BIOS25328

Cancer Genetics and Genomics BIOS-25328

This page contains material for the BIOS25328 Cancer Genetics and Genomics course, starting from 2024. 2023 and prior material is here

Lecture 8: Introduction to QTL Analysis

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lecture
Find the lecture notes here
Apr 21, 2025
Haky Im

 

homework 4 - polygenic risk scores

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homework
In this section, you will complete the practical implementation of polygenic risk scoring using PRSice software as done in Lab 04. As a reminder, it involves:
Apr 18, 2025
Haky Im

 

Lecture 7 - Polygenic additive models and Polygenic Risk Scores

lecture
bios25328
Find lecture notes here
Apr 16, 2025
Haky Im

 

Lecture 6 - Mixed Effects Models and LDSC

lecture
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Lecture 6 - Methods for correcting population structure in genetic association studies
Apr 14, 2025
Haky Im

 

homework 3 - population structure and GWAS

bios25328
homework
Calculate PCs using plink (10pt)
Apr 11, 2025
Haky Im

 

lecture 5 - population structure and principal component analysis

lecture
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Find the lecture slides here.
Apr 7, 2025
Haky Im

 

homework 2 - multiple testing

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homework
This assignment focuses on simulating multiple testing scenarios, understanding p-value distributions, and applying correction methods.
Apr 7, 2025
Haky Im

 

lecture 4 - statistical significance in gwas - addressing multiple testing

lecture
bios25328
Lecture 4
Mar 31, 2025
Haky Im

lecture 4 - multiple testing correction - with code

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notebook
Lecture 4
Mar 31, 2025
Haky Im

 

homework 1 - bash scripting

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homework
Homeworks problems for week 1
Mar 31, 2025
Haky Im

 

lecture 3

lecture
bios25328
Lecture 3
Mar 31, 2025
Haky Im

 

lecture 2

lecture
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Lecture 2: Cancer GWAS
Mar 26, 2025
Haky Im

 

homework 5

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homework
© HakyImLab and Listed Authors - CC BY 4.0 License
Apr 19, 2024
Haky Im

 

lab 4

lab
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In this lab we are going to use the PRSice software to take height GWAS results and predict height of the Personal Genome Project individuals using their genotype data.
Apr 12, 2024
Liz Gibbons

 

homework 4

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homework
© HakyImLab and Listed Authors - CC BY 4.0 License
Apr 12, 2024
Haky Im

lecture 8

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lecture
Lecture 8 notes link
Apr 10, 2024
Haky Im

 

lecture 7

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lecture
Lecture 7 notes link
Apr 8, 2024
Haky Im

 

lab 3

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lab
In this lab, you will run all the steps of a GWAS analysis using the Marees et al tutorial.
Apr 5, 2024

 

homework 3

bios25328
homework
Calculate PCs using plink (10pt)
Apr 5, 2024
Haky Im

 

lecture 6

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lecture
Lecture 6 notes link
Apr 3, 2024
Haky Im

 

lecture 5

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lecture
Lecture 5 slides link
Apr 1, 2024
Haky Im

 

lab 2

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lab
get started with simulations for homework 2
Mar 29, 2024

 

lecture 3

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lecture
Lecture 3 notes link
Mar 25, 2024
Haky Im

 

homework 2

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homework
Hint: use the code from the lecture slides or here
Mar 25, 2024
Haky Im

 

lecture 2

Dissection of Genetics & Prediction of Cancer Risk: Methods & Tools
Mar 20, 2024
Haky Im

 

lab 1 - command line and R

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lab
We will learn to use the command line by doing. Follow the instructions below.
Mar 18, 2024
Haky Im

 

homework 1

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homework
Homeworks problems for week 1
Mar 18, 2024
Haky Im
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© HakyImLab and Listed Authors - CC BY 4.0 License