trueallele ® computing: all the dna, all the time continuing professional development sydney,...
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TrueAllele® Computing: All the DNA, all the time
Continuing Professional DevelopmentContinuing Professional DevelopmentSydney, AustraliaSydney, Australia
March, 2014March, 2014
Mark W Perlin, PhD, MD, PhD Mark W Perlin, PhD, MD, PhD Cybergenetics, Pittsburgh, PACybergenetics, Pittsburgh, PA
Cybergenetics © 2003-2014Cybergenetics © 2003-2014
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DNA genotype
10, 121 2 3 4 5 6 7 8
ACGT
1 2 3 4 5
A genetic locus has two DNA sentences,one from each parent.
locus
Many alleles allow formany many allele pairs. A person's genotype is relatively unique.
motherallele
fatherallele
repeated word
An allele is the numberof repeated words.
A genotype at a locusis a pair of alleles.
9 10
6 7 8 9 101112
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One person, one genotype
7
14
locus
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DNA dataOne or two allele peaks at a locus
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DNA identification pathwayEvidence genotype
Known genotype
10 12
10, 12
10, 12
Lab Infer
Compare
Evidence item
Evidencedata
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Match information
Prob(evidence matches suspect)
Prob(coincidental match)before
data
(population)
after(evidence)
20
=100%
5%
=
At the suspect's genotype,identification vs. coincidence?
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Two people, two genotypes
7
14
10
12
locus
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DNA mixture dataQuantitative peak heights at a locus
peak size
peakheight
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DNA pathway brokenEvidence genotype
Known genotype
???
10, 12
Lab Infer
Compare
Evidence item
Evidencedata
+
7 10 12 14
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Human interpretation issues
Evidence• call good data inconclusive• peaks are too low for them• too many contributors to handle• potential examination bias
Database• hit by association, not by match• comparison: make false hits• restrict upload: lose true hits
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TrueAllele® Casework
Evidence• preserve data information• use all peaks, high or low• any number of contributors• entirely objective, no bias
Database• hit based on LR match statistic• sensitive: find true hits• specific: only true hits
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DNA pathway restoredLab InferEvidence
itemEvidence
data
7 10 12 14
+
Known genotype
10, 10 @ 30%10, 12 @ 50%10, 14 @ 20%
10, 12
Compare
Evidence genotype
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Match information preserved
Prob(evidence matches suspect)
Prob(coincidental match)before
data
(population)
after(evidence)
10
= 50%
5%
=
At the suspect's genotype,identification vs. coincidence?
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Gang DNA from 5 crime scenes
Food mart • gun • hat
Hardware • safe • phone
Jewelry • counter • safe Convenience
• keys • tape
Market • hat 1 • hat 2 • overalls • shirt
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Laboratory DNA processing
• gun • hat • safe • phone • counter • safe • keys • tape • hat 1 • hat 2 • overalls • shirt
10 reference items5 victims • V1 • V2 • V3 • V4 • V55 suspects • S1 • S2 • S3 • S4 • S5
12 evidence itemsScene 1
Scene 2
Scene 3 Scene 4 Scene 5
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Cybergenetics TrueAllele® timeline
Day Activity1 Received evidence data from lab2 Started computer processing4 Replicated evidence results9 Received known references10 Calculated DNA match statistics12 Reported match results to lab
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TrueAllele computer matches
Food mart • gun • hat
Hardware • safe • phone
Jewelry • counter • safe Convenience
• keys • tape
Market • hat 1 • hat 2 • overalls • shirt
Suspects: S1, S2, S3, S4, S5
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DNA match statistic:553 million
People of California v. People of California v. Charles Lewis LawtonCharles Lewis Lawtonand Dupree Donyell Langstonand Dupree Donyell Langston
November, 2012November, 2012Bakersfield, CABakersfield, CA
Admissibility hearingAdmissibility hearingand trial testimonyand trial testimony
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Peer-reviewed validationsPerlin MW, Sinelnikov A. An information gap in DNA evidence interpretation. PLoS ONE. 2009;4(12):e8327.
Perlin MW, Legler MM, Spencer CE, Smith JL, Allan WP, Belrose JL, Duceman BW. Validating TrueAllele® DNA mixture interpretation. Journal of Forensic Sciences. 2011;56(6):1430-47.
Ballantyne J, Hanson EK, Perlin MW. DNA mixture genotyping by probabilistic computer interpretation of binomially-sampled laser captured cell populations: Combining quantitative data for greater identification information. Science & Justice. 2013;53(2):103-14.
