The DNA Information Pathway

TrueAlleleTrueAllele®® Workshop WorkshopApril, 2013April, 2013

Leicestershire, United KingdomLeicestershire, United Kingdom

Mark W Perlin, PhD, MD, PhD Mark W Perlin, PhD, MD, PhD Cybergenetics, Pittsburgh, PACybergenetics, Pittsburgh, PA

Cybergenetics © 2003-2013Cybergenetics © 2003-2013

Identification

Known reference

Compare

Evidence item

DNA IdentificationEvidence genotype

Known genotype

10 12

10, 12

10, 12

Lab Infer

Compare

Evidence item

Evidencedata

cellcell

nucleusnucleus

chromosomeschromosomes

locus

Short Tandem Repeat (STR)

genotype10, 12

alleles

Genotype

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?

DNA Mixture DataQuantitative peak heights at a locus

peak size

peakheight

Peak Thresholds

Threshold

Under threshold, don't use alleles

Allele Pair7, 77, 107, 127, 14

10, 100%10, 12

10, 1412, 1212, 1414, 14

Simplify data for human review

Allele Dropout

Threshold

Under threshold, use alleles anyway

Allele Pair7, 77, 107, 127, 14

10, 10> 0% 10, 12

10, 1412, 1212, 1414, 14

Conjure phantom peaks

DNA Pathway BrokenEvidence genotype

Known genotype

???

10, 12

Lab Infer

Compare

Evidence item

Evidencedata

+

7 10 12 14

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

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

Validation Studies

Perlin 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.

Perlin MW, Belrose JL, Duceman BW. New York State TrueAllele® Casework validation study. Journal of Forensic Sciences. 2013;58(6):in press.

TrueAllele® Casework

ViewStationUser Client

DatabaseServer

Interpret/MatchExpansion

Visual User InterfaceVUIer™ Software

Parallel Processing Computers

Separate Mixture Contributors

25% 75%

GenotypeThorough: consider every possible genotype solutionObjective: does not know the comparison genotype

Explain thepeak pattern

Betterexplanationhas ahigher likelihood

Victim's allele pair

Another person's Another person's allele pairallele pair

Allele Pair7, 77, 107, 127, 14

10, 1050%10, 12

10, 1412, 1212, 1414, 14

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

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?

Massereene Barracks Attack

PatrickAzimkar

MarkQuinsey

Real Irish Republican Army claimed responsibility

Homicide victims

March 7, 2009 in Antrim, Northern Ireland

Abandoned Burned Car

Touch DNA Evidence

passenger sidesafety belt buckle

cell phone incenter console

match stickat side of road

Data Ambiguity

DNAmixture

low DNAquantity

alleledrop out

D21 D18D8

vWAD3 D18 D2

FGATH01D18no DNAvisible

Much Data,Little Consensus

No Match Statistic

a b c

0 2 1

BrianShivers

Combine DNA Evidence

a

b

c

a

b

c

a b

a

c

singles pairs all threedata

10 20 30

b

c a b c

1.1 million

6.04

STR tests

40,000

4.60

26,000

4.42

560

2.75

25

1.40

27

1.43

6

0.75

Explain All the Data

TH01 locus3 times

test 1

test 2

test 3

Try All Possible Genotypes

TH01 locus3 times

test 1

test 2

test 3

Evidence GenotypeObjective genotype determined

solely from the DNA data. Never sees a suspect.

82%

12%6%

DNA Match Statistic

How much more does the suspect match the evidencethan a random person?

Probability(evidence match)

Probability(coincidental match)6x

13%

82%

Statistic at 10 Loci

A match between the matchstick and Brian Shivers is1.1 million times more probable than coincidence.

Computer's Match Statistics

5.91 trillion

6.01 billion

1.1 million

ColinDuffy

BrianShivers

Admissibility Ruling

I am satisfied that the stage has now been reached in the case of this system where it can be regarded as being reliable and accepted, and I am satisfied that Dr Perlin has given his evidence in a credible and reliable fashion. In the light of these conclusions I can see no basis on which I could properly exercise my discretion … to exclude this evidence, and I therefore admit it in evidence.

December 1, 2011The Honorable Mr. Justice Hart

18 page ruling on TrueAllele, concluding:

World Trade Center AttackSeptember 11, 2001 in New York City, USA

al-Qaeda claimed responsibility

Over 2,700 victims

Identify Victim Remainsbiological material

Identify Missing Peoplebiological material

personaleffects

familyreferences

Match Biological Materialvictim remains missing people

match

Damaged Victim Remains

Damaged Personal Effectsvictim remains missing people

data

a b

ab

bb

1/10

9/10

match

Available Family Referencesvictim remains missing people

ab cc

ac bc?1/2 1/2

geneticmatch

Match Genotypesvictim remains missing people

match

TrueAllele in Criminal Trials

Court testimony:• state• federal• military• foreign

Over 100 case reports filed on DNA evidence

Crimes:• armed robbery• child abduction• child molestation• murder• rape• terrorism• weapons

TrueAllele Information Pathway

Known

Compare

Evidence

Knowns database

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Evidence database

Magazine Reading

Perlin MW. Forensic science in the information age. Forensic Magazine. 2012;9(2):17-21.

Perlin MW, Galloway J. Computer DNA evidence interpretation in the Real IRA Massereene terrorist attack. Evidence Technology Magazine. 2012;10(3):20-23.

Perlin MW. Easy reporting of hard DNA: computer comfort in the courtroom. Forensic Magazine. 2012;9(4):32-37.

Book Chapters

Perlin MW, DNA identification science, in Forensic Sciences, Wecht CH, editor. Albany, NY: LexisNexis® Matthew Bender®; 2012; Chapter 37C.

Perlin MW, The Blairsville slaying and the dawn of DNA computing, in Death Needs Answers: The Cold-Blooded Murder of Dr. John Yelenic, Niapas A, New Kensington, PA: Grelin Press, 2012.

Human-Computer Partnership

Current TrueAllele applications• eliminate DNA backlogs• reduce forensic costs• solve crimes• find criminals• convict the guilty• free the innocent• create a safer society

Objective, reliable truth-seeking computer• solves the DNA mixture problem• handles low-copy and degraded DNA• provides accurate DNA match statistics• automates DNA evidence interpretation

More Information

perlin@cybgen.com

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