Medical Diagnostics Applications
Intro to Genetics and Molecular Diagnostics
Spring 2010
Syllabus
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The University of Texas at El Paso
College of Health Sciences
Clinical Laboratory Science Program
Winter/Spring 2010
Course:
CLSC
2211: Medical Diagnostic Applications
Molecular Diagnostics
Instructor: William Lewis, M.A., H(ASCP), CLS(NCA)
Instructor Contact Information:
E-Mail Address: wlewis@utep.edu
Cell Phone: 917-347-3167
Schedule: There are NO face-to-face scheduled classes; all instruction will be
computer-based using the UTEP Blackboard learning system and the web
conferencing tool, Illuminate Live. The schedule for submitting assignments and
taking exams is listed under “Course Schedule”.
OFFICE HOURS: There are no scheduled office hours. All appointments
must be scheduled with me via email or by phone. I will respond to you within 8
hours, if between the hours of 7 AM and 6 PM. All meetings will take place in
the Illuminate Live conference room.
COURSE DESCRIPTION
This course will encompass molecular-based diagnostic applications and their use
and interpretation in patient care. Basic mathematical principles and calculations
used in the clinical laboratory will also be discussed. Areas covered will include:
genetics, molecular techniques, laboratory mathematics/statistics, quality control
and quality assurance.
Course goals:
At the end of this course the student will have an understanding of basic
concepts in molecular genetics, learn principles of molecular-based assays
and their importance in the diagnosis of disease.
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To provide the student with basic mathematical principles and calculations
used in clinical laboratory testing as well as those associated with quality
assurance, quality control and method comparison.
To stimulate professional and self-development, thus students will be
successful in their careers and enjoy life-long learning.
Train to develop analytical thinking and problem solving to be able to
identify troubleshoot and discuss laboratory findings.
Instill love and understanding of their profession , ethical responsibility in
order to provide the best health care possible.
Promote the need to engage in their community, professional activities and
civil matters.
COURSE OBJECTIVES:
A. Cognitive
1. State the rules and perform mathematical calculations using/involving
scientific notation.
2. Describe units of measure commonly used in the clinical laboratory in
terms of their relationship to the applicable system of measure and the
relationship of the unit to the system; i.e., measurement of length, weight,
mass and temperature.
3. Recognize, describe major types of solutions; calculate, determine all
components related to dilutions, titers, concentrations and volumes.
4. Define the molarity, normality, mole, molar, molality, equivalent weight
and be able to calculate the above concentrations in solutions.
5. Describe quality assurance and quality control in the clinical laboratory.
Define and calculate various parameters used QA/QC assessment.
6. Plot QC results on a Levy-Jennings chart and evaluate the acceptability of
results using Westgard rules.
7. Compare and contrast systematic and random errors.
8. Apply mathematical calculations to specific clinical areas in the laboratory;
i.e. chemistry, hematology, urinalysis, immunohematology and
microbiology.
9. Describe the phases of the cell cycle.
10. List and Explain the stages of Mitosis.
11. List and explain the stages of meiosis. What is the difference between
mitosis and meiosis?
12. Define the following terms: gene, genotype, phenotype, independent
assortment, allele, codominance, homozygous, heterozygous, mutation.
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13. Understand Mendel‟s laws of independent segregation and random
assortment and how he developed them.
14. Correlate the ideas of dominant and recessive traits.
15. Determine the inheritance pattern of a given trait by examination of the
pedigree analysis.
16. Distinguish between X-linked and autosomal traits and how each is
inherited.
17. Diagram the structure of nitrogen bases, nucleosides and nucleotides.
18. Differentiate between DNA and RNA structures.
19. Describe in detail the processes of replication, transcription and translation
and know the basic mechanism of each.
20. Be familiar with various types of genetic mutations.
21. Understand the cell‟s different mechanisms to correct mutations.
22. Compare and contrast organic, inorganic and solid-phase approaches for
isolating DNA.
23. Explain the principle of electrophoresis as it applies to nucleic acids.
24. Explain what restriction enzymes are.
25. Briefly describe the procedures of Southern blot and Northern blot.
26. List three methods of DNA amplification.
27. Explain the principle of the PCR technique.
28. Describe some of the applications of DNA technology in the Clinical
laboratory.
29. Understand the importance of molecular technology for the diagnosis of
disease.
B. Affective
To show the appropriate responsible behaviors, students will demonstrate:
1. A positive attitude by being prepared for lecture and laboratory sessions
completing assigned tasks on time and displaying self-motivation.
2. Organization by utilizing time effectively, sequencing and prioritizing
tasks for completion with time constraints and maintaining a neat clean
work.
3. Attention to detail by diligently pursuing accuracy and documenting data
accurately and legibly.
4. Problem solving ability by explaining purpose of each step in diagnosis,
interpretation, procedure, recognizing discrepancies in techniques or
procedures and repeating necessary lab tests when necessary.
5. Dependability by following directions, working independently after being
given directions.
