Syllabus (Genome 361 Summer 2012) - UW Courses Web Server

Genome 361: Fundamentals of Genetics and Genomics Summer 2012
Instructors
Frances Cheong, kcheong3@uw.edu
Mary Kuhner, mkkuhner@uw.edu
Teaching Assistants
Renee Agatsuma, ragatsum@uw.edu
Caitlin Scoville, cwscov@uw.edu
Jeff Vierstra, jeffrv@uw.edu
Chad Weisbrod, weisbc@uw.edu
Course overview
Genetics is the scientific study of heredity, and over the last century many genetic methods
have been developed for understanding basic biological processes. However, genetics is
much more than a set of methodological tools. Rather, it provides a coherent framework
for thinking about biology, medicine, and evolution. In addition, genetics permeates our
everyday lives, and chances are that you have already thought about or have been exposed
to genetics-related topics (such as forensics, genetic testing for inherited diseases, human
cloning, stem cell research, and genetically modified foods). A recurring theme of the
course will be how genotypes (the genetic composition of organisms) determine
phenotypes (observable traits or characteristics). The curriculum will cover basic
Mendelian genetics, elements of probability and statistics fundamental to interpreting
genetic data, genetic variation, the use of model organisms in genetics, basic molecular
genetics, and approaches to mapping genes for specific phenotypes or diseases.
Office Hours
Weekly office hours are held at the following times:
Jeff Vierstra Tuesday 11:30am – 12:30pm in Foege S040
Caitlin Scoville Wednesday 8:30 – 9:30am in Foege S040
Mary Kuhner Wednesday 2:30 – 3:30pm in Foege S110
Frances Cheong Wednesday 3:30 – 4:30pm in Foege S110
Renee Agatsuma Thursday 8:30 – 9:30am in Foege S040
Chad Weisbrod Thursday 1:00 – 2:00pm in Foege S040
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Schedule
Lectures are on Tuesday and Thursday in Foege S060 from 9:40am to 11:10am. Typically
we will take a short break in the middle of each lecture. In addition, all students should be
enrolled in a quiz section that will be held in Hitchcock 443. On the following pages, the
tentative schedule of lecture and quiz section topics for each week is shown. Exam dates
are also indicated. Problem sets will be handed out in quiz section every week, and
answers will be posted on the course website (see below). Although problem sets will not
be graded, we strongly suggest that you work through them each week before the answers
are posted; this will provide an important opportunity to assess your understanding of
material and to prepare for exams. In addition, every Monday a quiz section pre-activity
will be posted on the course website. Do this pre-activity before coming to quiz section.
Week 1
Tuesday, Jun. 19 Lecture 1 (FC) Introduction to genetics; Mitosis and meiosis
What do we mean by Genetics? Cell division; cell
cycle; chromosomal segregation in mitosis and
meiosis
Quiz Section 1 Meiosis
Problem Set 1
Thursday, Jun. 21 Lecture 2 (FC) Mendelian genetics and probability I
Mendelian ratios; principle of genetic segregation;
product and sum rules
Week 2
Tuesday, Jun. 26 Lecture 3 (FC) Mendelian genetics and probability II
Principle of independent assortment; chi-squared
analysis
Quiz Section 2 Mendelian genetics
Problem Set 2
Thursday, Jun. 28 Lecture 4 (FC) Mendelian genetics and probability III
X-linked inheritance
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Week 3
Tuesday, July 3 Lecture 5 (FC) Central dogma
Transcription; translation; looking for ORFs
No quiz section Central dogma take-home exercise
Thursday, July 5 EXAM 1
Week 4
Tuesday, July 10 Lecture 6 (MK) Mutation and complementation
Loss of function; gain of function; mutagenesis;
complementation
Quiz Section 3 Mutagenesis and complementation
Problem Set 3
Thursday, July 12 Lecture 7 (MK) Epistasis
Genetic interactions and dihybrid ratios
Week 5
Tuesday, July 17 Lecture 8 (MK) PCR & cloning
Molecular methods
Quiz Section 4 Epistasis & molecular techniques
Problem Set 4
Thursday, July 19 Lecture 9 (MK) DNA sequencing
Making a genomic library; DNA sequencing
technology; genome sequencing
Week 6
Tuesday, July 24 Lecture 10
(FC)
Genetic linkage
Testcrosses; genetic linkage; parental and
recombinant types
Quiz Section 5 Introduction to genetic linkage
Problem Set 5
Thursday, July 26 Exam 2
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Week 7
Tuesday, July 31 Lecture 11
(FC)
Thursday, Aug. 2 Lecture 12
(MK)
Week 8
Quiz Section 6 Cancer genetics
Problem Set 6
Genetic and physical maps
Constructing genomic maps based on
recombination and physical distance
Molecular markers
Tuesday, Aug. 7 Lecture 13 Guest lecture on genetic counseling
Thursday, Aug. 9 Lecture 14
(MK)
Week 9
Tuesday, Aug. 14 Lecture 15
(MK)
Quiz Section 7 Molecular markers
Problem Set 7
Human pedigrees & LOD score analysis
Mapping human genetic diseases using pedigrees
Population genetics
Quiz Section 8 LOD score analysis
Problem Set 8
Thursday, Aug. 16 Exam 3
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Course Website
A course website has been created and is available at
http://courses.washington.edu/gs361sum
Much of the material used in lectures will end up on the class web site, but there may be a
lag of several days. The website also includes a link to a Go Post discussion board that has
been set up for the class. Audio podcasts will be made available for the class. The audio
podcasts, the course website and discussion board should be used to complement lectures,
not as a substitute.
