Personal Genomics for Bioinformaticians - Winter 2017

[course syllabus]


Course description

Genome-sequencing is quickly becoming a commodity, and more than a million people have already analyzed their own genomes through direct-to-consumer companies. This course provides an introduction to current bioinformatics techniques for analyzing and interpreting human genomes. We will learn how to interpret a single genome in the context of an entire population, based on the often quoted concept: interpreting one genome requires tens of thousands of genomes. Topics covered include an introduction to human medical and population genetics, human ancestry, finding and interpreting disease-causing variants, genome-wide association studies, genetic risk prediction, analyzing next generation sequencing data, and how to scale current genomics techniques to analyze hundreds of thousands of genomes. We will also discuss the social impact of the personal genomics revolution.


Module Date Lecture Homework
Introduction to personal genomics 01-10 (Th) Introduction to your genome ps1 out
What can I do with my genome? 01-12 (Th) Basic population genetics ps1 due, ps2 out
01-17 (T) Determining ancestry
01-19 (Th) Phasing and imputation
01-24 (T) Genetic Genealogy, Web 2.0 Genomics
01-26 (Th) Social impact of personal genomics (Guest lecture) ps2 due
Complex traits 01-31 (T) Introduction to GWAS ps3 out
02-02 (Th) Risk prediction
02-07 (T) Missing heritability project out
02-09 (Th) Scaling GWAS to millions of genomes ps3 due
Next-gen sequencing and big data 02-14 (T) Introduction to NGS ps4 out
02-16 (Th) Short read alignment and variant calling proposal due
02-21 (T) Long read sequencing technologies
02-23 (Th) Functional genomics - ChIPseq (Guest lecture)
02-28 (T) Storing, querying, visualization ps4 due
Mutation hunting 03-02 (Th) Introduction to genetic mapping ps5 out
03-07 (T) Filtering and prioritizing variants
03-09 (Th) De novo mutations and constraint ps5 due
03-14 (T) Interpreting non-coding variants
Final project 03-16 (Th) Project presentations project due

Resources for problem sets

Class material

Lecture 1: Introduction to your genome

Lecture 2: Basic population genetics

Lecture 3: Determining ancestry

Lecture 4: Phasing and Imputation

Lecture 5: Mitochondria and Y chromosome analysis, Web 2.0 Genomics

Lecture 6: Social impact of personal genomics

Lecture 7: Introduction to GWAS

Lecture 8: Risk prediction

Lecture 9: Missing heritability

Lecture 10: Scaling GWAS to millions of samples

Lecture 11: Intro to NGS

Lecture 12: Short read alignment and variant calling

Lecture 13: Long read sequencing technologies

Lecture 14: Functional genomics - ChIP sequencing (Guest lecture Alon Goren)

Lecture 15: Storing, querying, visualization (+RNAseq)

Lecture 16: Intro to mutation hunting

Lecture 17: Filtering and prioritization

Lecture 18: De novo mutations and constraint

Lecture 19: Interpreting non-coding variants

Lecture 20: Final Project Presentations