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6. Stability and self-confidence by approaching and performing routine tasks
confidently without assistance and maintaining composure.
7. Appropriate interpersonal skills by cooperating and communicating
effectively with classmates and instructors and displaying courteous,
considerate behavior and appropriate appearance.
8. Ethical behavior and integrity by respecting confidentiality of patient
information, complying with professional standards and code of ethics,
adhering to safety policies and abiding by all rules and regulations of the
institution.
Methods of Course Instruction:
All course content is presented in the required textbook, on UTEP‟s Blackboard
on-line course system, Illuminate Live, and other Internet Resources. Blackboard
and e-mail are used for submission of assignments, taking quizzes and exams, as
well as for the instructor's evaluation and comments.
Required Materials:
Students must be able to access on-line materials via a computer with Internet
access, either from home or some other place, such as a library or learning
resource center. High-speed Internet connection such as DSL, RoadRunner,
Fios is preferable to more quickly download information. Visit the UTEP
Blackboard website to see the computer system requirements and for any
software downloads. The schedule (including open lab hours) for the Health
Sciences Computer Lab (Room 109) may be found at:
http://irp.utep.edu/Default.aspx?tabid=40432 or you can contact the ILC at:
College of Health Sciences 109
http://academics.utep.edu/ilc
ilc@utep.edu
747-7211
Required Texts:
Molecular Diagnostics: Fundamentals, methods and clinical Applications.
2007. Buckingham, L., and Flaws M.L. F.A. Davis, Philadelphia, PA.
Lorraine J. Doucette. Mathematics for the Clinical Laboratory. 1st ed. W.B.
Saunders Company. 1997.
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Suggested readings
Recommended books:
An A to Z of DNA Science. 2001. Witherly, J.L., G.P. Perry, and D.L. Leja.
CSHL Press, New York.
DNA Simplified: The Hitchhicker‟s guide to DNA. 1996. D.H. Farkas. AACC
Press, Washingtons, D.C.
Should be available in the UTEP library.
Web sites:
American Society for clinical Laboratory Science ASCLS
American society for Clinical Pathology ASCP
American society for Microbiology ASM
COURSE POLICES:
Class Schedule and Communications: This is an on-line, self paced course and
although there are no on-site classes, UTEP‟s Blackboard provides several built-in
communication tools which will be used for interaction and communication. We will
use a web conferencing tool (Illuminate Live) to meet as a class for 2 hours, once each
week. The meeting schedule will be determined during the first week of class.
I will communicate mainly using the Announcements and Discussions tools. You may
send personal concerns or questions to me using the course email tool. I will reply to
your emails or Discussion board messages within one working day under normal
circumstances.
Grading Information
Exams:
A total of 3 online quizzes and 3 online exams will be given (via
Blackboard) during the semester. All quizzes and exams will be
posted on Fridays at 8:00 AM and must be completed by that
Sunday at 8:00 PM. Please see the “Course Schedule” for exam
dates.
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If you cannot take an exam for a legitimate reason (death, illness
etc.) inform me as soon as possible and we will arrange a future time
for you to access the exam. If you fail to take an exam during the
scheduled time with no notification, 10 points will be deducted from
your make-up exam score. Make-up exams/quizzes, while they may
cover the same material, may differ from the exam/quiz taken by the
rest of the class in organization, format, or specific item data.
Dates of Quizzes / Exams and Material to be covered:
Math Quiz 1 - chapters 1-3 and must be completed by Sunday, 1/31/2010 at 8 pm.
Math Quiz II – chapters 4-6 and must be completed by Sunday, 2/7/2010 at 8 pm.
Math Quiz III – chapters 12-13 and must be completed by Sunday, 2/14/2010 at 8 pm.
Exam I – see „course schedule‟ and must be completed by Sunday, 3/14/2010 at 8 pm.
Exam II – see „course schedule‟ and must be completed by Sunday, 4/4/2010 at 8 pm.
Exam III – see „course schedule‟ and must be completed by Sunday, 5/8/2010 at 8 pm.
Weights
The average of the three quizzes account for 25% of the overall grade.
Each exam will account for 25% of the overall grade. There will be no midterm or final exams.
Grading Criteria
Grades are as follows:
A
90 -100
B
80 -89
C
70 -79
D
60 – 69 *
F
below 60
* If a grade of a D is obtained in this course, the student will not be able to apply
to the CLS Program. A grade of a C or better is required for admission to the
UTEP CLS Program.
Accessing Grades
Students can check their grades by clicking “My Grades” under Course
Tools after the grade for each assessment task is released.
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Online Quizzes/Exams
You can access quizzes/exams by clicking the Assessments link on the course
menu or see the quiz/exam icon on the designated page. Each quiz is timed and
can be accessed only one time within the scheduled time window. Please read the
on-screen instructions carefully before you click “Begin Assessment”. After each
quiz/exam is graded and released, you may go back to the Assessments page and
click “View All Submissions” to review your quiz/exam results.
