MAT 394 – Forensic DNA Analysis

Fall 2015

Instructor: Dr. Jay Taylor; office: PSA 447; phone: 965-2641; e-mail: jetaylo6@asu.edu
Time: Mondays and Wednesdays 4:35-5:45
Location: LL 230
Office Hours: Wednesdays 11:00-1:00 in PSA 447; also by appointment.
Text: Statistical DNA Forensics: Theory, Methods and Computation (2008) by Wing Kam Fung and Yu-Qing Hu. The lectures will also cover some of the material in the book Weight-of-Evidence for Forensic DNA Profiles (2005) by David Balding; a PDF of this book is available online through the ASU library.

Course Description: This course will provide an introduction to the mathematical and statistical foundations of forensic DNA analysis. After covering background material on probability theory, hypothesis testing, and molecular and population genetics, we will examine four forensic problems that involve genetic data: (1) identification of individuals from DNA samples; (2) maternity and paternity testing; (3) kinship determination; and (4) interpretation of DNA mixtures. In each case, we will see how probabilistic models of genetic processes can be used to assess the evidentiary value of DNA data for a collection of competing hypotheses. Phylogenetic inference will be introduced in the final part of the course, and we will see how gene genealogies can be used to investigate crimes involving domestic animals, wildlife, and infectious disease.

Problem Sets: These will be announced in class and posted at the following link. Solutions will also be posted here a few days after each set is collected.

Essay: You will need to write a short (4-6 page) article on a subject pertinent to forensic genetics. This will be due on 23 Nov and will be read and evaluated by your classmates.

Class Participation: Please attend and actively engage in class. Don't be shy about asking questions or participating.

Grading and Assignments: Grades will be determined by your scores on the problem sets (25%), the essay (25%), a take-home mid-term exam (25%), and the final exam (25%). The usual mapping between percentages and letter grades will be used: 90% and above will guarantee an A, 80% and above will guarantee a B, 70% and above will guarantee a C, etc.

Final Exam: Monday, Dec 7, 2:30 – 4:20 in LL 230.

Lecture notes: These can be found here here.


Date

Topic

Readings, notes and slides

24 Aug

Overview and history of forensic genetics

Balding, p. 1-20; lecture notes

26 Aug

Human Genetics: DNA, chromosomes, and heredity

Jeffreys (2005); slides

31 Aug

Human Genetics: DNA, chromosomes, and heredity


2 Sept

Genetic Markers: STR's and SNP's

Balding, p. 43-54; slides

7 Sept

Labor Day


9 Sept

Genetic Markers: STR's and SNP's

Balding, p. 43-54; slides

14 Sept

Probability I: definitions and properties of probabilities

FH, p. 7-8

16 Sept

Probability II: conditional probabilities and Bayes' formula

FH, p. 9-11

21 Sept

Probability III: random variables; discrete distributions

FH, p. 12-20

23 Sept

Probability IV: continuous distributions; random vectors

lecture notes

28 Sept

Population Genetics I: Hardy-Weinberg equilibrium

FH, p. 23-45; Balding p. 69-75

30 Sept

Population Genetics II: drift and mutation

Balding, p. 56-63

5 Oct

Population Genetics III: structured populations

Balding, p. 63-69

7 Oct

Population Genetics IV: sampling distributions


12 Oct

Fall Break


14 Oct

Identification from DNA profiles: likelihood calculations

FH, p. 35-41; Balding, p. 82-93

19 Oct

Identification from DNA profiles: relatives

FH, p. 42-45; Balding, p. 94-101

21 Oct

Parentage Testing: trios

FH, p. 47-60

26 Oct

Parentage Testing: incorporating data from other relatives

FH, p. 61-68

28 Oct

Parentage Testing: exclusion probabilities

FH, p. 68-76

2 Nov

Kinship Testing: two persons (Midterm distributed)

FH, p. 79-90

4 Nov

Kinship Testing: three persons(Midterm due: solutions)

FH, p. 91-101

9 Nov

DNA Mixtures: examples

FH, p. 113-120

11 Nov

Veteran's Day

FH, p. 121-127

16 Nov

DNA Mixtures: general approach

FH, p. 121-127

18 Nov

Phylogenetic analysis: overview

lecture notes

23 Nov

Phylogenetic analysis: maximum likelihood and Bayesian inference

practical

25 Nov

Phylogenetic analysis: introduction to BEAST

BEAST Manual (2007)

30 Nov

Phylogenetic analysis: interpreting BEAST analyses

Metzker et al. (2002)

2 Dec

Forensic Epidemiology

slides; Rasko et al. (2011)