evaluating forensic dna evidence: essential elements of a competent defense review forensic...
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Evaluating forensic DNA evidence: essential
elements of a competent defense review
Forensic Bioinformatics (www.bioforensics.com)[email protected]
Dan E. KraneBiological Sciences, Wright State University,
Dayton OH 45435
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Three generations of DNA testing
DQ-alphaTEST STRIPAllele = BLUE DOT
RFLPAUTORADAllele = BAND
Automated STRELECTROPHEROGRAMAllele = PEAK
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DNA content of biological samples:Type of sample Amount of DNA
Blood 30,000 ng/mLstain 1 cm in area 200 ngstain 1 mm in area 2 ng
Semen 250,000 ng/mLPostcoital vaginal swab 0 - 3,000 ng
Hairpluckedshed
1 - 750 ng/hair1 - 12 ng/hair
Saliva
Urine5,000 ng/mL
1 - 20 ng/mL
2
2
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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
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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
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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
5 repeats: AATG AATG AATG AATG AATG
6 repeats: AATG AATG AATG AATG AATG AATG
4 repeats: AATG AATG AATG AATG
3 repeats: AATG AATG AATG
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Reading an electropherogramPeaks correspond to alleles
Electropherogram
D3 vWA FGA
D8 D21 D18
D5 D13 D7
BLUE
GREEN
YELLOW
RED
AmelogeninAmelogeninXX = femaleXY = male
75 100 139
150
160
200 245 300 bpsRed = ROX size standard
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Automated STR Test
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Crime Scene Samples & Reference Samples
Differential extraction in sex assault cases separates out DNA from sperm cells
• Extract and purify DNA
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Extract and Purify DNA
• Add primers and other reagents
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PCR Amplification
Groups of amplified STR products are labeled with different colored dyes (blue, green, yellow)
• DNA regions flanked by primers are amplified
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The ABI 310 Genetic Analyzer:SIZE, COLOR & AMOUNT
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ABI 310 Genetic Analyzer: Capillary Electrophoresis
•Amplified STR DNA injected onto column
•Electric current applied
•DNA separated out by size:
– Large STRs travel slower
– Small STRs travel faster
•DNA pulled towards the positive electrode
•Color of STR detected and recorded as it passes the detector
DetectorWindow
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Profiler Plus: Raw data
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Statistical estimates: the product rule
0.222 x 0.222 x 2
= 0.1
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Statistical estimates: the product rule
= 0.1
1 in 79,531,528,960,000,000
1 in 80 quadrillion
1 in 10 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
x x
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What more is there to say after you have said: “The chance of a
coincidental match is one in 80 quadrillion?”
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What more is there to say after you have said: “The chance of a
coincidental match is one in 80 quadrillion?”
• Two samples really do have the same source
• Samples match coincidentally• An error has occurred
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Sources of ambiguity in DNA testing results
• Mixtures: deconvolution and relatives• Degradation, inhibition• Background noise• Stutter (n+4)• Pull-up• Spikes and blobs
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Opportunities for subjective interpretation?
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Opportunities for subjective interpretation?
D3: 12, 17 vWA: 15, 17 FGA: 22, 26
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Sources of ambiguity in DNA testing results
• Mixtures: deconvolution and relatives• Degradation, inhibition• Background noise• Stutter (n+4)• Pull-up• Spikes and blobs
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Mixed DNA samples
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How many contributors to a mixture if analysts can discard a locus?
How many contributors to a mixture?
Maximum # of alleles observed in a 3 person mixture # of occurrences Percent of cases
2 0 0.00
3 310 0.00
4 2,498,139 5.53
5 29,938,777 66.32
6 12,702,670 28.14
There are 45,139,896 possible different 3-way mixtures of the 648 individuals in the MN BCI database.
8,151
1,526,550
32,078,976
11,526,219
0.02
3.38
71.07
25.53
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Sources of ambiguity in DNA testing results
• Mixtures: deconvolution and relatives• Degradation, inhibition• Background noise• Stutter (n+4)• Pull-up• Spikes and blobs
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Accounting for relatives
0.00%
2.00%
4.00%
6.00%
8.00%
10.00%
12.00%
14.00%
16.00%
18.00%
20.00%
1 3 5 7 9 11 13 15 17 19 21 23
Number of Shared Alleles
Percent of Total
Synthetic
Cousins
Siblings
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Likelihood ratios for allele sharing:
0.00%
10.00%
20.00%
30.00%
40.00%
50.00%
60.00%
70.00%
80.00%
90.00%
100.00%
1 3 5 7 9 11 13 15 17 19 21 23
Number of Shared Alleles
Likelihood
Synthetic
Cousins
Siblings
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Sources of ambiguity in DNA testing results
• Mixtures: deconvolution and relatives• Degradation, inhibition• Background noise• Stutter (n+4)• Pull-up• Spikes and blobs
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Degradation
• 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• Degradation is unusual.
LARGE
SMALL
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Degradation
The Leskie Inquest
• Undegraded samples can have “ski-slopes” too.
• How negative does a slope have to be to an indication of degradation?
• Experience, training and expertise.
• Positive controls should not be degraded.
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Degradation
The Leskie Inquest
• DNA profiles in a rape and a murder investigation match.
• Everyone agrees that the murder samples are degraded.
• If the rape sample is degraded, it could have contaminated the murder samples.
• Is the rape sample degraded?
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Degradation
The Leskie Inquest
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Sources of ambiguity in DNA testing results
• Mixtures: deconvolution and relatives• Degradation, inhibition• Background noise• Stutter (n+4)• Pull-up• Spikes and blobs
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Background noise
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Stutter peaks
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Pull-up (software differences)
Advanced Classic
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“Spikes” and “blobs”
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Spikes and blobs
Peak height
Peak
are
a
spike
blob
Peak Height
Pe
ak
Are
a
Blob: Peak Area / Peak Height > 10 +Spike: Peak Area / Peak Height < 4.5 -Blob: Peak Area / Peak Height > 10 +Spike: Peak Area / Peak Height < 4.5 -
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Resources
• Books– ‘Forensic DNA Typing’ by John M. Butler (Academic Press)
• Internet– Applied Biosystems Website: http://www.appliedbiosystems.com/ (see
human identity and forensics)– Forensic Bioinformatics Website: http://www.bioforensics.com/– 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)– Keith Inman (Forensic Analytical, Haywood, CA)
• Testing laboratories– Technical Associates (Ventura, CA)– Indiana State Police (Indianapolis, IN)
• Other resources– Forensic Bioinformatics (Dayton, OH)