6.881 Computational Personal Genomics: making sense of complete genomes
Spring 2016
Professor: Manolis Kellis
TA: Yaping Liu
Lecture: M 4-6 P.M. (32-124)
Information:
With the growing availability and lowering costs of genotyping and personal genome sequencing, the focus has shifted from the ability to obtain the sequence to the ability to make sense of the resulting information. This course is aimed at exploring the computational challenges associated with interpreting how sequence differences between individuals lead to phenotypic differences such as gene expression, disease predisposition, or response to treatment. It will cover the computational challenges associated with personal genomics, such as genotype phasing and haplotype reconstruction, exploiting linkage for variant imputation, ancestry painting for admixed genomes, predicting likely causal variants using functional or comparative genomics annotations of coding and non-coding elements, relating regulatory variation to gene expression or chromatin state changes, measuring recent evolution and human selection, using systems biology and network information for understanding weak contributions, and the challenge of deciphering complex multi-genic traits such as height, Alzheimer’s, diabetes, or cancer. Students will read and discuss seminal papers in the area, download and use existing tools, write their own software to interpret existing human genomes, and discuss limitations, challenges, and ethical, legal and social implications.
Announcements
Final project presentation schedule
Dear all,Please fill your final project presentation schedule information here before May 9:
https://docs.google.com/spreadsheets/d/1ESnd5H2Ii173zeK7Zvny2dLWrJRDuqaLroGbgEYWKzk/edit#gid=0
Thanks
Announced on 02 May 2016 6:07 p.m. by Yaping Liu
Lecture 9 - Ancestry
Dear all, Lecture 9 comments are now posted.Thanks for the many comments and discussion. You can find them under "Materials -> Student Comments"
Announced on 10 April 2016 10:22 p.m. by Yaping Liu
Lab 7 assignment extension
Dear All,1) Sorry about some problems in Lab 7 - QTL, Yongjin, Karthik and I re-edit the lab7.pdf and make the statement more clear now. For those of you who have not submitted Lab 7 assignment yet, please download the newest files from Homework in stella and submit it before next Monday 4pm (4/11)
2) For the option between final project and lab assignments, if you choose final project, you could skip up to 4 lab assignments: If you submitted all lab assignment before, you could skip rest of all lab assignments. If you have already skipped some lab assignments, please continue to submit them in the next few lectures.
Announced on 05 April 2016 11:47 a.m. by Yaping Liu
Options between final project and rest of lab assignment
Dear all,1). During today's lecture, Manolis mentioned that you could make the choice between final project and rest of lab assignment. If you choose lab assignment, please continue to submit them before each due date.
2). Some students mentioned that there is some problem to install PEER package for Lab 7 QTL. And also, there is some problem if you run the code directly without any modification from Nature protocol paper. I apologize that I have not test them completely before giving the assignment. Here is some tips for the package installation which i tried successfully:
##I test the installation of PEER on linux (Red Hat Enterprise
Linux Server release 6.7 in broad institute server)
## although the protocol claim that it could be run on Mac OS. I
could not install it on my Mac OSX (10.9.5), apologize about
it.
##installation:
##follow the pre-requisition here:
##https://github.com/PMBio/peer/wiki/Installation-instructions
##it is too difficult to build from scratch, so i just choose to
install package in R
## wget -c
https://github.com/downloads/PMBio/peer/R_peer_source_1.3.tgz
##i could not install it by " R CMD INSTALL
R_peer_source_1.3.tgz " at server in broad institute
## try it this way (also thanks tips from Beryl Cummings): open
R
setwd("/your/download/directory/")
install.packages("R_peer_source_1.3.tgz",repos=NULL,type="source")
##please allow it to install on your own personal R library if you do it at broad server or other public server without root permission.
Announced on 04 April 2016 10:06 p.m. by Yaping Liu
Lecture 8 - Heritability
Dear all, Lecture 8 comments are now posted.Thanks for the many comments and discussion. You can find them under "Materials -> Student Comments"
Announced on 03 April 2016 11:04 p.m. by Yaping Liu
