1. JS 196e Forensic Molecular Biology
Welcome and Introductions
Steven Lee- Instructor
Overview of the course
Description- Requirements
Small Groups-Your background, interests
First “case” assignment
Introduction to DNA typing
Why DNA?
Learn the main uses of DNA in Forensics
Progression and Comparison of DNA markers
Overview of DNA typing
Brief History of DNA typing

2. My Background Who am I? Scientist, Teacher and Dad
Consultant -Director of R&D, Biotech (MiraiBio)
Adjunct Prof Chem FIU, Adjunct Prof Biology SFSU
Blessed to have been a mentor to my students
Husband and Dad to 4
Interests: music, running, meditation
How did I get here? Research and Teaching Experience
CA DOJ DNA (94-99), Adjunct SFSU (96- ), Biology UNC (92-94)
SUNYB, AECOM, NYU, Columbia, UCB, UGA
Courses: Mol Genetics, Genetics of Forensic DNA typing (UC Davis), Chem. of DNA typing (Web Based- FIU- F 2001, Sp 2003)
Forensic Experience? All in DNA
CA DOJ DNA Research, Validation and Training
Served on TWGDAM
AFDIL mtDNA QA, ASCLD-LAB certified, AAFS full member, CAC full member
Qualified expert DNA witness

3. Contact Information
Instructor: Dr. Steven Lee, Associate Professor
Office MH 521
Office Hrs: W
Set 20 minute appointments via
Phone

4. Overview of the Course
Course Description: This course covers history, scientific concepts, methods, practices, instrumentation, interpretation, statistics and court issues of forensic DNA analysis via lectures, hands-on activities/laboratories, and videos. Collection, documentation and preservation of biological evidence, bioethics, QA, validation, admissibility and training will also be covered.

5. Course Texts: Required Texts:
Forensic DNA Typing: Biology and Technology Behind STR Markers John Butler PhD ISBN: , 688pp. Academic Press
Forensic DNA Analysis. Rudin, N. and K. Inman. 2nd Edition ISBN: Publisher: CRC Press; 2nd edition (December 21, 2001) 312 pp.
Forensic Biology Laboratory Protocols. Steven Lee. Crime laboratory protocols (publicly available). Protocols will be handed out and utilized for laboratory and hands-on exercises.

6. Required reading and internet materials:
Journal articles and other readings will be accessible at the SJSU library, on reserve or will be accessible on line. Citations and URLs for on line materials will be provided in assignments and on the greensheet. These will include:
Molecular Biology Resource Page:
Protocol Page:
Excellent On-Line Course at Rhodes College in Molecular Biology
Several pages within the course will be assigned as additional reading
Harvard DNA project:
President’s DNA Initiative:
M.A. Jobling, and P. Gill Encoded Evidence: DNA in Forensic Analysis. Nature Reviews. 5:
Kaye, DH and ME. Smith, 2003, Wisc Law Rev - 3:
NIST STRBase:
NCJRS publications -
DOJ links: :
Human Genome Project Links- and others
: and
Genetic Witness: Forensic Uses of DNA Testing, Office of Technology Assessment;
Supplementary Texts (Optional)- Course material may include citations from the following:
Review Readings from:
Molecular Biology of the Gene, 5th Ed., Watson, et al., Pearson/Benjamin Cummings, 2004.
Self-paced Review Material
- DNA as the Genetic Material C2
- Nature of Chemical Bonds- C3, 4
- Protein Structure C 5
- Structure of DNA and RNA C 6 (See Rhodes college page for review of topics on line)
The Evaluation of Forensic DNA Evidence Committee on DNA Forensic Science: An Update, National Research Council 272 pages, 6 x 9, 1996, ISBN National Academies Press- Available on-line for free-
Criminalistics: An Introduction to Forensic Science (College Version), 9/E, Copyright 2007, ISBN , RE. Saferstein, Ph.D, Prentice Hall, 672pp.
Techniques of Crime Scene Investigation, Seventh Edition Barry Fisher. ISBN X, 544 pages. CRC Press

7. Course Format:
The course will include lectures by the instructor and guest lectures including scientists from crime laboratories, hands-on laboratories and activities, discussions, videos, and small-group hands-on activities. If possible, on-line chats and a visit to a crime lab will be scheduled (TBA).