Attendance
Although there are no on-site classes for this course, the student will be expected
to attend the weekly Illuminate Live class sessions, communicate with the
instructor via email, post communications on the Blackboard Discussion Board at
assigned intervals, and complete all assignments and exams by the deadlines
posted in the Course Schedule.
STUDY TIPS:
1. TIME MANAGEMENT - It is critical that you manage your time
wisely. Plan in advance to study EVERY DAY. Organize yourself by
planning a schedule. In this schedule you may want to record times for
reading, reviewing and studying for tests. Adjust your schedule as the
course progresses. Pace the course workload evenly. Use a study
location free of distractions and review periodically.
2. MAKING USEFUL NOTES - Identify new ideas, summarize main
ideas from lecture or text, create outlines, flow charts, trees, concepts;
underline selectively and rewrite your notes.
3. READING TO LEARN - Determine your purpose for reading;
preview the text (titles, summaries, diagrams); turn titles and headings
into questions; read for main ideas; re-read, visualize, relate; review.
4. STUDY WITH OTHERS - Study groups are one of the best ways of
learning. Review the subject, formulate questions and discuss main
ideas. Share notes and quiz each other for knowledge. Explain what
you have learned to others. Synergism works with people and the
group can inspire individuals to greater achievement and build
confidence.
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5. SEEK COUNSEL - If you are having difficulties, email or call me so
that we can discuss them.
6. STRESS REDUCTION - When taking tests always study several
times and over several days before taking the test. Overnight cramming
produces confusion, anxiety, and poor learning. If you have test
anxiety, learn relaxation techniques to calm yourself so that you can
perform at your best. Make sure you are well nourished and rested.
Take a walk or do other physical activity to release anxiety.
Scholastic Honesty
The University has policies and discipline procedures regarding scholastic dishonesty.
Detailed information is available on the UTEP‟s Dean of Students‟ Guidelines:
http://www.utep.edu/dos/acadintg.htm All students are expected to maintain a high
level of responsibility with respect to academic honesty. Students who violate
University rules on scholastic dishonesty are subject to disciplinary penalties, including
the possibility of failure in the course and/or dismissal from the University. Since such
dishonesty harms the individual, all students and the integrity of the University, policies
on scholastic dishonesty will be strictly enforced.
Academic Integrity
The faculty expects from its students a high level of responsibility and academic
honesty. Because the value of an academic degree depends upon the absolute integrity
of the work done by the student for that degree, it is imperative that a student
demonstrate a high standard of individual honor in his or her scholastic work.
Scholastic dishonesty includes, but is not limited to, statements, acts or omissions
related to applications for enrollment or the award of a degree, and/or the submission as
one‟s own work or material that is not one‟s own. As a general rule, scholastic
dishonesty involves one of the following acts: cheating, plagiarism, collusion and/or
falsifying academic records. Students suspected of academic dishonesty are subject to
disciplinary proceedings.
Plagiarism, especially from the web, from portions of papers for other classes, and from
any other source is unacceptable and will be dealt with under the university‟s policy on
plagiarism (see general catalog for details). This course will use the resources of
turnitin.com, which searches the web for possible plagiarism and is over 90% effective.
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Course Evaluation
As required by UT academic regulations, every student must complete an evaluation for
each enrolled course at the end of the semester. An online instructional assessment form
will be made available for your confidential use. Please look for the course evaluation
link on the course Homepage towards the end of the course.
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Molecular Diagnostics
Class Schedule
Winter/Spring 2010
TBA, one 2 hour session every week
Date
Week of
Jan 19
Jan
25
Room: Illuminate Live Conf.
Topic
Course Introduction, schedule, policies
Chapter 1: Basic Mathematics
Chapter 2: Scientific Notation, exponents and logarithms
Chapter 3: Systems of Measure and Temperature Conversions
Quiz #1 will be posted for chapters 1-3 on Jan. 29th
Feb 1
Chapter 4: Dilutions
Chapter 5 & 6: Solutions, Molarity and Normality
Quiz #2 will be posted for chapters 4-6 on Feb. 5th
Feb
8
Chapter 12: Quality Assurance & Basic Statistical Concepts
Chapter 13: Quality Assurance & Quality Control in the Clinical
Laboratory
Quiz #3 will be posted for chapters 12-13 on Feb. 12th
Feb
15
Intro to Molecular Diagnostics
The Flow of Life
Feb
22
Chemical structure of Nucleic Acids
DNA Structure
RNA Structure
Mar
1
DNA: lab applications, techniques
RNA: lab applications techniques
Mar
8
Exam I will be posted on March 12th
Mar 15
Spring Break
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Mar 22
Proteins
Lab applications and techniques
Mar 29
Specimen Collection
Exam II will be posted on April 2nd
Apr
5
Nucleic Acid extraction
Analysis and characterization of nucleic acids
Apr
12
Amplification techniques
Non-amplification methods
Apr
19
Future Technology
Apr
26
Medical Applications
May 3
Exam III will be posted on May 6th