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Graduate Course Proposal Form Submission Detail - PHC6572

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Current Status: SCNS Liaison Notified of Graduate Council Approval - 2016-06-15
Campus: Tampa
Submission Type: New
Course Change Information (for course changes only):
Comments: In review by OGS; Required for MSPH in Genetic Counc Conc.. Approved; To USF Sys 4/21/16; to SCNS after 4/28/16. Description truncated, needs rev. Emailed 6/15/16. Recd 6/17. Corrected 9/30/16 resubmit to SCNS


  1. Department and Contact Information

    Tracking Number Date & Time Submitted
    5305 2015-10-16
     
    Department College Budget Account Number
    Global Health PH 640800
     
    Contact Person Phone Email
    Rays Jiang 8139744541 Jiang2@health.usf.edu

  2. Course Information

    Prefix Number Full Title
    PHC 6572 Quantitative Genomics and Genetics

    Is the course title variable? N
    Is a permit required for registration? N
    Are the credit hours variable? N
    Is this course repeatable? N
    If repeatable, how many times? 0

    Credit Hours Section Type Grading Option
    3 C - Class Lecture (Primarily) R - Regular
     
    Abbreviated Title (30 characters maximum)
    Quan Genomics & Genetics
     
    Course Online? Percentage Online
    C - Face-to-face (0% online) 0

    Prerequisites

    None.

    Corequisites

    None.

    Course Description

    This course will introduce quantitative genetic and genomic concepts and skills to health students. Through real world case studies and student projects, students will develop effective analytical skills to handle fundamental problems in genomics.


  3. Justification

    A. Please briefly explain why it is necessary and/or desirable to add this course.

    Needed for new program/concentration/certificate

    B. What is the need or demand for this course? (Indicate if this course is part of a required sequence in the major.) What other programs would this course service?

    This will be a required course for the proposed MSPH in Genetic Counseling which will ideally begin admitting new cohorts of students each fall beginning with Fall 2016. Additionally, this course will be required in the proposed sequence to meet the accreditation requirements of the Accreditation Council for Genetic Counseling (ACGC).

    C. Has this course been offered as Selected Topics/Experimental Topics course? If yes, how many times?

    No

    D. What qualifications for training and/or experience are necessary to teach this course? (List minimum qualifications for the instructor.)

    To teach in this course individuals should have a terminal degree in Genomics, Public Health, Biology or related field.


