Difference between revisions of "Biostatistics 666: Main Page"
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== Objective == | == Objective == | ||
| − | Gene mapping studies | + | 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. |
| − | Biostatistics 666 | + | For additional information, see also [[Biostatistics 666: Core Competencies|Core Competencies in Biostatistics Program covered by this course]]. |
== Target Audience == | == Target Audience == | ||
| − | Students in Biostatistics 666 should be | + | 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 == | == 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]] - [[Media:666.2017.01 - Introductory Lecture.pdf|PDF]] | |
| − | + | [[Biostatistics 666: Hardy-Weinberg Equilibrium]] - [[Media:666.2017.02 - Hardy Weinberg Equilibrium.pdf|PDF]] | |
| − | |||
| − | + | [[Biostatistics 666: Linkage Disequilibrium]] - [[Media:666.2017.03 - Linkage Disequilibrium.pdf|PDF]] | |
| − | |||
| − | + | [[Biostatistics 666: Introduction to the Coalescent]] - [[Media:666.04 - The Coalescent.pdf|PDF]] | |
| − | + | Lectures below have not yet been updated for 2017. | |
| − | |||
| − | |||
| − | |||
| − | |||
[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.05.pdf|PDF]] | [[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.05.pdf|PDF]] | ||
| Line 52: | Line 46: | ||
[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]] | [[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]] | ||
| − | |||
| − | |||
[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]] | [[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]] | ||
| Line 60: | Line 52: | ||
[[Biostatistics 666: Analysis of Low Pass Sequence Data]] - [[Media:666.2010.05.pdf|PDF]] | [[Biostatistics 666: Analysis of Low Pass Sequence Data]] - [[Media:666.2010.05.pdf|PDF]] | ||
| + | |||
| + | [[Biostatistics 666: Analysis of Copy Number Using Sequence Data]] - [[Media:666.2011.02.pdf|PDF]] | ||
| + | |||
| + | [[Biostatistics 666: Introduction to De Novo Assembly]] - [[Media:666.2012.01.pdf|PDF]] | ||
| + | |||
| + | [[Biostatistics 666: Rare Variant Burden Tests]] - [[Media:666.2011.01.pdf|PDF]] | ||
| + | |||
| + | [[Biostatistics 666: Variance Component Analyses]] - [[Media:666.20.pdf|PDF]] | ||
| + | |||
| + | [[Biostatistics 666: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|PDF]] | ||
== Older Lectures == | == Older Lectures == | ||
| Line 67: | Line 69: | ||
[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]] | [[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]] | ||
| − | [[Biostatistics 666: Hardy | + | [[Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium]] - [[Media:2011.666.01.pdf|PDF]] |
[[Biostatistics 666: Advanced Coalescent, Changing Population Size]] - [[Media:666.07.pdf|PDF]] | [[Biostatistics 666: Advanced Coalescent, Changing Population Size]] - [[Media:666.07.pdf|PDF]] | ||
| Line 83: | Line 85: | ||
[[Biostatistics 666: Applications of the Lander-Green Algorithm]] - [[Media:666.19.pdf|PDF]] | [[Biostatistics 666: Applications of the Lander-Green Algorithm]] - [[Media:666.19.pdf|PDF]] | ||
| − | == | + | == Problem Sets == |
| − | + | [[Media:666.Worksheet 1.pdf|Problem Set 1]] | |
| − | == | + | == 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 == | == Standards of Academic Conduct == | ||
| Line 101: | Line 99: | ||
''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.'' | ''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. | + | 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 == | == Course History == | ||
| − | This course is typically taught every year. | + | 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: | Goncalo Abecasis taught it in the following academic years: | ||
| − | * 2001/2002 (jointly with Jeff Long) | + | * 2001/2002 (jointly with [http://www.unm.edu/~anthro/people_faculty_jeff_long.html Jeff Long], who is now at the University of New Mexico) |
* 2002/2003 | * 2002/2003 | ||
* 2003/2004 | * 2003/2004 | ||
| Line 118: | Line 116: | ||
* 2010/2011 | * 2010/2011 | ||
* 2011/2012 | * 2011/2012 | ||
| + | * 2012/2013 | ||
| − | He | + | He last taught it in the 2012/2013 academic year. For previous course notes, see [[http://www.sph.umich.edu/csg/abecasis/class Goncalo's older class notes]]. |
Revision as of 05:54, 18 September 2017
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
Lectures below have not yet been updated for 2017.
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: Haplotype Association Tests - PDF
Biostatistics 666: Association Tests in Structured Populations - PDF
Biostatistics 666: Power of Genomewide Association Studies - 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
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
He last taught it in the 2012/2013 academic year. For previous course notes, see [Goncalo's older class notes].
