Genome Analysis Wiki - User contributions [en]

File:666.Worksheet 5.Solution.pdf

2017-12-11T05:31:33Z

Goncalo: Goncalo uploaded a new version of File:666.Worksheet 5.Solution.pdf

Biostatistics 666: Main Page

2017-12-10T14:16:34Z

Goncalo: /* Problem Sets */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|PDF]]

Biostatistics 666: Kinship Coefficients and Relatedness - [[Media:666.2017.12_-_Kinship_Coefficients.pdf|PDF]]

[[Biostatistics 666: Variance Component Analyses]] - [[Media:666.2017.13_-_Variance_Component_Models.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2017.14_-_Affected_Sibling_Pairs.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2017.15_-_Genotype_Imputation.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2017.16_-_Introduction_to_Sequencing.pdf|PDF]]

[[Biostatistics 666: Functional Genomics (Guest lecture)]] - [[Media:Biostat666FunctionalGenomics_v4(2017).pdf|PDF]]

[[Biostatistics 666: Introduction to De Novo Assembly]] - [[Media:666.2012.01_-_De_Novo_Assembly.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.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: Rare Variant Burden Tests]] - [[Media:666.2011.01.pdf|PDF]]

[[Biostatistics 666: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|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]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]] -- [[Media:666.Worksheet_4.Solution.pdf|Solution]]

[[Media:666.Worksheet_5.pdf|Problem Set 5]] -- [[Media:666.Worksheet_5.Solution.pdf|Solution]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|Sample Mid-Term]]

[[Media:666.SampleMidterm02.pdf|2nd 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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.Worksheet 5.Solution.pdf

2017-12-10T14:15:46Z

Goncalo:

File:666.Worksheet 4.Solution.pdf

2017-12-10T14:15:23Z

Goncalo:

Biostatistics 666: Main Page

2017-12-04T07:57:33Z

Goncalo: /* Sample Mid-Term */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|PDF]]

Biostatistics 666: Kinship Coefficients and Relatedness - [[Media:666.2017.12_-_Kinship_Coefficients.pdf|PDF]]

[[Biostatistics 666: Variance Component Analyses]] - [[Media:666.2017.13_-_Variance_Component_Models.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2017.14_-_Affected_Sibling_Pairs.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2017.15_-_Genotype_Imputation.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2017.16_-_Introduction_to_Sequencing.pdf|PDF]]

[[Biostatistics 666: Functional Genomics (Guest lecture)]] - [[Media:Biostat666FunctionalGenomics_v4(2017).pdf|PDF]]

[[Biostatistics 666: Introduction to De Novo Assembly]] - [[Media:666.2012.01_-_De_Novo_Assembly.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.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: Rare Variant Burden Tests]] - [[Media:666.2011.01.pdf|PDF]]

[[Biostatistics 666: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|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]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

[[Media:666.Worksheet_5.pdf|Problem Set 5]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|Sample Mid-Term]]

[[Media:666.SampleMidterm02.pdf|2nd 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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.SampleMidterm02.pdf

2017-12-04T07:56:48Z

Goncalo:

Biostatistics 666: Introduction to De Novo Assembly

2017-12-04T07:38:01Z

Goncalo: /* Slides */

== Overview ==

Introduces the issues surrounding de novo assembly of complex genomes, with a particular focus on issues related to variant discovery. Also provides a brief overview of the results of Lander and Waterman on contig length.

== Slides ==

[[Media:666.2012.01_-_De_Novo_Assembly.pdf|Slides in PDF Format]]

== Recommended Reading ==

Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature Genetics'' '''44''':226-232

Lander E and Waterman M (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. ''Genomics'' '''2''':231-239

Biostatistics 666: Whole Genome Sequencing

2017-12-04T07:37:36Z

Goncalo: /* Lecture Notes */

== Objective ==

Introduce the statistical and computational challenges of contemporary whole genome sequencing.

== Lecture Notes ==

[[Media:666.2017.16_-_Introduction_to_Sequencing.pdf|Slides in PDF Format]]

== Recommended Reading ==

The 1000 Genomes Project (2010) A map of human genome variation from population-scale sequencing. ''Nature'' '''467''':1061-73

Biostatistics 666: Main Page

2017-12-04T07:37:23Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|PDF]]

Biostatistics 666: Kinship Coefficients and Relatedness - [[Media:666.2017.12_-_Kinship_Coefficients.pdf|PDF]]

[[Biostatistics 666: Variance Component Analyses]] - [[Media:666.2017.13_-_Variance_Component_Models.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2017.14_-_Affected_Sibling_Pairs.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2017.15_-_Genotype_Imputation.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2017.16_-_Introduction_to_Sequencing.pdf|PDF]]