Textbooks
There is no required textbook for this course. Each lecture will be accompanied by a
handout that covers all of the in-class material. For students who would like to have a
general reference book to supplement course material, the following textbooks will be put
on reserve in Suzallo library:
• Griffiths, A. J. F., Wessler, S. R., Lewontin, R. C., and Carroll, S. B. 2008.
Introduction to genetic analysis. 9th ed. W. H. Freeman and Company, New York,
NY. ISBN: 139780716768876
• Hartwell, L. H., Hood, L., Goldberg, M. L., Reynolds, A. E., Silver, L. M., and
Veres, R. C. 2006. Genetics from genes to genomes. 3rd ed. McGraw-Hill, Boston,
MA. ISBN-10: 0073227382
• Klug, W. S., Cummings, M. R., and Spencer, C. A. 2006. Concepts of genetics. 8th
ed. Pearson Prentice Hall, Upper Saddle River, NJ. ISBN: 0131918338.
Grading
The final grade will be determined by exams and participation points for lecture and quiz
sections.
Exams. There will be a total of three exams, each worth 100 points. Exams are not
designed to be cumulative, but they will end up being somewhat cumulative because the
later course material assumes that you understand the earlier material. We will allow you
to bring hand written notes on one 4x6 index card, but that really doesn't mean much—if
you don’t understand the material, having notes won’t be much help. We will give you an
index card to use; it will be handed out during the lecture preceding the exam.
Class participation points. Each lecture will involve several clicker questions. If you
attend at least 9 lectures, as determined by your participation in answering the clicker
questions, you will receive 10 points. Otherwise, you will receive zero points. Having
someone take your clicker to class and click for you when you are not there is a violation
of the Honor Code. We will report any breach of conduct to the University Disciplinary
Board. Both the clicker-giver and the clicker-receiver will be reported. The clicker receiver
channel is 41.
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Quiz section participation points. If you attend at least 6 out of the 8 quiz sections, you
will receive 10 points. Otherwise, you will receive zero points. You must attend your
registered section to receive credit.
Final grade. The total number of points available is 320 (300 points from exams, 10 points
from class participation, and 10 points from quiz section participation). The curve will be
set so that the median score is a 2.8. The lowest passing grade will be set at half the
median.
Conflict policy. Make-up exams are not automatically given for scheduling conflicts. Our
policy is to allow students to schedule a make-up exam, at the instructors’ discretion, for
only a few reasons:
• Medical/family emergencies. Visiting relatives on their birthdays does not count as
a family emergency!
• Academic events – the student must be interviewing for a job or medical/graduate
school, or presenting academic research that was conducted at the University at a
conference.
• University-sponsored sporting events – the student must be part of a University
sponsored team. University clubs do not count as university-sponsored sports
teams; if in doubt, check with the Athletics department.
Airline reservations do not constitute a valid excuse. If you will need to reschedule an
exam (for one of the reasons listed above), you must fill out an exam conflict form and
return it to Frances by June 21. If an exam is missed because of a medical or other
emergency, there will be NO opportunity to take a written make-up exam after the
scheduled exam date. The instructors may choose to give an oral exam in cases of
unforeseeable emergencies. If you cannot meet the exam schedule, you should not take this
class.
Re-grades. If you feel that an error was made in grading an exam, state your case in an
email to Frances (kcheong3@uw.edu) within one week after the graded exam was returned
to you. We reserve the right to re-grade the entire exam, not just the question in contention.
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Code of Conduct
Honesty is a highly valued principle in science. In Genome 361 we strive to create an
environment where individual achievement and honesty are rewarded. In this spirit, we
expect that each student will do his or her own work on exams and only use a clicker when
present in class. During exams and lectures, we will circulate to answer your questions. If
we observe behavior that does not meet our standards of honesty, we will take actions to
remedy the situation (e.g. by taking exams or clickers away). For these reasons, please
keep your eyes on your own paper and do not give your clicker to another student. We
reserve the right to report any breach of conduct to the University Disciplinary Board. If
they find that an infraction has occurred during an exam, the exam in question will be
given a zero. As a further deterrent to altering exams after they are graded, and as an aid
for grading them rapidly, we keep photocopies of exams. Please refer to the University’s
Policy on Academic Honesty if you have questions about the code of conduct.
Please be aware that university email is not considered a secure way to communicate
private and sensitive matters. If you wish to discuss confidential matters related to the
course, please set up an appointment with the instructors.
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