1. How TrueAllele ® Works (Part 2) Degraded DNA and Allele Dropout Cybergenetics Webinar November, 2014 Mark W Perlin, PhD, MD, PhD Cybergenetics, Pittsburgh, PA Cybergenetics © 2003-2014

3. Commonwealth v. Lyons homicide: DNA mixture evidence Victim's blood spatter pulsating spray from severed carotid artery 70% victim 30% other

4. Copy DNA with PCR Copy intact DNA

5. Degraded DNA Can’t copy broken DNA break

6. Longer molecules copy less With degradation, a longer DNA molecule has a greater chance of having a break

7. Break density & copy probability the break density p = Pr(break at a nucleotide) q = Pr(no break at a nucleotide) = 1 – p q n = Pr(no break in n nucleotides) the copy probability

8. Decay factor λ pqλ100200400n 1/2.0001.000.0001.000 ∞.001.999.001.904.819.670693.002.998.002.819.670.450346.005.995.005.606.367.135138.010.990.010.366.134.01869 copy probabilitybreak density

9. DNA decay curve DNA size Observed DNA With degradation, a longer DNA molecule makes fewer DNA copies half length signal decay λ =.0035 n 1/2 = 200 (100 bp)

10. Reduced match information Degraded DNA Lower peak height Greater data variation More genotype uncertainty Diffused genotype probability Reduced match information

11. Differential mixture degradation computer separates decay curves

12. Affects mixture weight, genotypes

13. Degraded mixture separation Degraded other DNA Victim DNA likelihood priorposterior

14. Mixture weight separation w 2 = 30%w 1 = 70%30:70 vs 15:85 likelihood priorposterior

15. likelihood priorposterior Genotype separation

16. Information comparison A match between the suspect and the evidence is a trillion times more probable than coincidence. (TrueAllele solving for degradation) A match between the suspect and the evidence is a billion times more probable than coincidence. (TrueAllele not solving for degradation) Combined probability of inclusion of 42 thousand. (Human review with thresholds)

17. Likelihood ratio 9 ban 12 ban

18. Hierarchical mixture modeling template weight locus weights WkWk W k,1 W k,2 W k,N … k th contributor W0W0 prior probability experiment data d k,1 d k,2 d k,N …

20. Allele dropout 713 An allele present in a contributor genotype is not seen as a peak in the STR data. ?

21. Genotype modeling Compare patterns: fixed data vs possible explanations

22. Faithful data 2022

23. Genotype & LR 22

24. Imbalanced data 1012

25. Genotype & LR 1.5

26. Drop out data 713

27. Genotype & LR.35

28. TrueAllele result, but no CPI log(LR) Count YESNO Locus free of drop-out or imbalance? 0.659 (0.664) N = 68 – 0.755 (0.346) N = 29 How inclusion interpretation of DNA mixture evidence reduces identification information. Perlin MW, Dormer K, Hornyak J, Meyers T, Lorenz, W, American Academy of Forensic Sciences, Washington, DC, 2013.

29. Separating truth from noise Simple two person mixture, 10% minor contributor An investigation of software programs using “semi-continuous” and “continuous” methods for complex DNA mixture interpretation. Coble M, Myers S, Klaver J, Kloosterman A, Leiden University, The Netherlands, 9th International Conference on Forensic Inference and Statistics, 2014.

30. Separating truth from noise Simple two person mixture, 10% minor contributor Threshold and drop parameter An investigation of software programs using “semi-continuous” and “continuous” methods for complex DNA mixture interpretation. Coble M, Myers S, Klaver J, Kloosterman A, Leiden University, The Netherlands, 9th International Conference on Forensic Inference and Statistics, 2014.

31. How TrueAllele Works perlin@cybgen.com http://www.cybgen.com/information/webinar/page.shtml Part 1, 16-Oct-2014 Genotype modeling and the likelihood ratio Part 2, 20-Nov-2014 Degraded DNA and allele dropout Part 3, 18-Dec-2014 Kinship, paternity and missing persons