Genetics and genomics
BIO-373
Media
Course syllabus:
- Genetics (Sebastian Waszak): 3 sessions
- Sept 8th: Introduction to genetics. Mendelian genetics. Extension of Mendelian genetics.
- Sept 15th: X-linked heredity. Extranuclear inheritance. Population genetics.
- Sept 22nd: No class this week - Lundi du jeûne fédéral
- Sept 29th: Chromosomes variation. Mutation and DNA repair. Cancer genetics.
- Bioinformatics analysis of genetics and genomics data - An Introduction (Vincent Gardeux): 2 sessions
- Oct 6th: Introduction to Python for bioinformatics.
- Oct 13th: Data analysis applied to genetics & genomics.
- Oct 20th: No class this week - Holiday week
- Genomics (Bart Deplancke): 4 sessions
- Oct 27th: Introduction to genomics. Sequencing technologies. Comparative genomics.
- Nov 3rd: Genomic variations. Complex traits. GWAS.
- Nov 10th: Gene Regulatory networks. Regulatory elements. Transcription factors.
- Nov 17th: Genomic diseases and therapeutics. Precision medicine.
- Bioinformatics analysis of genetics and genomics data - G&G Projects (Vincent Gardeux): 4 sessions
- Nov 24th + Dec 1st: Group project in genetics
- Dec 8th + 15th: Group project in genomics
- Written exam
- Jan 2025: TBD
- Course overview (File)
- Introduction to genetics (File)
- Mendelian genetics (File)
- Extension of Mendelian Genetics (File)
- Questions for Week 1 (File)
- Questions & Answers for Week 1 (File)
Genetics - part II
- X-linked heredity and sex determination (File)
- Extranuclear inheritance (File)
- Population genetics (File)
- Questions for Week 2 (File)
- Questions & Answers for Week 2 (File)
No class this week - Lundi du jeûne fédéral
Genetics - part III
- Mutation & DNA Repair (File)
- Chromosome variation (File)
- Cancer Genetics (File)
- Questions for Week 3 (File)
- Questions & Answers for Week 3 (File)
Python for bioinformatics analysis of genetics and genomics data
Structure
This Python introduction will be split in two sessions and will be decomposed as follows:
- Python introduction (this week)
- One genetics practice exercise (next week)
It is meant as an introduction and a preparatory exercise for the four sessions at the end of the course (after the genomics part).
Course content
Supporting documents for the courses and the exercises are available on Moodle in the form of Jupyter notebooks (In .ipynb, .pdf and .html formats).
Software requirements
As described in the first lesson 01., in this course, we will use Python in Jupyter notebooks (a shorthand for Julia, Python and R).
To get and use Jupyter notebooks, we recommend Anaconda distribution, which is available for the most common operating systems. To install Anaconda, check out this link.
After installing, you can either open the Jupyter via the app, or execute the jupyter notebook command in the terminal to start a Jupyter server.
Then, you will need to install some packages for Python. Please check out lesson 03 to know how to proceed.
- 01.introduction_to_jupyter.ipynb (File)
- 01.introduction_to_jupyter.pdf (File)
- 01.introduction_to_jupyter.html (File)
- 02.a.extended_introduction_to_python.ipynb (File)
- 02.a.extended_introduction_to_python.html (File)
- 02.b.quick_python_overview.ipynb (File)
- 02.b.quick_python_overview.pdf (File)
- 02.b.quick_python_overview.html (File)
- 03.useful_python_packages_and_examples.ipynb (File)
- 03.useful_python_packages_and_examples.pdf (File)
- 03.useful_python_packages_and_examples.html (File)
- 04.python_hands_on_genetics.pdf (File)
- 04.python_hands_on_genetics.html (File)
- resources (Folder)
Python for bioinformatics analysis of genetics and genomics data
No class this week - Holiday week
- Slides Lecture 1: Intro to the Genome (File)
- Questions Lecture 1 (File)
- Answers to questions Lecture 1 (File)
- Reading material (Folder)
- Genomics video (URL)
- Illumina sequencing (URL)
- Answers Interactive Questions Lecture 1 (File)
- Slides Lecture 2: Genomic variation (File)
- Questions Lecture 2 genetic variation 2024 (File)
- Answers questions Lecture 2 genetic variation 2024 (File)
- Answers to interactive questions Lecture 2 (File)
- Reading material for part 2 (Folder)
- Slides Lecture 3: Gene regulatory networks (File)
- Questions Lecture 3: Gene regulatory networks (File)
- Lecture 3 Answers to Questions: Gene regulatory networks (File)
- Lecture 3 Answers to Interactive Questions (File)
- Reading Material for gene regulatory networks (TFs and networks) (Folder)
- Reading Material for gene regulatory networks (genomic elements) (Folder)
Lecture 4: Regulatory variation & Precision Medicine
- Slides Lecture 4 - Regulatory variation & Precision medicine (File)
- Questions Lecture 4_2024 (File)
- Answers Lecture 4_2024 (File)
- Lecture 4: Interactive questions (File)
- Reading Material Lecture 4 (Folder)
- Genomics exam 2021-2022 with answers (File)
Project 1 - Genetics
Structure
This project will span over 2 sessions and will be graded by groups of 2-3 students.
The deadline to submit Project 1 (one report per group) is Sunday December 7th - 23:59pm.
You will have to submit your code, the output figures, and your answers to the questions. You can for example submit your Jupyter notebook file and a PDF or an HTML generated from your Jupyter Notebook file, that would serve as a report.
Description
In this project, you will analyze genotyping data from 284 individuals, all of whom also have corresponding caffeine consumption information. Your task involves conducting a Genome-Wide Association Study (GWAS) analysis to identify the genetic variants that influence caffeine consumption.
Resources
You need to download the resources folder, where you will find three files:
- genotypes.txt
- annotations.txt
You will find in this week's materials a detailed description of the provided resources, the project, and the steps you need to follow.
Good luck!
- Resources (Folder)
- Genetics Project - Tasks (File)
- Genetics Project - Background & Report Instructions (File)
Project 1 - Genetics
Assignment: Genetics project provided last week.
Project 2 - Genomics
Structure
This project will span over 2 sessions and will be graded by groups of 2-3 students.
The deadline to submit Project 2 (one report per group) is Sunday December 22th at 23:59. Late submissions are subject to point reductions.
You will have to submit your code, the output figures, and your answers to the questions in a nicely organized PDF file. You can for example submit your Jupyter notebook file and a PDF or an HTML generated from your Jupyter Notebook file, that would serve as a report.
Description
In this exercise, we are working with a single-cell transcriptomics dataset containing 5’462 single cells from 2 different human cell types. Additionally, a subset of the cells were treated with a cytokine, to study its effect.
Your overall objective is to identify the two cell types present in the dataset and determine which cytokine was used to treat some of the cells.
Resources
We are giving you two files:
- single_cell_count_matrix.tsv, which contains the transcriptomics count matrix.
- metadata.tsv, which contains additional information on the cells.
Project 2 - Genomics
Assignment: Genomics project provided last week.