Perlin MW, Belrose JL, Duceman BW. New York State TrueAllele® Casework validation study. Journal of Forensic Sciences. 2013;58(6):1458-66.
Perlin MW, Dormer K, Hornyak J, Schiermeier-Wood L, Greenspoon S. TrueAllele® Casework on Virginia DNA mixture evidence: computer and manual interpretation in 72 reported criminal cases. PLOS ONE. 2014:in press.
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Expected match statistic
DNA mixture weight
Number of zerosin the DNA
match statistic
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Specific match statistic
Number of zeros in a nonmatching DNA statistic
Numberof
occurrences
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Computers can use all the dataQuantitative peak heights at locus D8S1179
peakheight
peak size
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People may use less of the data
Threshold
Over threshold, peaks are labeled as allele events
All-or-none allele peaks,each given equal status
Under threshold, alleles vanish
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How the computer thinksConsider every possible genotype solution
Explain thepeak pattern
Better explanationhas a higher likelihood
One person’s allele pair
Another person's Another person's allele pairallele pair
A third person's allele pairA third person's allele pair
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Objective genotype determined solely from the DNA data.
Never sees a reference.
Evidence genotype
51%
1%2%1% 1% 3%
20%
1% 2% 3% 1% 1% 2% 3% 3% 1% 1% 1%1%
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DNA match information
Prob(evidence match)
Prob(coincidental match)
How much more does the suspect match the evidencethan a random person?
8x
51%
6%
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Match information at 15 loci
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Is the suspect in the evidence?
A match between the front counterand Dupree Langston is:
553 million times more probable than a coincidental match to an unrelated Black person
731 million times more probable than a coincidental match to an unrelated Caucasian person
208 million times more probable thana coincidental match to an unrelated Hispanic person
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TrueAllele reinterpretation
Virginia reevaluates DNA evidence in 375 casesJuly 16, 2011
“Mixture cases are their own little nightmare,” says William Vosburgh, director of the D.C. police’s crime
lab. “It gets really tricky in a hurry.”
“If you show 10 colleagues a mixture, you will probably end up with 10 different answers”
Dr. Peter Gill, Human Identification E-Symposium, 2005
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Virginia validation study
• 72 criminal cases• 92 evidence items • 111 genotype comparisons
Criminal offense• 18 homicide• 12 robbery • 6 sexual assault• 20 weapon
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Mixture method comparison
CPI
11.05 (5.42)113 billion
6.83 (2.22)6.68 million
2.15 (1.68)140
mCPI
TrueAllele
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DNA mixture crisis
375 cases/year x 4 years = 1,500 cases320 M in US / 8 M in VA = 40 factor1,500 cases x 40 factor = 60,000 inconclusive
1,000 cases/year x 4 years = 4,000 cases320 M in US / 8 M in NY = 40 factor4,000 cases x 40 factor = 160,000 inconclusive
+ underreporting of DNA match statistics DNA evidence data in 100,000 casesCollected, analyzed & paid for – but unused
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20th century DNA database
Evidence
Allele database
Crime scene
Reference
Allele database
Criminals
Infer &Upload
Match &Report
+
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21st century DNA database
Evidence
Genotype database
Crime scene
Reference
Genotype database
Criminals
Infer &Upload
Match &Report
+
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TrueAllele in criminal trials
Court testimony:• state• federal• military• foreign
Over 150 case reports filed on DNA evidence
Crimes:• armed robbery• child abduction• child molestation• murder• rape• terrorism• weapons
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TrueAllele usage in the US
Casework systemInterpretation servicesAdmissibility hearing
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All the DNA, all the time
Currently used to:• eliminate DNA backlogs• reduce forensic costs• solve crimes• find criminals• convict the guilty• free the innocent• create a safer society
Objective, reliable truth-seeking tool• solves the DNA mixture problem• handles low-copy and degraded DNA• provides accurate DNA match statistics• automates DNA evidence interpretation
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TrueAllele today
Invented math & algorithms 20 years
Developed computer systems 15 years
Support users and workflow 10 laboratories
Used routinely in casework 3 labs
Validate system reliability 20 studies
Educate the community 50 talks
Train & certify analysts 200 students
Go to court for admissibility 5 hearings
Testify about LR results 20 trials
Educate lawyers and laymen 1,000 people
Make the ideas understandable 150 reports
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More TrueAllele information
http://www.cybgen.com/information
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http://www.youtube.com/user/TrueAlleleTrueAllele YouTube channel