Evaluating forensic DNA evidence

1. Evaluating forensic DNA evidence Dan E. Krane Biological Sciences, Wright State University, Dayton OH 45435 Forensic Bioinformatics (www.bioforensics.com) help@bioforensics.com

2. Three generations of DNA testing RFLP AUTORAD Allele = BAND DQ-alpha TEST STRIP Allele = BLUE DOT Automated STR ELECTROPHEROGRAM Allele = PEAK

3. Target Region for PCR A T T G A T C A DNA in the Cell cell chromosome nucleus Double stranded DNA molecule

4. DNA content of biological samples: Type of sample Amount of DNA Blood 30,000 ng/mL 2 stain 1 cm in area 200 ng 2 stain 1 mm in area 2 ng Semen 250,000 ng/mL Postcoital vaginal swab 0 - 3,000 ng Hair plucked 1 - 750 ng/hair shed 1 - 12 ng/hair Saliva 5,000 ng/mL Urine 1 - 20 ng/mL

5. Basic terminology: Genetics • DNA Polymorphism (“many forms”) • Regions of DNA which differ from person to person • Locus (plural = loci) • Site or location on a chromosome • Allele • Different variants which can exist at a locus • DNA Profile • The combination of alleles for an individual

6. Basic terminology: Technology • Amplification or PCR (Polymerase Chain Reaction) • A technique for ‘replicating’ DNA in the laboratory (‘molecular Xeroxing’) • Region to be amplified defined by PRIMERS • Can be ‘color coded’ • Electrophoresis • A technique for separating molecules according to their size

7. STR • Short tandem repeat • Describes a type of DNA polymorphism in which: • a DNA sequence repeats • over and over again • and has a short (usually 4 base pair) repeat unit • A length polymorphism -- alleles differ in their length 3 repeats: AATG AATG AATG 4 repeats: AATG AATG AATG AATG 5 repeats: AATG AATG AATG AATG AATG 6 repeats: AATG AATG AATG AATG AATG AATG

8. BLUE D3 vWA FGA D8 GREEN D21 D18 Amelogenin D5 YELLOW D13 D7 Amelogenin XX = female XY = male 75 100 139 200 245 300 bps 150 RED Red = ROX size standard 160 Electropherogram Reading an electropherogramPeaks correspond to alleles

9. Automated STR Test

10. Crime Scene Samples & Reference Samples Differential extraction in sex assault cases separates out DNA from sperm cells • Extract and purify DNA

11. Extract and Purify DNA • Add primers and other reagents

12. PCR Amplification Groups of amplified STR products are labeled with different colored dyes (blue, green, yellow) • DNA regions flanked by primers are amplified

13. The ABI 310 Genetic Analyzer:SIZE, COLOR & AMOUNT

14. Detector Window ABI 310 Genetic Analyzer: Capillary Electrophoresis • Amplified STR DNA injected onto column • Electric current applied • DNA pulled towards the positive electrode • DNA separated out by size: • Large STRs travel slower • Small STRs travel faster • Color of STR detected and recorded as it passes the detector

15. Profiler Plus: Raw data

16. D3 vWA FGA Am D8 D21 D18 • The type of this sample is: • D3: 16, 17 • vWA: 15, 15 • FGA: 21,23 D5 D13 D7 • Amelogenin: X, Y • D8: 16, 16 • D21: 28, 29 • D18: 14, 19 • D5: 8, 12 • D13: 11, 13 • D7: 10 10 RAW DATA • GENESCAN divides the raw data into a separate electropherogram for each color: • Blue • Green • Yellow • Red • GENOTYPER identifies the different loci and makes the allele calls PROCESSED DATA

17. x 0.222 x 2 Statistical estimates: the product rule 0.222 = 0.1

18. x x 1 in 111 1 in 20 1 in 22,200 x x 1 in 100 1 in 14 1 in 81 1 in 113,400 x x 1 in 116 1 in 17 1 in 16 1 in 31,552 Statistical estimates: the product rule 1 in 10 = 0.1 1 in 79,531,528,960,000,000 1 in 80 quadrillion

