Human Genetics 236B - Advanced Human Genetics

Spring Quarter 2008

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

Exception: no class on Monday, 26 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)

31 March: Rita Cantor, Introduction to Complex Genetic Studies

02 - 07 Apr: Jerry Rotter, Introduction to Complex Traits: Inflammatory Bowel Disease Example

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

Presentation: Wednesday and Friday [pdf - warning Large file > 5 MB]

Presentation: Monday [pdf - warning Large file > 5 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]

09 - 11 Apr: Rita Cantor, Statistics Primer for Complex Genetic Studies

14 - 16 Apr: Jeanette Papp, Genotyping and Sequencing Technologies

Presentation: Monday and Wednesday [pdf - warning large file > 1 MB]

Homework Assignment [pdf]

Pertinent Articles:

• Bainbridge, et al.: Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach [pdf]
• Carter: Methods and strategies for analyzing copy number variation using DNA microarrays [pdf]
• Green, et al.: Analysis of one million base pairs of Neanderthal DNA [pdf]
• Hoffman, et al.: DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations [pdf]
• Parameswaran, et al.: A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing [pdf]

18 Apr: Eleazar Eskin, Bioinformatics Tools

21 - 25 Apr: Eric Sobel, Linkage Analysis for Complex Traits

Presentation: Monday, Wednesday, and Friday

Homework Assignment [pdf]

Homework Mendel Files [zip]

28 Apr - 02 May: Thomas Drake, Mouse Models of Complex Genetics

Session Overview [pdf] - Includes required reading assignments

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

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

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

Homework [as PDF document]

Homework [as Word document]

Articles:

• Peters, et al.: The mouse as a model for human biology: a resource guide for complex trait analysis [pdf]
• Hillebrandt, et al. 2002: Genome-wide analysis of hepatic fibrosis in inbred mice identifies the susceptibility locus Hfib1 on chromosome 15 [pdf]
• Hillebrandt, et al. 2005: Complement factor 5 is a quantitative trait gene that modifies liver fibrogenesis in mice and humans [pdf]
• Flint, et al.: Strategies for mapping and cloning quantitative trait genes in rodents [pdf]
• Liu, et al.: Candidate lung tumor susceptibility genes identified through whole-genome association analyses in inbred mice [pdf]
• Rockman and Kruglyak: Genetics of global gene expression [pdf]
• Chen, et al.: Variations in DNA elucidate molecular networks that cause disease [pdf]
• Silver: Mouse Genetics [http]

05 - 07 May: Janet Sinsheimer, Analysis of Quantitative Trait Loci

Presentation [pdf]

Homework [pdf]

Homework Data File (Vitamin_D_transport2.in) [text]

09 - 14 May: Chiara Sabatti, Population Genetics

Presentation [pdf - warning large file > 1 MB]

Homework [pdf]

19 - 21 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]

23 May: Steve Horvath, Expression Data and Its Analysis

Presentation [pdf - warning large file > 1 MB]

FBAT Homework [pdf]

28 May - 02 June: Rita Cantor, Whole Genome Association

Articles:

• For background: Kruglyak: The road to genome-wide association studies [pdf]
• For class discussion: Rioux, et al.: Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis [pdf]
• For homework: Duerr, et al.: A genome-wide association study identifies IL23R as an inflammatory bowel disease gene [pdf]

04 - 06 June: Ed McCabe, Individualized Medicine

Presentation on Systems Biology [pdf - warning Large file > 3 MB]

Presentation on Individualized Medicine [pdf - warning Large file > 3 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]