Cancer Genomics (BIOS 25328)
Unprecedented technological progress over the last decade, especially high throughput sequencing technologies, has transformed the basic and translational research of cancer as well as other diseases. In this course, we will introduce the current state of the field, discuss how germline and somatic factors drive cancer initiation and progression, and demonstrate how to use omics data to advance our understanding of cancer. We will review recent literature in cancer genetics and genomics, learn about the standing questions in the field, and practice the analytical techniques to address these questions. Computational exercises will be an integral part of the course and provide you with a hand-on experience of state-of-the-art techniques.
Find more information in the 2024 class syllabus here
Lecture 9 - Mendelian Randomization
2022-04-25
Haky Im
𝕙ttps://docs.google.com/presentation/d/16aMKkcAX1QifQabgBSBR_xr8LuoLwnsj9eEBFXi6EYk/edit?usp=sharing
[…] See slides
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PRSice and the Personal Genome Project
2022-04-21
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.
Goals
[…] library(tidyverse) ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ## ✓ …
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Lecture 8 - Functional Genomics to Inform GWAS
2022-04-20
Haky Im
𝕙ttps://docs.google.com/presentation/d/1fXQYo1sXa_FkiisLrd5CjusMkL_42XTG/edit?usp=sharing&ouid=100565019341850449624&rtpof=true&sd=true
[…] See slides
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GWAS catalog analysis 2022
2022-04-20
Haky Im
𝕤uppressMessages(library(tidyverse)) suppressMessages(library(glue)) PRE = "/Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data" ## COPY THE DATA AND SLUG FROM THE HEADER DATA = glue("{PRE}/2022-04-20-gwas-catalog-analysis-2022") …
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Lecture 7 - Predicting Complex Diseases - PRS
2022-04-18
Haky Im
𝕙ttps://docs.google.com/presentation/d/11oe2nZIFqs9TOXT_QDqdpsFhZYJeVVLm/edit?usp=sharing&ouid=100565019341850449624&rtpof=true&sd=true
[…] See slides
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Homework 3
2022-04-15
Haky Im
𝔸ssignment
[…] See below for additional information on the assignment.
Links
[…] Lecture 5 https://docs.google.com/presentation/d/1VYfx0coU5HKQLXwbo5yr7XvgJeqt8Hdf/edit#slide=id.p1
[…] Lecture 6 …
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Calculate Z-score, P-value, Chi2 stat from GWAS
2022-04-13
Haky Im
\[Y = \beta \cdot X + \epsilon\] GWAS summary statistics will contain an estimate of the regression coefficient \(\hat\beta\) and its standard error \(\text{se}(\hat\beta)\) for each SNP in the GWAS.
We distinguish the true \(\beta\) from the estimated value \(\hat\beta\) using a hat.
[…] \[ …
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Lecture 6 - mixed effects - LDSC
2022-04-13
Haky Im
𝕙ttps://docs.google.com/presentation/d/1I0-4u_6PAG5Q9LNi3mfQNnvZsVgf16tO/edit?usp=sharing&ouid=100565019341850449624&rtpof=true&sd=true
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Lab_2_Plink_and_QC
2022-04-13
Margaret Perry
𝕋his Lab will cover the quality batch portion of the QC and will be using the 1_Main_scripts_QC_GWAS.txt from Marees et al A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis.
[…] We will follow the tutorial published here by Marees et al A …
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Lecture 5 - Population Structure - PCA
2022-04-11
Haky Im
𝕙ttps://docs.google.com/presentation/d/1VYfx0coU5HKQLXwbo5yr7XvgJeqt8Hdf/edit?usp=sharing&ouid=100565019341850449624&rtpof=true&sd=true
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