Biostatistics 666: Main Page

Objective

Gene mapping studies study the relationship between genetic variation and susceptibility to human disease. These studies can be used to elucidate the biochemical basis of medically interesting traits leading to knowledge that will, ultimately, help us improve treatment and management of human disease. Biostatistics 666 is a Masters level course that introduces many of the concepts, statistical models and numerical methods useful for studies.

For additional information, see also Core Competencies in Biostatistics Program covered by this course.

Target Audience

Students in Biostatistics 666 should be comfortable with simple algebra and, ideally, have previous exposure to maximum likelihood. Previous knowledge of Genetics is helpful, but not required. Most students registering for the course are Master or Doctoral students in Human Genetics, Bioinformatics, Statistics or Biostatistics.

Scheduling

Final grades will take into account performance in written in-class assessments, take home problem sets, as well as participation in class and any class projects.

Class Notes

Biostatistics 666: Contemporary Human Genetics - PDF

Biostatistics 666: Hardy-Weinberg Equilibrium - PDF

Biostatistics 666: Linkage Disequilibrium - PDF

Biostatistics 666: Introduction to the Coalescent - PDF

Biostatistics 666: Modeling Variation in the Coalescent - PDF

Biostatistics 666: Modeling Recombination and Migration in the Coalescent - PDF

Biostatistics 666: Maximum Likelihood Allele Frequency Estimation - PDF

Biostatistics 666: Introduction to the E-M Algorithm - PDF

Biostatistics 666: Haplotype Estimation - PDF

Biostatistics 666: Advanced Haplotype Estimation - PDF

Biostatistics 666: Power of Genomewide Association Studies - PDF

Biostatistics 666: Kinship Coefficients and Relatedness - PDF

Lectures below have not yet been updated for 2017.

Biostatistics 666: Haplotype Association Tests - PDF

Biostatistics 666: Association Tests in Structured Populations - PDF

Biostatistics 666: Linkage Analysis in Sibling Pairs - PDF

Biostatistics 666: Multipoint Analysis in Sibling Pairs - PDF

Biostatistics 666: Relationship Checking - PDF

Biostatistics 666: Genotype Imputation - PDF

Biostatistics 666: Whole Genome Sequencing - PDF

Biostatistics 666: Analysis of Low Pass Sequence Data - PDF

Biostatistics 666: Analysis of Copy Number Using Sequence Data - PDF

Biostatistics 666: Introduction to De Novo Assembly - PDF

Biostatistics 666: Rare Variant Burden Tests - PDF

Biostatistics 666: Variance Component Analyses - PDF

Biostatistics 666: Likelihood Calculations for Large Pedigrees - PDF

Older Lectures

These lectures were used in previous years, but have been replaced in the most recent edition of the course.

Biostatistics 666: Introductory Lecture - PDF

Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium - PDF

Biostatistics 666: Advanced Coalescent, Changing Population Size - PDF

Biostatistics 666: Advanced Coalescent, Computation with the Coalescent - PDF

Biostatistics 666: Copy Number Variation - PDF

Biostatistics 666: Linkage Tests for Pairs of Individuals - PDF

Biostatistics 666: The Possible Triangle Constraint - PDF

Biostatistics 666: The Lander-Green Algorithm - PDF

Biostatistics 666: Applications of the Lander-Green Algorithm - PDF

Problem Sets

Problem Set 1 -- Solution

Problem Set 2 -- Solution

Problem Set 3 -- Solution

Problem Set 4

Sample Mid-Term

Sample Mid-Term

Office Hours

For the 2017 Fall Term, office hours are tentatively schedule for Friday afternoons at 3pm. I will provide free coffee to anyone who turns up.

Standards of Academic Conduct

The following is an extract from the School of Public Health's Student Code of Conduct [1]:

Student academic misconduct includes behavior involving plagiarism, cheating, fabrication, falsification of records or official documents, intentional misuse of equipment or materials, and aiding and abetting the perpetration of such acts. The preparation of reports, papers, and examinations, assigned on an individual basis, must represent each student’s own effort. Reference sources should be indicated clearly. The use of assistance from other students or aids of any kind during a written examination, except when the use of books or notes has been approved by an instructor, is a violation of the standard of academic conduct.

In the context of this course, any work you hand-in should be your own and any material that is a transcript (or interpreted transcript) of work by others must be clearly labeled as such.

Course History

This course was started by Ken Lange and Mike Boehnke and is typically taught every year.

Goncalo Abecasis taught it in the following academic years:

• 2001/2002 (jointly with Jeff Long, who is now at the University of New Mexico)
• 2002/2003
• 2003/2004
• 2004/2005
• 2005/2006
• 2006/2007
• 2009/2010
• 2010/2011
• 2011/2012
• 2012/2013
• 2017/2018

He last taught it in the 2017/2018 academic year. For previous course notes, see [Goncalo's older class notes].