[[Biostatistics 666: Functional Genomics (Guest lecture)]] - [[Media:Biostat666FunctionalGenomics_v4(2017).pdf|PDF]]

[[Biostatistics 666: Introduction to De Novo Assembly]] - [[Media:666.2012.01_-_De_Novo_Assembly.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.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: Rare Variant Burden Tests]] - [[Media:666.2011.01.pdf|PDF]]

[[Biostatistics 666: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|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]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

[[Media:666.Worksheet_5.pdf|Problem Set 5]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.2012.01 - De Novo Assembly.pdf

2017-12-04T07:35:49Z

Goncalo:

File:666.2017.16 - Introduction to Sequencing.pdf

2017-12-04T07:34:07Z

Goncalo:

Biostatistics 666: Whole Genome Sequencing

2017-11-27T13:28:54Z

Goncalo: /* Lecture Notes */

== Objective ==

Introduce the statistical and computational challenges of contemporary whole genome sequencing.

== Lecture Notes ==

[[Media:666.2017.16_-_Introduction_to_Sequencing.pptx|Slides in PDF Format]]

== Recommended Reading ==

The 1000 Genomes Project (2010) A map of human genome variation from population-scale sequencing. ''Nature'' '''467''':1061-73

Biostatistics 666: Main Page

2017-11-27T13:28:35Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|PDF]]

Biostatistics 666: Kinship Coefficients and Relatedness - [[Media:666.2017.12_-_Kinship_Coefficients.pdf|PDF]]

[[Biostatistics 666: Variance Component Analyses]] - [[Media:666.2017.13_-_Variance_Component_Models.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2017.14_-_Affected_Sibling_Pairs.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2017.15_-_Genotype_Imputation.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2017.16_-_Introduction_to_Sequencing.pptx|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.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: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|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]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

[[Media:666.Worksheet_5.pdf|Problem Set 5]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.2017.16 - Introduction to Sequencing.pptx

2017-11-27T13:27:32Z

Goncalo:

Biostatistics 666: Main Page

2017-11-20T13:11:45Z

Goncalo: /* Problem Sets */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|PDF]]

Biostatistics 666: Kinship Coefficients and Relatedness - [[Media:666.2017.12_-_Kinship_Coefficients.pdf|PDF]]

[[Biostatistics 666: Variance Component Analyses]] - [[Media:666.2017.13_-_Variance_Component_Models.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2017.14_-_Affected_Sibling_Pairs.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2017.15_-_Genotype_Imputation.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|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]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

[[Media:666.Worksheet_5.pdf|Problem Set 5]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

Biostatistics 666: Genotype Imputation

2017-11-20T13:10:59Z

Goncalo: /* Slides */

== Overview ==

Genotype imputation is one of the most commonly used tools for the analysis of genomewide association studies. This lecture introduces the basic ideas behind genotype imputation, together with some examples of its practical applications.

== Slides ==

[[Media:666.2017.15_-_Genotype_Imputation.pdf|Slides in PDF Format]]

== Recommended Reading ==

* Chen and Abecasis (2007) Family based association tests for genome wide association scans. Am J Hum Genet 81:913-926

* Li et al (2010) Using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genetic Epidemiology 34:816-834

Biostatistics 666: Main Page

2017-11-20T13:10:42Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|PDF]]

Biostatistics 666: Kinship Coefficients and Relatedness - [[Media:666.2017.12_-_Kinship_Coefficients.pdf|PDF]]

[[Biostatistics 666: Variance Component Analyses]] - [[Media:666.2017.13_-_Variance_Component_Models.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2017.14_-_Affected_Sibling_Pairs.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2017.15_-_Genotype_Imputation.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|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]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.2017.15 - Genotype Imputation.pdf

2017-11-20T13:09:28Z

Goncalo:

File:666.Worksheet 5.pdf

2017-11-20T13:08:43Z

Goncalo:

Biostatistics 666: Linkage Analysis in Sibling Pairs

2017-11-15T13:30:49Z

Goncalo: /* Slides */

== Outline ==

This lecture introduces Neil Risch's Maximum Lod Score (MLS) test for linkage and its refinement using Peter Holman's possible triangle constraint.

