Genetics and genomics
BIO-373
Media
Media
Course syllabus:
- Genetics (Jacques Fellay): 3 sessions
- Sept 9th: Introduction to genetics. Mendelian genetics. Extension of Mendelian genetics.
- Sept 23rd: X-linked heredity. Extranuclear inheritance. Population genetics.
- Oct 7th: Chromosomes variation. Mutation and DNA repair. Cancer genetics.
- Genomics (Bart Deplancke): 4 sessions
- Oct 14th: Introduction to genomics. Sequencing technologies. Comparative genomics.
- Oct 28th: Genomic variations. Complex traits. GWAS.
- Nov 11th: Gene Regulatory networks. Regulatory elements. Transcription factors.
- Nov 18th: Genomic diseases and therapeutics. Precision medicine.
- Bioinformatics analysis of genetics and genomics data (Vincent Gardeux): 6 sessions
- Sept 30th: Introduction to Python for bioinformatics.
- Nov 4th: Data analysis applied to genetics & genomics.
- Nov 25th + Dec 2nd: Group project in genetics
- Dec 9th + 16th: Group project in genomics
- Written exam
- Jan 20th 2025: from 09h15 to 12h15 (BCH2201)
Monday September 9th
- Intro to genetics (File)
- Mendelian genetics (File)
- Extension of Mendelian genetics (File)
- Interactive question - week 1 (File)
- Questions week 1 (File)
- Questions week 1 with answers (File)
Monday September 23rd
Genetics - part II
- X-linked heredity (File)
- Extranuclear inheritance (File)
- Population genetics (File)
- Questions week 2 (File)
- Questions week 2 with answers (File)
- Interactive questions week 2 (File)
Monday September 30th
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 (September 30th)
- One genetics practice exercise (November 4th)
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)
- 03.useful_python_packages_and_examples_with_solutions.ipynb (File)
- 03.useful_python_packages_and_examples_with_solutions.pdf (File)
- 04.python_hands_on_genetics.pdf (File)
- 04.python_hands_on_genetics.html (File)
- resources (Folder)
Monday October 7th
Genetics - part III
- Chromosomal variation (File)
- Mutations and DNA repair (File)
- Cancer genetics (File)
- Week3_questions (File)
- Week3_questions_with_answers (File)
- Interactive questions week 3 (File)
Start Genomics - Monday October 14th
- 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)
Monday, October 21st
No class this week
Monday October 28th
- Slides for Human genetic variation and its contribution to complex traits 2024 (lecture 2) (File)
- Questions Lecture 2 genetic variation 2024 (File)
- Answers questions Lecture 2 genetic variation 2024 (File)
- Interactive questions Lecture 2 (File)
- Reading material for part 2 (Folder)
Monday, November 4th
Python for bioinformatics analysis of genetics and genomics data
Assignment: Genetics exercise provided on September, 30th
Monday November 11th
- Gene regulatory networks Lecture 3 2024 (File)
- Lecture 3 Questions: Gene regulatory networks (File)
- Lecture 3 Answers to Questions: Gene regulatory networks (File)
- Reading Material for gene regulatory networks (TFs and networks) (Folder)
- Reading Material for gene regulatory networks (genomic elements) (Folder)
Monday November 18th
Lecture 4: Regulatory variation & Precision Medicine
- Slides Lecture 4: Regulatory variation & Precision Medicine (File)
- Questions Lecture 4_2024 (File)
- Answers Lecture 4_2024 (File)
- Reading Material Lecture 4 (Folder)
Monday November 25th - December 2nd
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 December 9th - 00:00am.
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!
Monday December 9th - 16th
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 51 cells, from 3 different mice cell types.
The goal is to find out what cell type, or tissue, these 3 groups of cells belong to. Do they belong to the heart, brown fat, or the brain cortex?
Resources
We are giving you two files:
- single_cell_count_matrix.txt, which contains the transcriptomics count matrix
- gene_name.txt, which contains the annotation of the genes used in the transcriptomics dataset