Human Genetics 236B - Advanced Human Genetics

Spring Quarter 2009

Monday, Wednesday, and Friday at 9:00 AM - 9:50 AM in 5303 Gonda Genetics Research Center.

Exception: no class on Monday, 25 May, Memorial Holiday.

Course organizers: and .

Course Syllabus [pdf]

(Adobe Reader version 6 or greater is recommended for reading the PDF files linked from this website.)

Highly recommended textbook: Human Molecular Genetics, 3rd edition, by Strachan and Read (hereafter referred to as HGM3)

M   30 Mar:      Rita Cantor, Introduction to Complex Genetic Studies

WFM 01 - 06 Apr: Jerry Rotter, Introduction to Complex Traits: Inflammatory Bowel Disease Example

Session Overview [pdf] - Includes required reading and homework assignments

Presentation [pdf - warning Large file > 20 MB]

Articles: (please see Session Overview [pdf] for article assignments)

• Hugot, et al.: Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease [pdf]
• Duerr, et al.: A genome-wide association study identifies IL23R as an inflammatory bowel disease gene [pdf]
• Abreu, et al.: Mutations in NOD2 are associated with fibrostenosing disease in patients with Crohn's disease [pdf]
• Devlin, et al.: NOD2 variants and antibody response to microbial antigens in Crohn's disease patients and their unaffected relatives [pdf]
• Sugimura, et al.: A novel NOD2/CARD15 haplotype conferring risk for Crohn's disease in Ashkenazi Jews [pdf]
• McGovern, et al.: Genetic epistasisof IL23/IL17 pathway genes in Crohn's disease [pdf]
• Taylor, et al.: IL23R haplotypes provide a large population attributable risk for Crohn's disease [pdf]

WF  08 - 10 Apr: Rita Cantor, Statistics Primer for Complex Genetic Studies

M   13 Apr:      Jeanette Papp, Genotyping and Sequencing Technologies

Presentation [pdf - warning Large file > 20 MB]

WF  15 - 17 Apr: Eleazar Eskin, Bioinformatics Tools

Homework Assignment [pdf]

MWF 20 - 24 Apr: Eric Sobel, Linkage Analysis for Complex Traits

Presentation [pdf]

Homework Assignment [pdf]

Homework Mendel Files [zip]

MWF 27 Apr - 01 May: Jake Lusis, Mouse Models of Complex Genetics

Session Overview [pdf] - Includes required reading assignments

Presentation #1 [pdf - warning large file > 5 MB]

Presentation #2 [pdf - warning large file > 1 MB]

Presentation #3 [pdf - warning large file > 1 MB]

Articles:

• Silver: Mouse Genetics [http]
• Flint, et al.: Strategies for mapping and cloning quantitative trait genes in rodents [pdf]
• Keller, et al.: A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility [pdf]

MW  04 - 06 May: Janet Sinsheimer, Analysis of Quantitative Trait Loci

Presentation [pdf]

Homework [pdf]

Articles:

• Cho, et al.: A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits [pdf]
• Cho, et al.: Supplementary Material [pdf - warning large file > 1 MB]

FMW 08 - 13 May: Chiara Sabatti, Population Genetics

Presentation [pdf - warning large file > 1 MB]

Homework [pdf]

F   15 May:      Ken Lange, Ethnic Admixture Analysis

Presentation [pdf]

M   18 May:      Steve Horvath, Family-based Association Testing

Presentation [pdf]

FBAT Software Tutorial [pdf]

FBAT Software Manual [pdf]

FBAT Homework [pdf]

Example Data Set for FBAT Homework [zip]

WF  20 - 22 May: Steve Horvath, Expression Data and Its Analysis

Presentation [pdf - warning large file > 1 MB]

FBAT Homework [pdf]

WFM 27 May - 01 Jun: Rita Cantor, Whole Genome Association

Articles:

• For class discussion: Rioux, et al.: Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis [pdf]
• Rioux, et al.: supplementary material [pdf]

WF  03 - 05 Jun: Ed McCabe, Personalized Medicine

Presentation on Systems Biology [pdf - warning large file > 1 MB]

Presentation on Personalized Medicine [pdf - warning large file > 1 MB]

Homework [pdf]

Articles:

• Dipple and McCabe: Phenotypes of patients with simple mendelian disorders are complex traits: thresholds, modifiers, and systems dynamics [pdf]
• Dipple, et al.: Consequences of complexity within biological networks: robustness and health, or vulnerability and disease [pdf]
• Khoury, et al.: Population screening in the age of genomic medicine [pdf]
• McCabe and McCabe: Direct-to-consumer genetic testing: access and marketing [pdf]
• MacLennan, et al.: Targeted disruption of glycerol kinase gene in mice: expression analysis in liver shows alterations in network partners related to glycerol kinase activity [pdf]