== Slides ==

[[Media:666.2017.14_-_Affected_Sibling_Pairs.pdf|Slides in PDF Format]]

== Recommended Reading ==

Risch (1990) Linkage Strategies for Genetically Complex Traits. III. The Effect of Marker Polymorphism on Analysis of Affected Relative Pairs. ''Am J Hum Genet'' '''46''':242-253

Risch (1990) Linkage strategies for genetically complex traits. I. Multi-locus models. ''Am J Hum Genet'' '''46''':222-228

Holmans (1993) Asymptotic Properties of Affected-Sib-Pair Linkage Analysis. ''Am J Hum Genet'' '''52''':362-374

Biostatistics 666: Main Page

2017-11-15T13:30:31Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|PDF]]

Biostatistics 666: Kinship Coefficients and Relatedness - [[Media:666.2017.12_-_Kinship_Coefficients.pdf|PDF]]

[[Biostatistics 666: Variance Component Analyses]] - [[Media:666.2017.13_-_Variance_Component_Models.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2017.14_-_Affected_Sibling_Pairs.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|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]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.2017.14 - Affected Sibling Pairs.pdf

2017-11-15T13:29:17Z

Goncalo:

Biostatistics 666: Variance Component Analyses

2017-11-13T13:38:01Z

Goncalo: /* Lecture Notes */

== Objective ==

Introduce the principles of variance component analysis. Introduce kinship coefficients.

== Lecture Notes ==

[[Media:666.2017.13_-_Variance_Component_Models.pdf|Slides in PDF Format]]

== References ==

Amos (1994) ''Am J Hum Genet'' '''54''':535-543

Hopper and Matthews (1982) ''Ann Hum Genet'' '''46''':373–383

Lange and Boehnke (1983) ''Am J Med Genet'' '''14''':513-24

Biostatistics 666: Main Page

2017-11-13T13:37:38Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|PDF]]

Biostatistics 666: Kinship Coefficients and Relatedness - [[Media:666.2017.12_-_Kinship_Coefficients.pdf|PDF]]

[[Biostatistics 666: Variance Component Analyses]] - [[Media:666.2017.13_-_Variance_Component_Models.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|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]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.2017.13 - Variance Component Models.pdf

2017-11-13T13:36:42Z

Goncalo:

File:666.2017.12 - Kinship Coefficients.pdf

2017-11-13T13:36:21Z

Goncalo: Goncalo uploaded a new version of File:666.2017.12 - Kinship Coefficients.pdf

Biostatistics 666: Main Page

2017-11-08T13:44:33Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|PDF]]

Biostatistics 666: Kinship Coefficients and Relatedness - [[Media:666.2017.12_-_Kinship_Coefficients.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.2017.12 - Kinship Coefficients.pdf

2017-11-08T13:43:39Z

Goncalo:

File:666.2010.01 - Power of Genomewide Studies.pdf

2017-11-01T12:59:59Z

Goncalo: Goncalo uploaded a new version of File:666.2010.01 - Power of Genomewide Studies.pdf

Biostatistics 666: Power of Genomewide Association Studies

2017-11-01T08:28:36Z

Goncalo: /* Lecture Notes */

== Objective ==

This lecture discusses power calculations in the context of genomewide association studies. It also introduces the concept of two stage designs and the tradeoffs between replication based and two stage analyses. The "Winner's Curse" makes a brief ''cameo'' appearance.

== Lecture Notes ==

[[666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|Slides in PDF Format]]

== Recommended Reading ==

Skol el al (2006) Joint analysis is more efficient than replication based analysis for two-stage genomewide association studies. ''Nature Genetics'' '''38''':209-13

Biostatistics 666: Main Page

2017-11-01T08:28:08Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01_-_Power_of_Genomewide_Studies.pdf ‎|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

Biostatistics 666: Main Page

2017-11-01T08:27:14Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.2010.01 - Power of Genomewide Studies.pdf

2017-11-01T08:26:30Z

Goncalo:

Biostatistics 666: Advanced Haplotype Estimation

2017-10-23T12:16:13Z

Goncalo: /* Slides */

== Objective ==

This lecture introduces modern methods for haplotype estimation, which based on an idea introduced by Na Li and Matthew Stephens in 2003. This approach models each haplotype in the sample as an imperfect mosaic of other haplotypes. It typically favors solutions that involve longer mosaic pieces and where there are fewer mismatches between each haplotype and its template.

== Slides ==

[[Media:666.2017.10_-_Advanced_Haplotyping.pdf|Slides in PDF Format]]

== Recommended Reading ==

Li and Stephens (2003) ''Genetics'' '''65''':2213-33.

Li et al (2010) ''Genetic Epidemiology'' '''34''':816–34

Biostatistics 666: Advanced Haplotype Estimation

2017-10-23T12:15:35Z

Goncalo: Created page with "== Objective == This lecture introduces modern methods for haplotype estimation, which based on an idea introduced by Na Li and Matthew Stephens in 2003. This approach models..."

== Objective ==

This lecture introduces modern methods for haplotype estimation, which based on an idea introduced by Na Li and Matthew Stephens in 2003. This approach models each haplotype in the sample as an imperfect mosaic of other haplotypes. It typically favors solutions that involve longer mosaic pieces and where there are fewer mismatches between each haplotype and its template.