  4. Other Course Information

    A. Objectives

    Week 1: Course introduction and expectations for this skill-based course

    1. Define quantitative genetics and genomics

    2. Explain why genetics, high throughput technology and quantitative skills are important

    Week 2: Understanding population genetics

    3. Learn basic principles of population genetics

    4. Understand Hardy-Weinberg equilibrium.

    5. Learn how to use allele frequencies to study population genetics

    Week 3: Understanding evolutionary genetics

    6. Learn Darwinian evolution in the context of modern genetics

    7. Understand basic phylogeny constructions.

    8. Learn basic principle of Last Common Ancestor (LCA) construction

    Week 4: Understanding how genes and the environment interact

    9. Learn nature vs nurture debate in genetic history

    10. Learn relationships between genotypes and phenotypes

    11. Understand genetic penetrance

    Week 5: Familiarizing students with concept of risk assessment

    12. Learn genetic risks and assessment

    13. Learn Bayesian statistics based genetic risk estimations

    Week 7: Learning comparative genomics

    14. Understand the importance of comparing genomes and other genomic data

    15. Learn methods of measuring sequence divergence

    16. Learn methods of estimating genetic distances

    Week 8: Learning epigenetics and how it is impacting genomics

    17. Learn different aspects of epigenetics in DNA and histone modifications

    18. Understand the difference between genetics and epigenetics

    19. Learn basic methods of studying epigenetics

    Week 9: Learning how genomics are integrated into epidemiology

    20. Understand fundamentals of epidemiology

    21. Learn how genomics are conducted at a population level

    22. Learn the challenges and promises of population genomics

    Week 10: Learning types of genetic variations and analytical methods

    23. Understand different types of genetic variation

    24. Learn how to detect variants in large genomic datasets

    25. Learn how to use variant analysis for health research and disease diagnosis

    Week 11: Learning Quantitative trait analysis

    26. Learn basic principles of quantitative traits analysis

    27. Learn likelihood analysis for multiple loci traits

    28. Learn different types of quantitative traits such as expression quantitative traits

    Week 12: Learning sequencing technology with hands-on experience

    29. Learn how sequencing works in real research setting

    30. Understand how sequencing technology is transforming research and health practices

    31. Learn the work flow of generating genomic data

    Week 13: Gaining skills of genomic sequence analysis

    32. Learn basics of data handling and storage

    33. Learn basic computational pipeline operations for genomics sequences

    34. Learn basic sequence analyzing algorithms for genomics

    Week 14-15: Student initiated learning and presentation

    35. Learn how to design genomic studies

    36. Learn how to integrate different aspects of genetics and genomics

    37. Learn how to handle conflicting data

    38. Learn how to present research data

    B. Learning Outcomes

    Demonstrate and utilize a depth and breadth of understanding and knowledge of genetics and genomics core concepts and principles

    Assess individualsí and relatives probability of conditions with a genetic component or carrier status based on pedigree, test results, and other pertinent information.

    Use relevant knowledge and data based on pedigree analysis, inheritance, genetic epidemiology, quantitative genetic principles, and mathematical calculations.

    Identify and integrate relevant information about environment and lifestyle factors into risk assessment

    C. Major Topics

    Population and quantitative genetics, Use of genetics literature, bioinformatics, and computerized tools, Modalities, methods, and self‐studys of genomic technologies, Risk assessment

    D. Textbooks

    Clark DL & Hartl D (2006) Principles of Population Genetics, Fourth Edition

    Recommended:

    Lesk A (2012) Introduction to Genomics - Arthur Lesk

    Do K-A, Qin S, & Vannucci M (2013) Advances in Statistical Bioinformatics (Cambridge University Press)

    E. Course Readings, Online Resources, and Other Purchases

    N/A

    F. Student Expectations/Requirements and Grading Policy

    Pre-class assignments: 10% (10 points total)

    Class participation: 30% of grade (30 points total)

    Two exams: 40% of grade (2 at 20 points each)

    Workshop and hands-on experiences: 5% (5 points total)

    Student research projects: 15: (14 points total)

    Total points = 100

    Course Grading Scale:

    A = 100-89.5%†††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††

    B = 89.49-79.5%††††††††††††††††††††††††††††††††††††††††††††††††††††††

    C = 79.49-69.5%†††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††††

    D = 69.49-59.5%†††††††††††††††††††††††††††††††††††††††††††††††††††††

    F =

    G. Assignments, Exams and Tests

    1. Pre-class assignments.

    Prior to each class, students will be given a set of 1-3 short questions with reading materials to start their own thinking, reading, and research. These preparations will prepare the students for the topics of each class and help the students to engage in the course materials.

    2. Content lectures, and in class discussions.

    The fundamental topics of quantitative genetics and genomics will be taught in a combination of lecturing and in class discussion. Students will learn the key concepts in a lecturing format; and students will be required to make their own assessment and discussion with each major topic. Students will learn both classical principles and current research.

    3. Two written exams

    A mid-term exam will examine the studentís understanding of basic concepts. A final exam will test the knowledge and skills covered in the course.

    4. Workshop and hands-on experiences

    A workshop will be given with equipment used in real research settings. Students will have the opportunities to learn the workflow of genomic data generation. Students will be required to perform their own basic genomic data analysis.

