Genome 361: Fundamentals of Genetics and Genomics Fall 2015

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1 Genome 361: Fundamentals of Genetics and Genomics Fall 2015 Instructor Frances Cheong, Teaching Assistants Michael Bradshaw, Colby Samstag, Emily Youngblom, 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, 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 in Foege S040 at the following times: Michael Bradshaw: Emily Youngblom: Frances Cheong: Colby Samstag: Monday 2:00 3:00 pm Tuesday 1:00 2:00 pm Wednesday 2:30 3:30 pm Friday 1:30 2:30 pm 1

2 Schedule Lectures are on Tuesday and Thursday in Foege S060 from 11:00am to 12:20pm. Typically we will take a short break in the middle of each lecture. In addition, all students should be enrolled in a quiz section held in Health Sciences Building T365. The tentative schedule of lecture and quiz section topics for each week is shown below. Exam dates are also indicated. Problem sets will be handed out in quiz sections 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 week a quiz section pre-activity will be handed out in class and also posted on the course website. Do this pre-activity and submit it online before coming to quiz section. Beginning with quiz section 2, attendance credit will only be awarded if you have submitted the pre-activity before coming to quiz section. Note: Quiz Section 6 is a take-home exercise that should be submitted in class. There will be no quiz section meeting that week. Eating in class: There are students in our class with severe food allergies. Eating is not permitted in the auditorium; but if you have food with you, please sit in the left-most section facing the podium. Week 1 Th, Oct. 1 Lecture 1 Introduction to genetics; central dogma What do we mean by genetics? Biology as information flow; transcription; translation; looking for ORFs Week 2 Tu, Oct. 6 Lecture 2 Mitosis and meiosis Cell division; cell cycle; chromosomal segregation in mitosis and meiosis Quiz Section 1 Central dogma Problem Set 1 Th, Oct. 8 Lecture 3 QUIZ 1 Chromosomal abnormality and Mendelian genetics and probability I Meiotic nondisjunction; Mendelian ratios; principle of genetic segregation 2

3 Week 3 Tu, Oct. 13 Lecture 4 Mendelian genetics and probability II Product and sum rules; Principle of independent assortment Quiz Section 2 Meiosis Problem Set 2 Th, Oct. 15 Lecture 5 Non-Mendelian inheritance I X-linked inheritance Week 4 Tu, Oct. 20 Lecture 6 Non-Mendelian inheritance II Maternal inheritance; Y-linked inheritance; different types of mutations Quiz Section 3 Mendelian genetics Problem Set 3 Th, Oct. 22 EXAM 1 Week 5 Tu, Oct. 27 Lecture 7 Mutations and complementation Loss of function; gain of function; mutagenesis; complementation Quiz Section 4 Mutagenesis and complementation Problem Set 4 Th, Oct. 29 Lecture 8 Epistasis Genetic interactions and dihybrid ratios 3

4 Week 6 Tu, Nov. 3 Lecture 9 DNA cloning Making a genomic library & other molecular methods Quiz Section 5 Epistasis & molecular techniques Problem Set 5 Th, Nov. 5 Lecture 10 DNA sequencing & PCR DNA sequencing technology; genome sequencing Week 7 Tu, Nov. 10 Lecture 11 Genetic linkage I Testcrosses; genetic linkage; parental and recombinant types Quiz Section 6 No quiz section meeting. Submission of exercise worksheet required for attendance credit. Problem Set 6 Th, Nov. 12 Lecture 12 Genetic linkage II Chi-squared analysis; Constructing genomic maps based on recombination and physical distance; introduction to molecular markers Week 8 Tu, Nov. 17 Lecture 13 Molecular markers ASO, microsatellites, RFLP Quiz Section 7 Genetic mapping Problem Set 7 Th, Nov. 19 EXAM 2 4

5 Week 9 Tu, Nov. 24 Lecture 14 Mapping human genes I Quiz Section 8 Molecular markers Problem Set 8 Th, Nov. 26 NO CLASS (Thanksgiving holiday) Week 10 Tu, Dec. 1 Lecture 15 Mapping human genes II Interpreting and calculating LOD scores Quiz Section 9 Cancer genetics Problem Set 9 Th, Dec. 3 Lecture 16 QUIZ 2 Week 11 Cancer genetics Tu, Dec. 8 Lecture 17 Genetic association studies Case/control studies Quiz Section 10 LOD score analysis Problem Set 10 Th, Dec. 10 Lecture 18 Wrap-up Week 12 (Final exam period ) Wed, Dec. 16 4:30 6:20 pm EXAM 3 5

6 Course Website A course website is available at Much of the material used in lectures will end up on the website, 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. The 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 the course material, the following textbooks will be put on reserve in Odegaard library under this course s listing: Griffiths, A. J. F., Wessler, S. R., Lewontin, R. C., and Carroll, S. B Introduction to genetic analysis. 9th ed. W. H. Freeman and Company, New York, NY. ISBN: Hartwell, L. H., Hood, L., Goldberg, M. L., Reynolds, A. E., Silver, L. M., and Veres, R. C Genetics from genes to genomes. 3rd ed. McGraw-Hill, Boston, MA. ISBN-10: Klug, W. S., Cummings, M. R., Spencer, C. A., and Palladino, M.A Concepts of genetics. 10th ed. Pearson Prentice Hall, Upper Saddle River, NJ. ISBN: Grading The final grade will be determined by quizzes, exams and participation points for lectures and quiz sections. Quizzes and Exams. There will be two quizzes (during lectures 3 & 16) and three exams (two during the quarter and one during finals week). Each quiz is worth 15 points, and each exam is worth 100 points. We will drop your lower quiz score, so there will be a total of 315 points from tests. Exams are not designed to be cumulative, but they will end up being somewhat cumulative because later course material assumes that you understand earlier material. We will allow you to bring handwritten notes on one 4x6 index card, but that really doesn't mean much if you don t understand the material, having notes there won t be much help. We will give you an index card to use; it will be handed out during the lecture before the exam. Class participation points. Each lecture will include several clicker questions. If you attend at least 12 lectures starting from lecture 3, as determined by your participation in answering 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. 6

7 Quiz section participation points. If you attend at least 8 out of the 10 quiz sections, you will receive 10 points. Otherwise, you will receive zero points. (Note that Quiz Section 6 is a takehome exercise and there is no quiz section meeting. You need to submit the exercise in class have your attendance counted.) You must attend your registered section and submit the preactivity online to receive credit. Final grade. The total number of points available is 335 (300 points from exams, 15 points from one quiz, 10 points for class participation, and 10 points for quiz section participation). The curve will be set so that the median score yields roughly a 2.8. The lowest passing grade is set at half the median. Conflict policy. We do not offer make-up quizzes. Our policy is to allow students to schedule a make-up exam, at the instructor s 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 October 6. If an exam is missed for medical or other emergencies without a doctor s note, there will be NO opportunity to take a written make-up exam after the scheduled exam date. The instructor 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 to Frances ([email protected]) within one week after the graded exam was returned to you. We reserve the right to regrade the entire exam, not just the isolated question in contention. 7

8 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 a quiz or exam, the exam in question will be given a zero, which may not be dropped. As a further deterrent to altering exams after they are graded, and as an aid for grading them rapidly, we keep photocopies of student papers. Please refer to the University s Policy on Academic Honesty if you have questions about the code of conduct. Additional Resources Lecture screencasts will be available online through the course website. They are not meant to be a substitute for attending lectures, but are intended to help you in case you missed something in class. Please be aware that university 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. 8