Genome 361: Fundamentals of Genetics and Genomics Winter 2021

Instructors Teaching Assistants

Colin Manoil (he/him), manoil@uw.edu
Bonita Brewer (she/her), bbrewer@uw.edu
Course Coordinator
Hannah Jordt (she/her), hljordt@uw.edu
Note: for ALL logistical questions, contact Hannah
Robin Aguilar (they/them), eaguil@uw.edu
Yuzhen Liu (she/her), yliu234@uw.edu
Phoebe Parrish (she/her), pparrish@uw.edu
Sam Smukowski (he/him), samsmuko@uw.edu

Course overview _
Genetics is the scientific study of heredity. In 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 issues (in areas such as forensics, genetic testing for inherited diseases, human cloning, stem
cell research, COVID-19, and genetically modified foods, to name just a few). A recurring theme of the course
will be how genotypes (the genetic makeup 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 used to map genes for specific phenotypes or diseases.

Office Hours _
Weekly office hours are held via Zoom at the following times, unless otherwise noted. All Zoom links can be
found on our Canvas website.

• Dr. Jordt: Wednesdays, 3:00-4:00pm

• Dr. Brewer: Thursdays, 2:00-3:00pm
• Dr. Manoil: Can be arranged by email

Extra office hours can be arranged via email, and TAs will offer additional office hours during exam weeks.

Schedule _
Lectures:
• Mon – synchronous – 12:30-1:50pm – Zoom link found on Canvas
• Fri – asynchronous – available on Canvas by at least Fri 12:30pm
o Short lecture quizzes due 11:59pm the day of each lecture (Mon & Fri).
o Exams occur Friday, January 22nd, Friday, February 19th, and Thursday, March 18th (finals week)
You will have 4 hours (12:30-4:30pm) to complete a take-home exam designed for 80 minutes.
o The asynchronous aspect of Friday lectures will be re-evaluated halfway through the course
depending on student and instructor experience.
Quiz sections:
• Tues OR Wed – synchronous – Zoom link found on Canvas
o Pre-activities due prior to your quiz section. Quiz section activity due 11:59pm the day of your
quiz section.
Practice exams:
• Thurs - untimed, available 24 hours (between 12:00am and 11:59pm Thurs) on non-exam weeks.

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We encourage you to set up a weekly schedule. Below is a suggested outline: :
Monday 12:30 am – 1:50 pm: Attend synchronous Zoom lecture, submit lecture quiz
Before your quiz section: Complete and submit section pre-activity
Tuesday/Wednesday: Attend quiz section, submit section activity
Before practice exam: Work on weekly problem set
Thursday Complete and submit practice exam
Friday afternoon: Watch asynchronous Zoom lecture, submit lecture quiz

The tentative schedule of topics is shown below. Exam dates are also indicated. Problem sets will be posted every
week by Friday, and answers will be posted on the course website. Although problem sets will not be graded, we
strongly suggest that you work through them each week before looking at the answers; this will provide an
important opportunity to assess your understanding of material and to prepare for exams.

Week 1

Monday, Jan. 4 Lecture 1 (CM) Introduction to genetics; central dogma

What do we mean by genetics? Biology as
information flow; transcription; translation; looking
for ORFs

Quiz Section 1 Central dogma

Practice Problem Set 1 (ungraded)

Week 1 practice exam (graded for effort)

Friday, Jan. 8 Lecture 2 (CM) Mitosis and meiosis

Cell division; cell cycle; chromosomal segregation in
mitosis and meiosis

Week 2

Monday, Jan. 11 Lecture 3 (CM) Mendelian genetics and probability I

Mendelian ratios; principle of genetic segregation;
product and sum rule

Quiz Section 2 Meiosis & introduction to Mendelian genetics

Practice Problem Set 2 (ungraded)

Week 2 practice exam (graded for effort)

Friday, Jan. 15 Lecture 4 (CM) Mendelian genetics and probability II

Principle of independent assortment; chi-square; sex-
linked inheritance

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Week 3

Monday, Jan. 18 NO CLASS (MLK Day)

Quiz Section 3 Mendelian genetics

Practice Problem Set 3 (ungraded)

Friday, Jan. 22 EXAM 1

Week 4

Monday, Jan. 25 Lecture 5 (CM) Mutations and complementation

Quiz Section 4 Mutagenesis and complementation

Practice Problem Set 4 (ungraded)

Week 4 practice exam (graded for effort)

