1. Chris Leibig February 1, 2018 Charles County Public Defender
DNA Interpretation
Chris Leibig
February 1, 2018
Charles County Public Defender

2. How to Read DNA Results
How DNA Results are Subjective
How the Raw Data Can Be Manipulated – Especially in Cases Involving Mixtures

4. DNA
DNA (deoxyribonucleic acid) is commonly referred to as the building block of life. DNA contains everything needed to determine what an individual will look like. DNA is found in skin cells, muscle, brain cells, bone, blood, teeth, hair, saliva, fingernails, urine, feces, organs, tissue and more. DNA is not found in red blood cells, but is found in white blood cells.

5. Short Tandem Repeats (STRs)
The human genome is full of repeated DNA sequences. These repeated sequences come in various sizes and are classified according to the length of the core repeat units, the number of contiguous repeat units, and/or the overall length of the repeat region. DNA regions with short repeat units (usually 2-6 bp in length) are called Short Tandem Repeats (STR). STRs are found surrounding the chromosomal centromere (the structural center of the chromosomes). STRs have proven to have several benefits that make them especially suitable for human identification.
Because of these characteristics, STRs with higher power of discrimination are chosen for human identification in forensic cases on a regular basis. It is used to identify victim, perpetrator, missing persons, and others.

7. LOCI USED IN FORENSIC ANALYSIS
Beginning in 1996, the FBI Laboratory launched a nationwide forensic science effort to establish core STR loci for inclusion within the national database known as CODIS (Combined DNA Index System). The 13 CODIS loci are CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51 and D21S11. These loci are nationally and internationally recognized as the standard for human identification.

8. Each person gets one allele at each locus from mother, one from father
Each person gets one allele at each locus from mother, one from father. PCR testing creates ghost alleles through the magnification process and people can debate what alleles are real. If an allele is too “weak” – below a certain, predefined “optical density”, DFS will not call it real even though it could be real.
DNA CHART

9. TYPES OF SAMPLES Buccal Swab or Drawn Blood Sperm from a scene
Blood from a scene
Other biological material from a scene – urine, skin cells, vaginal fluid, saliva, etc.
DNA TYPING IS THE SAME FOR EACH BIOLOGICAL SAMPLE FOR EACH PERSON

10. DNA TYPING CHART FOR MALE SUSPECT AND FEMALE VICTIM
Locus 1
9,10
11,13
Locus 2
8,9 12
Locus 3
8,10
14, 19
Locus 4
13,17 10
Locus 5
20,22
7,9
Locus 6
15, 21
13, 17
Locus 7
14, 18
16, 19
Locus 8
6, 11
8, 19
Locus 9
10, 13
Locus 10 7
12, 14
Locus 11
5, 11
12, 18
Locus 12 9
9, 10
Locus 13
12, 16
13, 19
Locus 14
8, 10
12, 13
Locus 15
7, 11
Amelogenin
X,X
X,Y

15. The stochastic threshold is the threshold at which the analyst can be confident. that if one peak for a heterozygote is above this threshold, then its sister allele will be present and should be at least above the analytical threshold.   REACTION FOR POWERPLEX® 16 HS AND IDENTIFILERTM PLUS promega.com

16. STOCHASTIC THRESHOLDS
In simple terms, the stochastic threshold means the percentage an “allele” must be (within a certain testing tool) of the largest allele at the locus before a scientist is allowed to call it real. For example:
FGA: 10%
TPOX:12%
CSF1PO: 9%
And so on….

17. DNA TYPING CHART FOR MALE SUSPECT AND FEMALE VICTIM
Locus 1
9,10 (8)(9%)
11,13 (10)(8%)
Locus 2
8,9 12
Locus 3
8,10
14, 19
Locus 4
13,17 (16)(7%) 10
Locus 5
20,22
7,9
Locus 6
15, 21
13, 17
Locus 7
14, 18
16, 19
Locus 8
6, 11(5)(4%)
8, 19
Locus 9
10, 13
Locus 10 7
12, 14
Locus 11
5, 11(9)
12, 18,
Locus 12
9 (15)
9, 10
Locus 13
12, 16
13, 19
Locus 14
8, 10
12, 13
Locus 15
7, 11 (6)(8%)
7, 11
Amelogenin
X,X
X,Y

18. TYPES OF ALLELE RESULTS AT A LOCUS
Single Contributor (Two alleles per locus – anything else is stutter or artifact)
Mixture (Two or more persons – far more complicated. (Three or more alleles at a locus mean at least two persons, five or more, at least three persons, and so on)
Results suggesting allelic dropout (A real allele that should be there is not)

22. IN THE UNITED STATES DISTRICT COURT
FOR THE DISTRICT OF HAWAII
UNITED STATES OF AMERICA,
Plaintiff,
vs.
NAEEM J. WILLIAMS,
Defendant.
CRIM. NO JMS/KSC
“Where the two samples at issue come from different people, however, Pizarro expressed concern that allelic dropout in one sample may lead to a false match that falsely incriminates an innocent defendant. Id. at For example, if the perpetrator is a heterozygous 14, 19 at a particular allele and the 19 is a mutant allele which drops out, the genotype will appear as a homozygous 14, 14. Id. If the defendant is a homozygous 14, 14, however, he will be considered a match at this allele. Although Pizarro recognized that “[w]e have not found reference to this scenario in the literature,” it asserted that “[i]f our conclusions are accurate, the widely held idea that allelic dropout cannot cause false results in a criminal case as long as the same primers/kit are used on both the defendant’s and the perpetrator’s DNA samples is a very serious falsehood based on the improper assumption that the defendant is guilty. Pizarro therefore suggested the scientific community consider null allele recovery where the analyst observes a homozygous genotype that raises the suspicion that a second allele has dropped out.”

