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CAMB 630 Topics in Human Genetics and Disease

Course Directors

Nancy Spinner, PhD

Prof of Human Genetics in Pediatrics
Univ. Penn. School of Medicine
CHOP ARC 1007A
(215) 590-4177, FAX (215) 590-3850
spinner@mail.med.upenn.edu

Marcella Devoto, PhD

Associate Prof Pediatrics and Epidemiology
Univ. Penn. School of Medicine
CHOP ARC 1002E
(267)-426-0124 FAX (215)590-3764devoto@email.chop.edu

Struan Grant, PhD

Associate Director, Center for Applied Genomics
CHOP ARC 1216F
(267) 426-2795, FAX (215) 590-3764 grants@chop.edu

Tamim Shaikh, PhD

Asst. Professor of Pediatrics
Univ. Penn. School of Medicine
CHOP ARC 1002
(215) 590-4274, FAX (215) 590-3764
tshaikh@mail.med.upenn.edu

Eileen Shore, PhD

Res. Assoc. Prof. Orthopaedic Surgery
Univ. Penn. School of Medicine
424 Stemmler
(215) 898-2331, FAX (215) 573-2133
shore@mail.med.upenn.edu

Building on the foundations of the Human Genome Project and parallel efforts in model organisms, research in human genetics and genomics is progressing rapidly.  Our understanding of basic concepts in genetics, and Mendelian and non-Mendelian human genetic disease is proceeding at an unprecedented pace.  This course will provide students with an overview to approaches to understanding current problems and techniques in human genetics and organisms modeling human disease.  The format will be an advanced seminar course, with directed reading and students presentations.

Prerequisites:
This course is designed for students with previous background in graduate level genetics, i.e., CAMB graduate students having taken CAMB550, or students in MD/PhD, veterinary, genetic counseling or nursing programs with equivalent courses.

Class Format:

(Thursdays, 1:30-3:30pm, BRBII/III 501, Fall Semester 2007)
Every week, students are expected to participate in a 2 hour class session, and two students will present recent publications in human genetics and disease.  After each session, instructors will meet with presenting students for 30 min. to provide individual feedback.  Course directors will attend each class, and guest preceptor with relevant scientific expertise may also participate.

Students will be assigned readings for the first half of the course, and then select their own papers for the second half of the course.  Presentations will be prepared in consultation with course directors.  Students must meet with instructors at least one to two weeks prior to the presentation date.

In class, the student discussion leaders will i.) present background information necessary to understand the assigned paper (10-15 min.), ii.) lead discussion of the paper, focusing on critical evaluation of the methods and results, and iii.) talk about the future directions for this research.

A short written assignment will be due by the end of the course.  This written work will be in the form of a review piece or “news and views” format commonly seen in scientific journals.  The topic of this review can be based on one of the two topics the student presents in class, or on a separate topic approved by the instructors.  The review should be approximately 1,000 words or less (no more than 4 double-spaced pages).

Minimum number of students 10, maximum 20. Fall semester, Thurs. 1:30-3:30 PM.

Grading:
Students will be evaluated based on class participation (25%), their first presentation (25%), their second presentation (25%), and the written assignment (25%).

Topics in Human Genetics and Disease:

1.  Genome architecture and instability (Shaikh, Spinner)

2.   Emerging Technologies (Grant, Shaikh)

3.   Mutations in Human Disease (Spinner, Shore)

4.   Epigenetics, gene regulation, and disease (Shore, Grant)

5.  Human genomic variation and disease (Devoto)

Date

Topic and paper

Instructors

9/13/07

Introductory meeting

ALL

9/20/07

I. Genome architecture and instability

Paper 1: Redon et al. (2006) Global variation in copy number in the human genome. Nature 444:444-454

Paper 2: Stankiewicz P et al. (2004) Serial segmental duplications during primate evolution result in complex human genome architecture. Genome Res 14:2209-2220

Additional reading:

Feuk et al. (2006) Structural variation in the human genome Nature Reviews Genetics 7: 85-97

Sharp et al (2006) Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nature Genet 38:1038-1042

Shaikh, Spinner

9/27/07

II. Emerging Technologies

Paper 1:  Robertson et al. 2007 Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods 4:651-657

Paper 2: Thomas et al. 2007 Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nature Med: 12:852-855.

Additional reading:

Bennett et al. 2005 Towards the $1000 genome. Pharmacogenomics 6:373-382

Margulies et al. 2005 Genome sequencing in microfabricated high-density picolitre reactors. Nature: 437:376-380

Grant, Shaikh

10/4/07

III. Mutations in human disease

 Paper 1: Welch et al. (2007) PTC 124 targets genetic disorders caused by nonsense mutations. Nature 447:87-91

Paper 2: Badano et al.(2006) Dissection of epistasis in oligogenic Bardet-Biedl syndrome Nature 439: 326-330

Additional reading: pending

Spinner, Shore

10/11/07

IV. Epigenetics, gene regulation and disease

Paper 1: Guenther et al. 2007 A chromatin landmark and transcription initiation at most promoters in human cells.  Cell 130: 77-88

Paper 2: Cui et al. 2003 Loss of IGF2 imprinting: a potential marker of colorectal cancer risk.  Science 299: 1753-1755

Additional reading:

Spivakov and Fisher (2007) Epigenetic signatures of stem cell identity. Nature Reviews Genetics 8:263-271

 Feinberg (2007) Phenotypic plasticity and the epigenetics of human disease Nature 447:433-440

Deadline for selection of papers for student presentations

Shore, Grant

10/18/07

V. Human genomic variation and disease

Paper 1: International MSGenetics Consortium (2007) Risk alleles for multiple sclerosis identified by a genome-wide study.  NEJM 357:1-12

Paper 2: Tishkoff et al. 2006 Convergent adaptation of human lactase persistence in Africa and Europe Nature Genetics

Devoto

10/25/07

ASHG meeting, no class

11/1/07

I.  Genomic architecture and human disease

Student selected papers

Shaikh, Spinner

11/8/07

II. Emerging technologies

Student selected paper

Grant, Shaikh

11/15/07

III. Mutations in human disease

 Student selected paper

Spinner, Shore

11/22/07

Thanksgiving holiday, no class

11/29/07

IV. Epigenetics, gene regulation and disease

Student selected paper

Shore, Grant

12/6/07

V. Human genomic variation and disease

Student selected paper

Devoto