Friday, Jan. 29 Lecture 6 (CM) Epistasis

Genetic interactions and dihybrid ratios

Week 5

Monday, Feb. 1 Lecture 7 (CM) PCR & cloning

Molecular methods; Making a genomic library

Quiz Section 5 Epistasis & molecular methods

Practice Problem Set 5 (ungraded)

Week 5 practice exam (graded for effort)

Friday, Feb. 5 Lecture 8 (CM) DNA sequencing

DNA sequencing technology; genome sequencing

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Week 6

Monday, Feb. 8 Lecture 9 (BB) Genetic linkage

Duchenne’s muscular dystrophy; sex linkage;
recombinant and parental gametes; linkage

Quiz Section 6 Linkage and recombination

Practice Problem Set 6 (ungraded)

Week 6 practice exam (graded for effort)

Friday, Feb. 12 Lecture 10 (BB) Constructing physical maps of chromosomes

Recombination mapping in flies; informative meioses
in human pedigrees; cloning; RFLPs; FISH

Week 7

Monday, Feb. 15 NO CLASS (President’s day)

Quiz Section 7 Chromosome mapping

Practice Problem Set 7 (ungraded)

Friday, Feb. 19 EXAM 2

Week 8

Monday, Feb. 22 Lecture 11 (BB) Mapping the DMD gene

Genetic vs. physical maps; cloning by subtractive
hybridization; chromosome translocations and
deletions

Quiz Section 8 RFLPs and human pedigrees

Practice Problem Set 8 (ungraded)

Week 8 practice exam (graded for effort)

Friday, Feb. 26 Lecture 12 (BB) The structure of the DMD gene

Chromosome walking, eukaryotic gene architecture,
cDNA clones

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Week 9

Monday, Mar. 1 Lecture 13 (BB) The dystrophin protein

Antibodies to study protein function; the link between
genotype and phenotype; different types of mutations

Quiz Section 9 Mutations in the dystrophin gene

Practice Problem Set 9 (ungraded)

Week 9 practice exam (graded for effort)

Friday, Mar. 5 Lecture 14 (BB) Model organisms with DMD

The mdx mouse and the GRMD dog; expressivity,
penetrance and suppressors; dissecting essential
functions in dystrophin

Week 10

Monday, Mar. 8 Lecture 15 (BB) Prenatal diagnosis, carrier detection and

population screening for DMD mutations
Serum CK levels; multiplex PCR techniques; targeted
DNA capture and next-generation sequencing

Quiz Section 10 DMD diagnosis and genetic counseling

Practice Problem Set 10 (ungraded)

Week 10 practice exam (graded for effort)

Friday, Mar. 12 Lecture 16 (BB) Mining the central dogma for a DMD cure
CRISPR/Cas9 editing; morpholinos for exon
skipping; non-sense bypass

Week 11 (Final Exam Period)

Thursday, Mar. 18 EXAM 3

8:30 – 10:20 am

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Course Website & Message Board _
Our course website is available at https://canvas.uw.edu/courses/1433150.
Please check this website frequently, since all class materials will be made available through Canvas.

The website also includes a link to a Piazza discussion board that has been set up for the class. Piazza is the best
and fastest place to: get administrative answers, start discussions with other students online, organize study
groups, and ask questions of the teaching staff of Genome 361. The Piazza message board will be temporarily
unavailable during exams, but other than that you will have constant access to it.

Textbooks _
There is no required textbook for this course. Lecture handouts will be available on Canvas.

Grading Guide _
Exams
There will be three exams (two during the quarter and one during finals Grade breakdown
week). Each is worth 80 points. Exams are not designed to be cumulative,
240 pts
but they will end up being somewhat cumulative because later course Exam 1, 2, & 3
(~15% each)
material assumes that you understand earlier material. The exams will be
open-note, open book. However, the exams must be completed solely by 70 pts
Practice exams
you, with no input from other individuals. Evidence of plagiarism, (~2% each)
working with others, or receiving help from others will result in an exam 32 pts Short lecture
grade of zero. Exams are meant to be 80 minutes long, but to facilitate (<1% each) quizzes
online exam-taking, you will be given 240 minutes (4 hours). Exams 1 and 90 pts
QS pre-activity
2 will be accessible online from 12:30 pm to 4:30 pm. You need to submit (~2% each)
your answers by 4:30 pm. Exam 3 will be accessible online from 8:30 am 90 pts
QS activity
to 12:30 pm. You need to submit your answers by 12:30 pm. (~2% each)

Practice Exams
There will be practice exams every Thursday on weeks that do not contain an exam. They are untimed and may be
completed between 12:00am and 11:59pm Thursday (24 hours). These are a proven effective way to increase your
understanding of course material. For each practice exam you will complete several exam-level questions, then
critique your own answers based on an instructor-supplied answer key and rubric. Grading will be based on
effort, not accuracy. Each is worth 10 points. In case of illness or technical problems with your computer, we
will drop each student’s lowest practice exam. See “practice exam instructions” on the course website for detailed
information about taking practice exams on Canvas.

