Fall 2015
Stony Brook University
Department of Ecology & Evolution
College of Arts and Sciences
Course Title: BIO 302, Human Genetics
Course Instructor: Brenna Henn
Course Location: Earth & Space 131
Course Time: 11:00am -11:53am, MWF
Office Hours: Wed. 2:30-3:30pm, and before class by appointment
Email: brenna.henn@stonybrook.edu Office Location: Life Sciences Building 640
TA: Shyamie Gopalan
Office Hours: Mon.
Office Location: , 6th floor, Life Sciences
TA contact information: shyamalika.gopalan@stonybrook.edu
COURSE DESCRIPTION:
An introduction to human genetics. Topics include the principles of inheritance, human
population genetics, molecular approaches for studying DNA, the genetic basis of mutations,
genetic diversity, using DNA to study ancient human history and human evolution. Human
genetic diseases are discussed and an introduction is given to human chromosome maps, the
Human Genome Project, and methods for mapping disease mutations. This class is meant to
introduce students to the major concepts in human genetic and genomic research. The course
will emphasize presentation skills and reading comprehension of current human genetics
literature. Students will be evaluated based on a combination of take-home assignments, pop
quizzes and a final project based on current scientific journal papers. Limited enrollment to 75
students.
Course Pre/Co-requisites:
BIO 201, BIO 202 core classes are required. BIO 204 [Fundamentals of Scientific Inquiry] is
advised, but not required.
Course Objectives:
This is an upper-division undergraduate course that emphasizes reading comprehension and
oral presentation of current human genetics literature. Students will be introduced to basic
population genetic statistics, human genomics from an evolutionary genetics standpoint and
standard forms of genome-wide data analysis. At the end of the course, students will know how
to:
1. read and organize the main components of a standard scientific article (All Weeks)
2. design a brief oral presentation to present scientific data and analysis (All Weeks)
3. understand the difference in genetic inheritance between haploid markers and
autosomal DNA (Week 2 – 5)
4. calculate mutation rates from pedigree or phylogenetic data (Week 4)
5. understand how principal components analysis and clustering algorithms to discriminate
population structure (Week 6 - 7)
6. understand the distribution of genetic diversity among human populations (Week 7-8)
7. apply population genetic statistics to discern the distribution of diversity within and
between populations (Week 5-9)
8. model the inheritance pattern of Mendelian disease and understand the shortcomings of
these models (Week 9-10)
9. use common genome browsers to identify pertinent information about human SNPs and
their locations relative to known genes (Week 11-12)
10. situate genomic patterns in their function and evolutionary context by contrasting interspecific genetic data (Week 14-15)
TEACHING SCHEDULE:
Week 1 [Aug. 24, 26, 28]: The human genome, what is a scientific paper?
Week 2 [Aug. 31, Sep. 2, 4]: Genome continued, Mutation models, what is a scientific
presentation?
Week 3 [Sep. 9, 11]: Population Structure, Origins of modern humans
Week 4 [Sep. 14, 16, 18]: Population genetic models: Hardy-Weinberg, migration
Week 5 [Sep. 21, 23, 25]: Population genetic models: Ne, genetic drift, [Oral presentation begin]
Week 6 [Sep. 28, 30, 2]: Genetic admixture and linkage disequilbrium
Week 7 [Oct. 5, 7, 9]: Genome technology
Week 8 [Oct. 12, 14, 16]: Heritability
Week 9 [Oct. 19, 21, 23]: Complex genetic diseases
Week 10 [Oct. 26, 28, 30]: Simple genetic diseases, FOXP2, pigmentation
Week 11 [Nov. 2, 4, 6]: Methylation
Week 12 [Nov. 9, 11, 13]: Human migrations: Part 1, networks
Week 13 [Nov. 16, 18, 20]: Human migrations: Part 2
Week 14 [Nov. 23]: Natural Selection
Week 15 [Nov. 30, Dec. 2, 4] Lactase persistence
Week 16 [Dec. 10]: Final Class (11:15am-1:45pm)
Course Material and Required Reading
Human Evolutionary Genetics, 2nd Edition, Jobling et al. Garland Science Publishing.
Readings from the primary literature will be assigned. Journal articles will be made freely
available via pdf to all students.