8. Small group formation 2-3 per team Gather emails and phone numbers
Find out the following
1) Name, Year (class), Major
2) Why are you interested in forensic molecular biology?
3) What are your career aspirations?
4) What molecular biology/genetics/biochem courses have you taken?
5) Something special/to remember you

9. Course requirements:
Exams-350 points: Three exams will be given in this course. Exams will be cumulative and will include all material covered up to the date of the exam. Exams may include multiple choice, matching, true/false, short answer, diagrams, drawings and sketches, short essay and/or long essay.
The final will be comprehensive. Exam 1 and exam 2 are both worth 100 points. The final is worth 150points
Exam 1: Mon. 03/05/07
Exam 2: Mon. 04/09/07
Final: 05/21/

10. Quizzes and Small Group Activities
Quizzes on assigned readings, small group activities and other assigned materials will be given during the semester. These will generally be multiple choice, matching, true/false and short answer but may also include essay questions.

11. Hands-on Laboratory Assignments/Reports - 40 points
Laboratories will be held throughout the semester. These will include: Safety, Measurements and Error, Proper collection methods, Microscopy/Presumptive tests, DNA Extractions, Quantification of DNA, multiplex PCR amplification of STRs (autosomal and Y), PAGE vs CE, computer STR data analysis, Mt DNA amplification and sequence analysis, and moot court testimony. Written reports for each of the activities will be required (see general guidelines for reports – handed out). During the semester, at least 1 report from each team will be collected and reviewed. At the end of the semester all laboratory reports entered in notebooks will be collected. Participation will also be considered in the grades.

12. Guidelines for Laboratory Reports:
All reports must contain the following sections: Abstract, Introduction, Materials and Methods, Results, Discussion with Conclusions, References, and Appendices with raw data. In general, documentation of all the activities should be complete enough so that an independent scientist could repeat all of the steps and understand the critical reasoning and analytical interpretation of the data and conclusions of your reports.

13. Guidelines for Laboratory Reports continued
All pages must be numbered, initialed and dated
All data must be inserted in the notebook with tape and sealed as you would evidence.
Report Grading: Reports will be graded using both administrative and technical criteria.

14. Participation point grading- 10 points
For in class and laboratory participation, you will be able to earn 10 points. You will be graded on your participation. For “outstanding” participation, you will be awarded 9-10 points. These will be awarded to students who participate fully each week including being on time, completing all assigned work, actively participating in group activities, providing several comments and questions during the activity/laboratory and on occasion, bringing to light additional information and references relevant to the topic.
For “good” participation, you will be awarded 6-8 points. This level will be achieved by those that are on time most of the time, completing nearly all assigned work, participating some in group activities and providing some comments and questions during the activities. “Fair” participation (some assigned work completed, a few comments or questions made, or students who participate considerably but arrive more than 15 minutes late or leave more than 15 minutes early or those missing 2-3 laboratory sessions) will be awarded 3-5 points. Minimal participation (very little completed work, almost no comments, consistently late arrival or early to leave) will be awarded 1-2 points. Students who are completely silent or are absent more than 4 times from laboratories will receive no participation points.

15. Grading Quizzes/Activities 100 points Exam 1 100 points
Lab Notebooks points
Participation points 10 points
Final exam points
Total required 500 points
Extra Credit A total of 10 points may be granted for additional extra credit small group assignments and other assignments during the semester. Each assignment will be worth 1-2 points each. These extra credit points may be used to augment your final point total.

16. Grading Policies
Make-up exams will not generally be permitted. However, under extraordinary circumstances, with proper documentation and approval by the instructor, a 15 page single-spaced term paper of an instructor assigned topic, may substitute for 1 exam.
A to 500 C to 399.9
A 467 to C 367 to 383.4
A- 450 to C- 350 to 366.9
B to D to 349.9
B 417 to D 317 to 333.4
B- 400 to D- 300 to 316.9
F <300

17. Course Schedule Section 1. Introduction/Overview- History
Basics of Physical and Biolgical Evidence / Collection and Preservation
Biochemistry of blood saliva and semen- Presumptive tests
Introduction to DNA and Basic Human Genetics
The Scientific Basis for DNA typing
DNA Extraction
Section 2
Quantification of DNA
RFLP, PCR
STRs, Repeat Slippage, Mutation Rates
DNA separation technologies: Gels/Capillaries
Section 3
Understanding STR results /Population Statistics- Hardy Weinberg
Databases, familial searching, cold hits, unsolved crimes
Additional DNA markers –mtDNA, Y chromosome markers
Quality Control, Validation, Training Standards
Admissibility, Court Testimony,
Legal and Ethical Implications of DNA testing- Innocence Project
Future of DNA typing
16 weeks- No classes – 03/2603/30 Exams 03/05, 04/09 and Final 05/21-Last class 5/16