Short lecture quizzes

These are designed to demonstrate, in 2-3 problems, what you should be able to do after each lecture. They will
become available in the morning before lecture and due by 11:59pm the evening of each lecture day. Questions
will be multiple choice and the assignment is intended to be low pressure. Answers are graded right/wrong, and
each lecture quiz is worth 2 points. In case of illness or technical problems with your computer, we will drop each
student’s lowest 2 lecture quizzes. You may work with others, but the most successful students in this course will
have attempted the problems on their own, prior to working with others.

Quiz section submissions

You are allowed to work with others on quiz section exercises, but you must submit your own work. They consist
of two parts:
• Pre-activity – These will be posted the Friday before quiz section and must be completed before your
quiz section. For example, if your quiz section starts at 1:30pm on Tuesday, the pre-activity is due at

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 1:30pm on Tuesday. Each pre-activity is worth 10 points and graded on completion. We will drop each
student’s lowest pre-activity score.
• Activity – These will be completed during quiz section and must be submitted on Canvas by 11:59pm
the day of your quiz section. Each week your TA will select a random question from the activity
submissions to grade for accuracy. The rest of the questions will be graded on completion. Each activity
is worth 10 points. We will drop each student’s lowest activity score.

Final Grade Determination _

The top 5% of students in the course will be awarded a 4.0. The Teaching Team will judge the lowest percentage
that represents acceptable performance for the class, and assign that score the lowest passing grade (0.7). Then,
grades will be determined by linear interpolation between the 4.0 and 0.7 scores. This system allows for any
number of students to achieve any non-4.0 grade, so it is relatively non-competitive compared to the strict curve
used in many departments. The median of the class will likely fall between a 2.8 and 3.0.

Exam Conflicts and Emergencies _

Exams must be taken at the scheduled times. Alternative arrangements may be made with proper documentation,
at the instructors’ discretion, for a few reasons. These include medical/family emergencies, University-sponsored
sporting events in which you are part of a university-sponsored team, or academic or professional interviews that
cannot be rescheduled. Please discuss with the course coordinator if you believe your conflict is not covered in
this policy and warrants further review. All requests must be communicated to the course coordinator as soon as
possible.

Class Recordings _
This course is scheduled to run synchronously at our scheduled Monday class time via Zoom. These sessions will
be recorded and student audio and video will be recorded if they share their computer audio and video during the
recorded session. The recordings will only be accessible to students enrolled in the course to review materials and
will not be shared with or accessible to the public.

The University and Zoom have FERPA-compliant agreements in place to protect the security and privacy of UW
Zoom accounts. Students who do not wish to be recorded should not share their audio or video during class and
might consider choosing a Zoom username that does not include any personal identifying information.

Access and Accommodations _

Your experience in this class is important to us. If you have already established accommodations with Disability
Resources for Students (DRS), please communicate your approved accommodations to Hannah at your earliest
convenience so we can discuss your needs in this course.

If you have not yet established services through DRS but have a temporary health condition or permanent
disability that requires accommodations (conditions include but not limited to; mental health, attention-related,
learning, vision, hearing, physical or health impacts), you are welcome to contact DRS at 206-543-8924 or
uwdrs@uw.edu or disability.uw.edu.

Religious Accommodations _
Washington state law requires that UW develop a policy for accommodation of student absences or significant
hardship due to reasons of faith or conscience, or for organized religious activities. The
UW’s policy, including more information about how to request an accommodation, is available at Religious
Accommodations Policy (https://registrar.washington.edu/staffandfaculty/religiousaccommodations-policy/).
Accommodations must be requested within the first two weeks of this course using the Religious
Accommodations Request form
(https://registrar.washington.edu/students/religious-accommodations-request/).

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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 their own
work on exams. If we observe behavior that does not meet standards of honesty, we will take actions to remedy
the situation. 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. Please refer to the
University’s Policy on Academic Honesty if you have questions about the code of conduct.