19. Profiler Plus D3S1358 VWA FGA AMEL D8S1179 D21S11 D18S51 D5S818 D13S317 D7S820

20. Cofiler D3S1358 D16S539 AMEL TH01 TPOX CSF1PO D7S820

21. Identifiler D8S1179 D7S820 CSF1PO D21S11 D2S1338 D3S1358 TH01 D13S317 D16S539 D19S433 VWA TPOX D18S51 AMEL D5S818 FGA

22. LOOKING AT A DNA REPORT

23. Components of a DNA report • The samples tested • Evidence samples (crime scene) • Reference samples (defendant, suspect) • The lab doing the testing • The test used: • Profiler Plus, Cofiler, Identifiler, mtDNA • The analyst who did the testing • Results and conclusions: • Table of alleles • Narrative conclusions

24. Table of alleles • Some labs include more information than others • Usually includes information about mixed samples • May also include: • Indication of low level results • Indication of results not reported • Relative amounts of different alleles (in mixed samples) • No standard format

25. Narrative conclusions • Indicates which samples match • Includes a statistical estimate • Identifies samples as mixed • May include an ‘identity statement’ i.e., samples are from the same source to a scientific degree of certainty (FBI) • May allude to problems (e.g. interpretative ambiguity, contamination)

26. Looking beneath the report

27. Sources of ambiguity in STR interpretation • Degradation • Allelic dropout • False peaks • Mixtures • Accounting for relatives • Threshold issues -- marginal samples

28. Degradation SMALL LARGE • When biological samples are exposed to adverse environmental conditions, they can become degraded • Warm, moist, sunlight, time • Degradation breaks the DNA at random • Larger amplified regions are affected first • Classic ‘ski-slope’ electropherogram • Peaks on the right lower than peaks on the left

29. Allelic Dropout 1500 Reference sample • Peaks in evidence samples all very low • Mostly below 150 rfu • Peaks in reference sample much higher • All well above 800 rfu • At D13S817: • Reference sample: 8, 14 • Evidence sample: 8, 8 • 14 allele has dropped out -- or has it? • Tend to see with ‘marginal samples’ Evidence sample 150 ?

30. False peaks & machine problems • False peaks: • Contamination • Dye blob • Electrical spikes • Pull-up • Machine problems: • Noise • Baseline instability • Injection failures

31. Mixed DNA samples

32. 0.02 8,151 25.53 11,526,219 71.07 32,078,976 3.38 1,526,550 How many contributors to a mixture if analysts can discard a locus? How many contributors to a mixture? There are 45,139,896 possible different 3-way mixtures of the 648 individuals in the MN BCI database.

33. How many loci must have six or fewer alleles to be confident there were only three contributors? Nine loci are commonly used. No kit tests at more than 16 loci. Approximately 144 loci must be examined for 95% confidence that there were only 3 contributors.

34. Opportunities for subjective interpretation?

35. Opportunities for subjective interpretation? D3: 12, 17 vWA: 15, 17 FGA: 22, 26

36. Opportunities for subjective interpretation?

37. Opportunities for subjective interpretation?

38. Opportunities for subjective interpretation?

39. Opportunities for subjective interpretation?

40. Accounting for relatives

41. Likelihood ratios for allele sharing:

42. Automatically runs GeneScan and GenoTyper • Presents all output in a web page • Performs expert analysis to identify problems • Generates a report detailing all testing issues

44. Genophiler output:

46. Genophiler also flags potential problems for further review:

47. Forensic BioInformatics (bioforensics.com) • Uses Genophiler to generate easily interpreted files • Objectively applies analysis parameters to all samples • Fast turn around times • Efficiently draws attention to problems requiring further review

48. Resources • Books • ‘Forensic DNA Typing’ by John M. Butler (Academic Press) • Internet • Applied Biosystems Website: http://www.appliedbiosystems.com/ (see human identity and forensics) • Promega Website: http://www.promega.com/ (see Genetic Identity) • STR base: http://www.cstl.nist.gov/biotech/strbase/(very useful) • Scientists • Larry Mueller (UC Irvine) • Simon Ford (Lexigen, Inc. San Francisco, CA) • William C. Thompson (UC Irvine) • William Shields (SUNY, Syracuse, NY) • Marc Taylor (Technical Associates, Ventura, CA) • Carll Ladd (Connecticut State Police) • Testing laboratories • Technical Associates (Ventura, CA) • Forensic Analytical (Haywood, CA) • Other resources • Forensic BioInformatics (Dayton, OH)