23. This seven does not have more optical density than other sevens
Jimmy in the clear – no mixtures. Everything where it should be. (Blue highlight is a homozygotic locus – same allele from mother and father):
SAMPLES
TPOX LOCUS
FGA LOCUS
CSFIPO LOCUS
Pajamas cut-out
8,10
10,12
7,10
Shirt cut-out
10, 12
Underwear cut-out
Buffy Buccal Swab
8.10
Jimmy Buccal Swab
9,11
15 (means 15,15)
7,11
This seven does not have more optical density than other sevens

24. This seven does not have more optical density than other sevens.
Jimmy in the clear and at least one other person in sample along with Buffy:
SAMPLES
TPOX LOCUS
FGA LOCUS
CSFIPO LOCUS
Pajamas cut-out
8,10 (17)(18)
10,12 (21)
7,10
Shirt cut-out
8,10, 17, 18
10, 12, 20, 21
Underwear cut-out
8,10, 17
10,12, 20
Buffy Buccal Swab
8.10
10,12
Jimmy Buccal Swab
9,11
15 (means 15,15)
7,11
This seven does not have more optical density than other sevens.

25. Jimmy, Buffy, and at least one other person included in the samples
TPOX LOCUS
FGA LOCUS
CSFIPO LOCUS
Pajamas cut-out
8,10, 9, 11, 21, 30
10,12, 15
7,10, (11), 9, 6
Shirt cut-out
8,10, 9, (11), (13), (19)
10, 12, 15, 21, 30
7,10, 11, 13, 9, 6
Underwear cut-out
8,10, (11), (13), (19)
Buffy Buccal Swab
8.10
10,12
7,10
Jimmy Buccal Swab
9,11
15 (means 15,15)
7,11
This seven has double the optical density than other sevens

26. Control samples shows, when compared with chart above, that the complex mixture which includes Buffy, Jimmy, and at least one other person is all over the place:
SAMPLES
TPOX LOCUS
FGA LOCUS
CSFIPO LOCUS
Control sample from pajama leg
8,10, 9, 11, 21, 30
10,12, 15
7,10, (110, 9, 6
Control sample from couch
8,10, 9, (11), (13), (19)
10, 12, 15, 21, 30
7,10, 11, 13, 9, 6
Control sample from pillow
8,10, (11), (13), (19)
Buffy Buccal Swab
8.10
10,12
7,10
Jimmy Buccal Swab
9,11
15 (means 15,15)
7,11

27. Underlying Chart from DFS Raw Data Shows: Bolded alleles NEVER PLACED ON FINAL CHART BY SCIENTIST because they were determined to be “stutter” (ghost alleles one number below a real one that appears). Red bolded, however, are not one number below and still called stutter by scientist.

28. They (maybe) should have been called real, meaning that another person is really included in the mixture. DFS makes these subjective, and attackable calls all the time:
SAMPLES
TPOX LOCUS
FGA LOCUS
CSFIPO LOCUS
Pajamas cut-out
8,10, 9, 11, 21, 30
10,12, 15
7,10, (110, 9, 6
Shirt cut-out
8,10, 9, (11), (13), (19)
10, 12, 15, 21, 30
7,10, 11, 13, 9, 6
Underwear cut-out
8,10, (11), (13), (19), (18), (12) (3)
10,12, 15, (6)
7,10, 11, 13, 9, 6, (2)
Buffy Buccal Swab
8.10, (7), (9)
10,12, (11)
7,10, (9)
Jimmy Buccal Swab
9,11, (8), (10)
15 (means 15,15) (14)
7,11

29. Here is how DFS uses protocols to show a deceptive result
Here is how DFS uses protocols to show a deceptive result. Pre-determined optical density for these loci is 10% (of the size of the “real” allele). Green are not called real because they are below the pre-determined optical density of 10%, but are likely real since they are Buffy’s alleles on her own underwear. Pink is called real, placing Jimmy on underwear, even though it is barely above the threshold at 11%. The predetermined OD has no inherent meaning.
SAMPLES
TPOX LOCUS
FGA LOCUS
CSFIPO LOCUS
Pajamas cut-out
8,10, 9, 11, 21, 30
10,12,
7,10
Shirt cut-out
8 (8% OD), 10
12 (6%), 10
7 (9%), 10
Underwear cut-out
8,10, (9) (11%)
10,12
7,10,
Buffy Buccal Swab
8.10
Jimmy Buccal Swab
9,11,
15 (means 15,15)
7,11

30. TPOX FGA
Suspect
9,10
11,12
Victim
16, 20
Victim Roommate
18,19
11,15
Underwear cut out
9, 10, 16, 18, 19, 20, (22)
8, 11,12, 15, 19,

31. TO DO LIST:
Locate the Typing Chart and Conclusions
Locate the Raw Data
Map all uncalled peaks
Find out the Stochastic Thresholds
Map all Alleles on Typing Chart According to Whether They Fall Above or Below Threshold
Form a Theory:
The mixture is more complicated then State suggests (more people in it, etc.)
The mixture is arguably less complicated (for example, client not in it)
State is overly inclusive of client
State is too conservative and leaves out contributors
Move for testing of control samples?
Hire DNA expert to Discuss the Above