    5. Student research projects and presentations

    Students will be required to choose their genomics research topics and use their quantitative skills to conduct a student research project. Students will gather genomics data, synthesize their theory and perform proof-of-principle hypothesis testing with quantitative genetics and genomics skills. The final outcome of these student research projects will be presented.

    H. Attendance Policy

    Course Attendance at First Class Meeting Ė Policy for Graduate Students: For structured courses, 6000 and above, the College/Campus Dean will set the first-day class attendance requirement. Check with the College for specific information. This policy is not applicable to courses in the following categories: Educational Outreach, Open University (TV), FEEDS Program, Community Experiential Learning (CEL), Cooperative Education Training, and courses that do not have regularly scheduled meeting days/times (such as, directed reading/research or study, individual research, thesis, dissertation, internship, practica, etc.). Students are responsible for dropping undesired courses in these categories by the 5th day of classes to avoid fee liability and academic penalty. (See USF Regulation Ė Registration - 4.0101,

    http://usfweb2.usf.edu/usfgc/ogc%20web/currentreg.htm)

    Attendance Policy for the Observance of Religious Days by Students: In accordance with Sections 1006.53 and 1001.74(10)(g) Florida Statutes and Board of Governors Regulation 6C-6.0115, the University of South Florida (University/USF) has established the following policy regarding religious observances: (http://usfweb2.usf.edu/usfgc/gc_pp/acadaf/gc10-045.htm)

    In the event of an emergency, it may be necessary for USF to suspend normal operations. During this time, USF may opt to continue delivery of instruction through methods that include but are not limited to: Blackboard, Elluminate, Skype, and email messaging and/or an alternate schedule. Itís the responsibility of the student to monitor Blackboard site for each class for course specific communication, and the main USF, College, and department websites, emails, and MoBull messages for important general information.

    I. Policy on Make-up Work

    All late assignments will be assessed a penalty of 1 point per day. Failure to complete any assignment will not be considered an excuse for being assigned an "I" grade in the course. Exceptions to this policy will be made only in the case of severe illness, documented family emergency, or similar problem.

    Disruption of the academic process and violations of the policies regarding academic integrity will not be tolerated. Review USF policies on Disruption of the Academic Process and the Academic Integrity of Students at:

    http://generalcounsel.usf.edu/regulations/pdfs/regulation-usf3.025.pdf

    Plagiarism will not be tolerated and is grounds for failure. Review USF Academic Dishonesty and Disruption of Academic Process Policy at:

    Undergraduate:

    http://www.ugs.usf.edu/pdf/cat1112/20112012.pdf#page=62

    Graduate:

    http://www.grad.usf.edu/inc/linked-files/USF_Grad_Catalog_2011-2012.pdf#page=39

    The University of South Florida has an account with an automated plagiarism detection service (Turnitin), which allows instructors and students to submit student assignments to be checked for plagiarism. I (the instructor) reserve the right to 1) request that assignments be submitted as electronic files and 2) submit studentsí assignments to Turnitin, or 3) request students to submit their assignments to Turnitin through the course site. Assignments are compared automatically with a database of journal articles, web articles, the internet and previously submitted papers. The instructor receives a report showing exactly how a studentís paper was plagiarized.

    NOTE: An institution may not release a paper to a plagiarism detection software without the studentís prior consent unless all personally identifiable information has been removed, such as a studentís name, social security number, student number, etc.. Note that a paper/essay is considered an educational record and an institution may not ask a student to waive their rights under FERPA for the purpose of submitting papers to a plagiarism detection software.

    For more information about Plagiarism and Turnitin, visit:

    Plagiarism tutorial: http://davon.etg.usf.edu/share/plagiarism/story.html

    Turnitin: http://turnitin.com/en_us/training/student-training/submitting-a-paper

    J. Program This Course Supports

    Master of Science in Public Health (MSPH) Genetic Couseling


  5. Course Concurrence Information



- if you have questions about any of these fields, please contact chinescobb@grad.usf.edu or joe@grad.usf.edu.