1. Lecture 15: Individual Identity and Paternity Analysis
October 15, 2012

2. Lab 7 Update Corrected instructions for lab 7 are on lab webpage
Up to 3 points extra credit if problem 2 is done correctly
New version of problem 2 can be answered with analysis that most people completed in lab
See lab open hours schedule on lab web page

3. Last Time Interpretation of F-statistics More on the Structure program
Principal Components Analysis
Population assignment

4. Today Population assignment examples
Forensic evidence and individual identity
Introduction to paternity analysis

5. Population Assignment: Likelihood
"Assignment Tests" based on allele frequencies in source populations and genetic composition of individuals
for homozygote AiAi in population l at locus k
Individual likelihood often summarized as:
-log10(P(G|Hn))
Low numbers mean higher probability of Hn
Likelihoods can be plotted against each other
for heterozygote AiAj in population l at locus k
for m loci

6. Population Assignment Example: Wolf Populations in Northwest Territories
Wolf populations sampled on island and mainland populations in Canadian Northwest Territories
Immigrants detected on mainland (black circles) from Banks Island (white circles)
Carmichael et al Mol Ecol 10:2787
-log likelihood from Banks Island
-log likelihood from Mainland

7. Population Assignment Example:Fish Stories
Fishing competition on Lake Saimaa in Southeast Finland
Contestant allegedly caught a 5.5 kg salmon, much larger than usual for the lake
Officials compared fish from the lake to fish from local markets (originating from Norway and Baltic sea)
7 microsatellites
Based on likelihood analysis, fish was purchased rather than caught in lake
Lake Saimaa
Market -

8. Individual Identity: Likelihood
Assume you find skin cells and blood under fingernails of a murder victim
A hitman for the Sicilian mob is seen exiting the apartment
You gather DNA evidence from the skin cells and from the suspect
What is H1 and what is H2?

9. Likelihood ratio for forensic DNA evidence
Matching a suspect to a piece of physical DNA evidence requires comparing likelihoods of two alternative hypotheses:
H1 is that the sample comes from the suspect
H2 is that the sample is from a person unrelated to the suspect
E is the DNA evidence
P(E|H1) =1 if the DNA profile of the suspect matches the DNA profile of the evidence
P(E|H2) is probability of observing the suspect genotype in an unrelated person in the population (i.e., the match probability)

10. Genetic typing in forensics
Highly polymorphic loci provide unique ‘fingerprint’ for each individual
Tie suspects to blood stains, semen, skin cells, hair
Revolutionized criminal justice in last 20 years
Also used in disasters and forensic anthropology
Principles of population genetics must be applied in calculating and interpreting probability of identity

11. Markers in Genetic Typing
Many sets of markers commonly used
Sets of highly polymorphic microsatellites (also called VNTR (Variable Number of Tandem Repeats), STR (Short Tandem Repeat) or SSR (Simple Sequence Repeat)) :
Profiler Plus, SGM Plus, Cofiler, Identifiler, PowerPlex16
Most are amplified in a single multiplex reaction and analyzed in a single capillary
Very high “exclusion power” (ability to differentiate individuals)

12. Match Probability for m loci
Probability of observing a genotype at locus k by chance in population is a function of allele frequencies:
Homozygote
Heterozygote
for m loci
Assumes unlinked (independent loci) and Hardy-Weinberg equilibrium

13. Probability of Identity
Probability 2 randomly selected individuals have same profile at locus k:
Homozygotes
Heterozygotes
for m loci
Exclusion Probability (E):
E=1-P

14. Does the general match probability apply to near relatives?
What if the slimy mob defense attorney argues that the most likely perpetrator is the mob hitman’s brother, who has conveniently “disappeared”?
Does the general match probability apply to near relatives?

15. Probability of identity for full sibs
2 alleles IBD
Homozygotes
2 alleles IBD
1 allele IBD
0 alleles IBD
Heterozygotes
0 alleles IBD
General Probability of Identity for Full Sibs:

16. Probability of identity for full sibs
Probability of identity unrelated individuals
For a locus with 5 alleles, each at a frequency of 0.2:
PID = 0.072
PIDsib = 0.368

17. What is minimum probability of identity for full sibs?

18. Application to bear and wolf populations
Loci
Probability of Identity
Collect anonymous hair samples in wild populations
Populations have high relatedness within restricted areas: family structure
Woods et al. 1999

19. Which allele frequency to use?
Human populations show some level of substructuring
FST generally < 0.03
Challenge is to choose proper ethnic group and account for gene flow from other groups
Illinois Caucasian
Georgia Caucasian
U.S. Black

20. Substructure in human populations
GST is quite high among the 5 major groups of human populations for CODIS microsatellites
Relatively low within groups, but not 0!

21. NRC (1996) recommendations
Use population that provides highest probability of observing the genotype (unless other information is known)
Correct homozygous genotypes for substructure within selected population (e.g., Native Americans, hispanics, African Americans, caucasians, Asian Americans)
No correction for heterozygotes
Homozygotes
Heterozygotes

22. Why is it ‘conservative’ (from the standpoint of proving a match) to ignore substructure for heterozygotes?

23. Example: World Trade Center Victims
Match victims using DNA collected from toothbrushes, hair brushes, or relatives
Exact matches not guaranteed
Allele dropout
Use likelihood to match samples to victims

24. Parentage Analysis: Paternity Exclusion
Determine multilocus genotypes of all mothers, offspring, and potential fathers
Determine paternal gamete by “subtracting” maternal genotype from that of each offspring.
Infer paternity by comparing the multilocus genotype of all gametes to those of all potential males in the population
Assign paternity if all potential males, except one, can be excluded on the basis of genetic incompatibility with the observed pollen gamete genotype
Unsampled males must be considered

25. Paternity Exclusion
YES NO
Locus 1
First step is to determine paternal contribution based on seedling alleles that do not match mother
Notice for locus 3 both alleles match mother, so there are two potential paternal contributions
Male 3 is the putative father because he is the only one that matches paternal contributions at all loci
Locus 2
Locus 3

26. Paternity Exclusion Analysis
Possible outcomes:
Male
Female ?
Consequences:
Only one male cannot be excluded
More than one male cannot be excluded
All males are excluded
Paternity is assigned
Analyze more loci
Conclude there is migration from external sources

27. Probabilities of Paternity Exclusion, Single Locus, 2 alleles, codominant
The paternity exclusion probability is the sum of the probability of all exclusionary combinations
Hedrick 2005
Probability of a falsely accused male of not matching for at least one of m loci:
See Chakraborty et al Genetics 118:527 for a more general calculation of exclusion power

28. Alleles versus Loci
For a given number of alleles: one locus with many alleles provides more exclusion power than many loci with few alleles
10 loci, 2 alleles, Pr = 0.875
1 locus, 20 alleles, Pr=0.898
Uniform allele frequencies provide more power

29. Characteristics of an ideal genetic marker for paternity analysis
Highly polymorphic, (i.e. with many alleles)
Codominant
Reliable
Low cost
Easy to use for genotyping large numbers of individuals
Mendelian or paternal inheritance