== Slides ==

[[Media:666.2017.10_-_Advanced_Haplotype_Estimation.pdf|Slides in PDF Format]]

== Recommended Reading ==

Li and Stephens (2003) ''Genetics'' '''65''':2213-33.

Li et al (2010) ''Genetic Epidemiology'' '''34''':816–34

File:666.Worksheet 4.pdf

2017-10-23T12:10:17Z

Goncalo:

Biostatistics 666: Main Page

2017-10-23T12:10:01Z

Goncalo: /* Problem Sets */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

[[Media:666.Worksheet_4.pdf|Problem Set 4]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

Biostatistics 666: Main Page

2017-10-23T12:04:35Z

Goncalo: /* Problem Sets */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]] -- [[Media:666.Worksheet_1.Solution.pdf|Solution]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]] -- [[Media:666.Worksheet_2.Solution.pdf|Solution]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]] -- [[Media:666.Worksheet_3.Solution.pdf|Solution]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.Worksheet 3.Solution.pdf

2017-10-23T12:03:30Z

Goncalo:

File:666.Worksheet 2.Solution.pdf

2017-10-23T12:03:05Z

Goncalo:

File:666.Worksheet 1.Solution.pdf

2017-10-23T12:02:39Z

Goncalo:

Biostatistics 666: Main Page

2017-10-11T12:50:48Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

[[Biostatistics 666: Advanced Haplotype Estimation]] - [[Media:666.2017.10_-_Advanced_Haplotyping.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.2017.10 - Advanced Haplotyping.pdf

2017-10-11T12:49:58Z

Goncalo:

Biostatistics 666: Haplotype Estimation

2017-10-09T12:37:27Z

Goncalo: /* Slides */

== Objective ==

This lecture introduces several strategies for estimating individual haplotypes and their frequencies. At heart, all population-based haplotyping algorithms look for haplotypes that are shared across multiple individuals. The simplest approach for haplotyping using this information is Clark's 1990 algorithm, which is intuitively simple but quite effective in a variety of settings. The E-M algorithm, which provides an important refinements at the cost of more computation, is also introduced. Further refined methods are also discussed.

== Slides ==

[[Media:666.2017.09_-_Haplotype_Estimation.pdf|Slides in PDF Format]]

== Recommended Reading ==

Clark (1990) ''Mol Biol Evol'' '''7''':111-122

Excoffier and Slatkin (1995) ''Mol Biol Evol'' '''12''':921-927

Biostatistics 666: Main Page

2017-10-09T12:37:16Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

Biostatistics 666: Main Page

2017-10-09T12:36:57Z

Goncalo: /* Class Notes */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[666.2017.09_-_Haplotype_Estimation.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

File:666.2017.09 - Haplotype Estimation.pdf

2017-10-09T12:36:20Z

Goncalo:

Biostatistics 666: Main Page

2017-10-06T19:53:08Z

Goncalo: /* Problem Sets */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.11.pdf|PDF]]

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]]

[[Media:666.Worksheet_3.pdf|Problem Set 3]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

Biostatistics 666: Main Page

2017-10-05T06:42:37Z

Goncalo: /* Course History */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.11.pdf|PDF]]

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].

Biostatistics 666: Main Page

2017-10-04T12:34:29Z

Goncalo: /* Sample MidTerm */

== 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 [[Biostatistics 666: Core Competencies|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]] - [[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]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.2017.07 - Maximum Likelihood Estimation.pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.2017.08 - The E-M Algorithm.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.11.pdf|PDF]]

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Power of Genomewide Association Studies]] - [[Media:666.2010.01.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2010.02.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2010.03.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2010.04.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 ==

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

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[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, Computation with the Coalescent]] - [[Media:666.08.pdf|PDF]]

[[Biostatistics 666: Copy Number Variation]] - [[Media:666.Zollner.CNV.pdf|PDF]]

[[Biostatistics 666: Linkage Tests for Pairs of Individuals]] - [[Media:666.14.pdf|PDF]]

[[Biostatistics 666: The Possible Triangle Constraint]] - [[Media:666.15.pdf|PDF]]

[[Biostatistics 666: The Lander-Green Algorithm]] - [[Media:666.18.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]]

[[Media:666.Worksheet_2.pdf|Problem Set 2]]

== Sample Mid-Term ==

[[Media:666.SampleMidterm.pdf|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 [http://www.sph.umich.edu/academics/policies/conduct.html]:

''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 [http://www.unm.edu/~anthro/people_faculty_jeff_long.html 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 [[http://www.sph.umich.edu/csg/abecasis/class Goncalo's older class notes]].