18. Full Service Crime Lab Services
Physical Science Unit- chemistry, physics, geology on drugs, glass, paint explosives and soil
Biology Unit- biologist and biochemists conduct serology and DNA testing of biological material (Fluids)
Firearms Unit- Examination of firearms, discharged bullets, cartridge cases, shotgun shells, ammo, and clothing for residues are performed
Document Examination Unit- handwriting and typewriting studies to ascertain authenticity or source
Photography Unit- Digital imaging, IR, UV X ray
Toxicology, Latent Fingerprints, Polygraph, Voiceprint, and Evidence collection units

19. Why DNA? Law Enforcement Criminal Investigation- Casework, Databanks
Reuniting immigrant families- Paternity
Missing persons
Evolutionary, Agricultural and Zoological applications
Assessing genetic diversity
Fingerprinting endangered species and pathogens
Assessing unrelatedness to breed for increasing genetic diversity
Assessing relationships for all biological predictions
Ancient DNA analyses for reconstructing history (how we populated the globe)
Other Human Applications
Making sense of the Human Genome project results- Bioinformatics
Developing rapid medical diagnostics such as those associated with triplet repeat diseases (STRs)- (Moxon et al Sci Amer. 280:94)
Understanding the molecular basis of development, disease and aging
Screening candidates for bone marrow/organ transplants and grafts

20. Human Identity Testing
Forensic cases -- matching suspect with evidence
Paternity testing -- identifying father
Historical investigations
Missing persons investigations
Mass disasters -- putting pieces back together
Military DNA “dog tag”
Convicted felon DNA databases
Forensic phenotype profiling

21. Progression of DNA Typing Markers
RFLP
multilocus VNTR probes
single locus VNTR probes (32P and chemi)
PCR
DQ-alpha (reverse dot blot)
PolyMarker (6 plex PCR; dots for SNPs)
D1S80 (AMP-FLPs)
singleplex STRs with silver staining
multiplex STRs with fluorescent dyes
mtDNA
Y chromosome markers

22. Comparison of DNA Typing Technologies
Speed of Analysis (Technology)
Power of Discrimination (Genetics)
Low
High
Slow
Fast
Markers Used (Biology)
RFLP
Single Locus Probes
Multi-Locus Probes
ABO
blood groups
Multiplex STRs
DQ
single STR
D1S80
mtDNA
PolyMarker

23. Overview of DNA typing Biology Technology Genetics
Sample Obtained from Crime Scene or Paternity Investigation
Biology
DNA
Extraction
DNA
Quantitation
PCR Amplification
of Multiple STR markers
Technology
Separation and Detection of PCR Products
(STR Alleles)
Sample Genotype Determination
Genetics
Comparison of Sample Genotype to Other Sample Results
Generation of Case Report with Probability of Random Match
If match occurs, comparison of DNA profile to population databases

24. Human Identity Testing Involves Comparing DNA Profiles
gender ID A B C D E F G H I J
DNA Size (base pairs)
probability of a random match: ~1 in 3 trillion
Results obtained in less than 5 hours with a spot of blood the size of a pinhead
Simultaneous Analysis of 10 STRs and Gender ID

25. Brief History of DNA Typing
Ray White describes first polymorphic RFLP marker
Alec Jeffreys discovers multilocus VNTR probes
first paper on PCR
FBI starts DNA casework
first STR paper
FSS starts UK DNA database
FBI launches CODIS database

26. Detailed History of Serology and DNA 1
Bloodstains AD
Blood groups 1888
Secretor status 1937

27. Detailed History of Serology and DNA 2

28. Small Group Exercise 1 What samples provide DNA?
DNA can be typed from a number of different types of samples and sources. You have a missing person and there are no known blood samples available as a reference.
In your small groups, list all types of samples you believe will provide DNA typing results that may provide a reference for the missing person. Start with the ones with the highest probability of typing.
You have 10 minutes to complete, review and edit your lists
Be sure that all members of your group sign and print their names and submit the list

29. DNA Chant The subject of the course today (me)
Is simply stated DNA (you)
Sugar-Phosphate backbone chains (me)
Hold the base pairs heres their names (you)
Chorus: AT(me)- AT(you)
GC(me)- GC(you)
ATGC, ATGC (together)
RFLP holy grail
Put bad guys away in jail
PCR can lend a hand
Amplifying those weak bands >Chorus
Blood, saliva, semen too,
Can be used as crucial clues
Fingernails and skin and hair
DNA is everywhere >Chorus

30. Office Hours Policies
Set up 15 minute appointments by
Weds
Benefits (to you and me)
Review the course material.
Show me how hard you are working
Provide feedback
Ask specific questions or Ask for help
Extra credit may be provided for coming to discuss questions on the reading, exams, DNA, assignments, forensics, news articles, department, college and campus scholarships…etc