READING SCHEDULE:
Week 1: HEG Chapter 1,2, Keller (2012, Nat Comm) [ancient DNA]
Week 2: HEG Chapter 3.2-3.3, 3.7, 5.2, 5.7, Kong (2012, Nature) [Mutation rate]
Week 3: HEG Chapter 9, 10.1 – 10.2, 11
Week 4: HEG Chapter 3.8, 5.5, Henn (2011, PNAS) [Origins]
Week 5: HEG Chapter 5.3, 6.1-6.3
Week 6: HEG Chapter 3.8, 5.2, 14
Week 7: HEG Chapter 4.0-4.6, Clark et al. (2011, Nature Biotechnology) [exomes]
Week 8: Visscher 2008 (Nature Review Genetics) [heritability]
Week 9: HEG Chapter 17
Week 10: HEG Chapter 15.3, 16.1-16.2, 8.3
Week 11: HEG Chapter 3.2 and TBD
Week 12: HEG Chapter 6.4, 11
Week 13: HEG Chapter 12
Week 14: HEG Chapter 5.6, 6.7, 10.3
Week 15: HEG Chapter 15.6, Tishkoff et al. (2007, Nature Genetics) [Lactase]
Assignments and Tests:
Three pop quizzes, in-class and open notes, will be given. Several homework assignments
based on exercises in the book will be assigned. Students have the option of a final oral
presentation, presented in class [10-15 min], or a final written review* [5 pages, single spaced
with 1 figure]. Presentation will involve reading and presenting a scientific paper from primary
literature; students will be encouraged to ask questions in class. Students must decide between
a written or oral review by the 3rd week of class in order to facilitate appropriate scheduling.
Decisions cannot be changed at a later date. Final review paper can be chosen from a range of
topics and must incorporate reading of current scientific literature. Students will meet once with
the course instructor or TA for individual preparation prior to the oral presentation.
*Upper-Division Writing Requirement
Students who elect to write a final review paper may consider this paper for the upper-division
writing requirement. BIO or EBH majors may submit a paper which has been deemed
satisfactory by the instructor (graded C or higher). The paper must be of appropriate length and
format. Students who wish to use a paper should present the necessary form to the course
director and obtain signatures on the form and the paper. The form and the original paper must
then be submitted to the Director of the program.
Attendance and Make Up Policy
If a student misses an in-class quiz, they must contact the TA and instructor to schedule a
make-up quiz during next available office hours. A make-up quiz is only allowed in the case of
1) verifiable illness, 2) verifiable family emergency, 3) University-sanctioned religious holiday,
or 4) participation in official University-sponsored events (for documented student athletes
only), excuse must be documented on official letterhead (as appropriate) and will be verified by
the instructor. Attendance at scheduled oral presentation is mandatory.
GRADING
The course grade will be based on the following components (list in parentheses is the percent
assigned to each component):
Pop Quizzes (30%)
Final oral presentation or Final review paper (30%)
Homework assignments (40%)
Oral presentations: 5 points for organization, 5 points for answering questions appropriately, 5
points for style, 15 points for conceptual understanding of topic
Review paper: 10 points for organization, 10 points for citation of appropriate scientific
literature, 20 points for answering chosen question/topic
Grades are based on the following scale:
A = 93-100, A- = 90-92
B+ = 88-89, B = 83-87, B- = 80-82
C+ = 78-79, C = 73-77, C- = 70-72
D+ = 68-69, D = 63-67, F <63
CLASS PROTOCOL
All electronic devices are to be turned off during class unless advance permission is given by
the instructor.
CLASS RESOURCES
E-mail / Blackboard will be used as the primary means of distribution for readings from the
primary literature and submission of assignments.
LETTERS of RECOMMENDATION
Given the size of the class and the limited interaction with any given student, I will not consider
writing a letter of recommendation for students unless exceptional circumstance apply.
UNDERGRADUATE TAs
If you are a sophomore or a junior, consider becoming an undergraduate TA next year. We will
select 1-2 individuals who performed well in the course to assist in teaching BIO302 next year.
http://sb.cc.stonybrook.edu/bulletin/current/policiesandregulations/special_academic_op/under
grad_teaching_assistantships.php
Americans with Disabilities Act
If you have a physical, psychological, medical or learning disability that may impact your course
work, please contact Disability Support Services, ECC (Educational Communications Center)
Building, room128, (631) 632-6748. They will determine with you what accommodations, if any,
are necessary and appropriate. All information and documentation is confidential. Students who
require assistance during emergency evacuation are encouraged to discuss their needs with
their professors and Disability Support Services. For procedures and information go to the
following website: http://www.stonybrook.edu/ehs/fire/disabilities]
Academic Integrity
Each student must pursue his or her academic goals honestly and be personally accountable
for all submitted work. Representing another person's work as your own is always wrong.
Faculty are required to report any suspected instances of academic dishonesty to the
Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology &
Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required
to follow their school-specific procedures. For more comprehensive information on academic
integrity, including categories of academic dishonesty, please refer to the academic judiciary
website at http://www.stonybrook.edu/uaa/academicjudiciary/
Critical Incident Management
Stony Brook University expects students to respect the rights, privileges, and property of other
people. Faculty are required to report to the Office of Judicial Affairs any disruptive behavior
that interrupts their ability to teach, compromises the safety of the learning environment, or
inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are
required to follow their school-specific procedures.