.

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Sequence analysis: interpretation

UZH BIO392 HS23 - Day 10

Morning

On the morning of day 10, the output of day 08's practical session (i.e., variant calls) will be analysed interpreted. Which variants were observed in the sequencing data you were provided and how can this be related to existing knowledge?

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Survival Analysis Exercise & Discussion

UZH BIO392 HS22 - Day 12

Survival analysis

This day and the following day of the course we will be working with survival datasets. Plan:

  • Introduction
  • Form groups (2-3 people)
  • Data download and prep
  • Work in groups
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Survival as a Measure in Cancer Genomics? Also: Cancer Classifications

UZH BIO392 HS22 - Day 09

Michael Baudis

This day provides some notes about the submitted notes, introduction to Kaplan-Meier survival analysis concepts and classification systems used to describe cancer types and clinical apperances.

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Sequence analysis: practical

UZH BIO392 HS23 - Day 08

Morning

The morning of day 08 will feature a hands-on practical of the bioinformatics pipeline discussed on the afternoon of day 07. The day will start with a brief refresher on the starting point of our pipeline: files with raw sequencing reads and a reference genome. After this, time will be spent on generating alignments and variant calls from the provided data, applying several widely used bioinformatics tools along the way.

Afternoon

The afternoon will be spent on reflecting on (or finishing) the steps from the practical. Afterwards, literature and/or slides will be provided to provide more background on Short Tandem Repeats (STRs); What are they? Why can they be problematic to analyse? Why is their variation relevant? These questions should prepare you for the morning of day 10, where the outputs of the bioinformatics pipeline will be analyses and interpreted.

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Genomic resource usage, sequence comparison, and sequence analysis

UZH BIO392 HS23 - Day 07

On this day, we will do hands-on exercises using some clinical variant annotation resources, and provide an overview of BLAST and a typical bioinformatics pipeline.

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Progenetix, Beacon+, EGA and Genome Resources

UZH BIO392 HS23 - Day 06

Michael Baudis

Today will be presentations about several topics, including Data Federation through the Beacon protocol as well as the Progenetix database. Another presentation will point to some online resources for genomics data.

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Genome Analysis Technologies

UZH BIO392 HS23 - Day 05

Michael Baudis

Some information about genomic analysis technologies, file formats ...

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Genomic File Formats, 1000 genomes project

UZH BIO392 HS22 - Day 04

Izaskun Mallona (email: izaskun.mallona at sib.swiss).

Morning

We will have a lecture and run a set of exercises (on site).

  • Overview of the standard genomics data formats
  • FASTA
  • FASTQ
  • SAM
  • BED
  • GFF
  • VCF
  • Basic file processing for bioinformatics
  • wc, grep, awk
  • Exercises
  • Project

Afternoon

Exercises and project.

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Terminal, Unix & Files

UZH BIO392 HS23 - Day 03

Izaskun Mallona (email: izaskun.mallona at mls.uzh.ch).

Morning (on site)

We will have two lectures and several sets of exercises (on site).

  • Unix + genomic formats lectures (exercises 1-4)
  • Unix and genomic formats exercises (5-14)

Afternoon

We will run the SIB Unix course using a Web browser. We encourage you to run the exercises of the course in a terminal of your own; either on a GNU/Linux or MacOS; or with a Web browser-based emulator of your choice, like cocalc.

  • SIB Unix course: UNIX for Bioinformatics
  • Chapter 1: What is UNIX
  • Chapter 2: The UNIX filesystem
  • Chapter 3: UNIX shell - first steps
  • Chapter 4: UNIX shell - filesystem commands
  • Chapter 5: UNIX shell - working with files
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Tools for programming

UZH BIO392 HS23 - Day 02

This day will introduce some tools for better software development such as Github and Atom, and basics of Python & R.

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Introduction & Technicalities

UZH BIO392 HS23 - Day 01

The first day of the "Bioinformatics of Sequence Variation" course (afternoon only) starts with a general introduction to the course's topics, timeline and procedures.

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Test...

UZH BIO392 HS22 - Day 14
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Genomic Privacy and Q & A

UZH BIO392 HS22 - Day 13

Michael Baudis

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Survival Analysis Exercise & Discussion

UZH BIO392 HS22 - Day 12
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Survival Analysis Exercise & Discussion

UZH BIO392 HS22 - Day 11
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From Sequence to Variants & Survival Analysis Introduction

UZH BIO392 HS22 - Day 10
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Survival as a Measure in Cancer Genomics? Also: Cancer Classifications

UZH BIO392 HS22 - Day 09

Michael Baudis

This day provides some notes about the submitted notes, introduction to Kaplan-Meier survival analysis concepts and classification systems used to describe cancer types and clinical apperances. Continue reading


Sequences Repeating Themselves - STRs et al.

UZH BIO392 HS22 - Day 08
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Sequence Search with BLAST & Clinical Variant Interpretation Resource

UZH BIO392 HS22 - Day 07

Morning

  • introduction of BLAST

  • excercise on using BLAST

Afternoon

get familiar with some clinical variant annotation resources.

  • introduction of ClinVar and ClinGen

  • exercise on using ClinVar and ClinGen

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Online Resources for Human Genomic Variations & Introduction to CNVs

UZH BIO392 HS22 - Day 06
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Genome Analysis Technologies

UZH BIO392 HS22 - Day 05

Michael Baudis

Some information about genomic analysis technologies, file formats ...

Continue reading

Genomic File Formats, 1000 genomes project

UZH BIO392 HS22 - Day 04

Izaskun Mallona (email: izaskun.mallona at sib.swiss).

Morning (on site, 9 am)

We will have a lecture and run a set of exercises (on site).

  • Overview of the standard genomics data formats
  • FASTA
  • FASTQ
  • SAM
  • BED
  • GFF
  • VCF
  • Basic file processing for bioinformatics
  • wc, grep, awk
  • Exercises
  • Project

Afternoon (on site or online)

Exercises and project.

Continue reading

Terminal, Unix & Files

UZH BIO392 HS22 - Day 03

Izaskun Mallona (email: izaskun.mallona at mls.uzh.ch).

Morning (on site, 9 am)

We will have two lectures and several sets of exercises (on site).

  • Unix + genomic formats lectures (exercises 1-4)
  • Unix and genomic formats exercises (5-14)

Afternoon (on site or online)

We will run the SIB Unix course using a Web browser. We encourage you to run the exercises of the course in a terminal of your own; either on a GNU/Linux or MacOS; or with a Web browser-based emulator of your choice, like cocalc. Continue reading


Github, Terminal & Editors

UZH BIO392 HS22 - Day 02

The second day of the "Bioinformatics of Sequence Variation" course, with some inroduction and setups of Github, Terminal & Editors.

  • 9:00 - 10:00: Introduction of Github things.
  • 10:00 - 11:00: Github exercise: create user specific directories & upload/edit test files using Markdown.
  • 11:00 - 12:00: Introduction to different interfaces eg atom, pycharm (lecture), editor setup exercise.

  • 13:00 - 14:00: Get familiar with R (lecture).

  • 14:00 - 15:00: Literature (genome variant review papers).
  • 15:00 - 16:30: Task: Answer the questions of literature review session and provide some notes (1-2 pages total) in a doc posted on Github (.md)
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Introduction & Technicalities

UZH BIO392 HS22 - Day 01

The first day of the "Bioinformatics of Sequence Variation" course (afternoon only) starts with a general introduction to the course's topics, timeline and procedures.

Continue reading