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Fundamentals of Forensic DNA Typing

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Chapter 1 Overview Fundamentals of Forensic DNA Typing Slides prepared by John M. Butler June 2009 – PowerPoint PPT presentation

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Title: Fundamentals of Forensic DNA Typing


1
Fundamentals of Forensic DNA Typing
Chapter 1 Overview
  • Slides prepared by John M. Butler
  • June 2009

2
Chapter 1 - Overview
  • Chapter Summary
  • Since its introduction in the mid-1980s,
    forensic DNA testing techniques have enabled
    crime scene evidence to be matched to
    perpetrators with increasing sensitivity and
    speed. An example is used to illustrate how DNA
    analysis aided the investigation of a sexual
    assault committed in Charlottesville, Virginia in
    1999. The role of forensic science and DNA
    testing are considered in the context of the
    criminal justice system. The steps in DNA sample
    processing are briefly reviewed and improvements
    to DNA testing are compared to advances in
    computer technology.

3
News Story on Montaret Davis DNA Database Match
to University of Virginia Student Rape
4
Overview of the Criminal Justice System
  • The criminal justice system consists of three
    broad areas
  • (1) law enforcement, (2) scientific analysis, and
    (3) legal proceedings
  • Detectives or investigators serving in police
    agencies submit evidence collected from crime
    scenes to forensic laboratories. This evidence is
    then compared to suspect reference samples (when
    available) or in the case of DNA or
    fingerprints -- searched against a database of
    previous offenders as performed in the Virginia
    case just described.
  • A scientific report of the analysis of the
    evidence and comparison to the reference samples
    is then produced. This report is used by law
    enforcement and the legal community (prosecutors
    or defense attorneys) to make further decisions
    that may result in the evidence being presented
    in a court of law.

5
Interactions between the Three Components of the
Criminal Justice System
Law Enforcement
Scientific Analysis
Legal Proceedings
Police Agencies (local, state, federal)
Forensic Laboratory
Court System
Legal framework and precedent
Validated scientific tests
Laws and police training
Other Forensic Disciplines
Judge
Investigators/ Detectives
CSI
Prosecution
John M. Butler (2009) Fundamentals of Forensic
DNA Typing, Figure 1.1
DNA Unit DNA Analysts
Defense
Scientific report(s) completed
Conviction or exoneration
Trial
Evidence submitted
Evidence returned
References submitted
Research (introduces new methods)
6
Historical Perspective on DNA Typing
2009 DNA is an important part of the criminal
justice system
www.dna.gov Presidents DNA Initiative (gt600M
from 2004-2008)
2009
2006
Identifiler 5-dye kit and ABI 3100
miniSTRs
2002
2004
Y-STRs
CODIS loci defined
PowerPlex 16 (16 loci in single amp)
1998
2000
STR typing with CE is fairly routine
FSS Quadruplex
1996
1994
First commercial fluorescent STR multiplexes
First STRs developed
mtDNA
1990
1992
Capillary electrophoresis of STRs first described
1985
PCR developed
Multiplex STRs
7
Stages of Forensic DNA Progression
Description
Time Frame
Stages
From John M. Butler (Feb 2009) Presentation at
AAFS session on Envisioning the Future
8
Lessons from the First Case Involving DNA Testing
  • Describes the first use of DNA (in 1986) to solve
    a double rape-homicide case in England about
    5,000 men asked to give blood or saliva to
    compare to crime stains
  • Connection of two crimes (1983 and 1986)
  • Use of DNA database to screen for perpetrator
    (DNA only done on 10 with same blood type as
    perpetrator)
  • Exoneration of an innocent suspect
  • DNA was an investigative tool did not solve the
    case by itself (confession of accomplice)

John M. Butler (2009) Fundamentals of Forensic
DNA Typing, D.N.A. Box 1.2
A local baker, Colin Pitchfork, was arrested and
his DNA profile matched with the semen from both
murders. In 1988 he was sentenced to life for the
two murders.
9
The Innocence Project
http//www.innocenceproject.org
John M. Butler (2009) Fundamentals of Forensic
DNA Typing, D.N.A. Box 1.1
  • Defense attorneys Barry Scheck and Peter Neufeld
    launched the Innocence Project in 1992 at the
    Benjamin N. Cardozo School of Law in New York
    City.
  • The Innocence Project promotes cases where
    evidence is available for post-conviction DNA
    testing and can help demonstrate innocence. The
    fact that truly innocent people have been behind
    bars for a decade or more has promoted
    legislation in a number of states and also at the
    federal level to fund post-conviction DNA
    testing.

10
Basis of DNA Profiling
The genome of each individual is unique (with the
exception of identical twins) and is inherited
from parents Probe subsets of genetic variation
in order to differentiate between individuals
(statistical probabilities of a random match are
used) DNA typing must be performed efficiently
and reproducibly (information must hold up in
court) Current standard DNA tests DO NOT look at
genes little/no information about race,
predisposal to disease, or phenotypical
information (eye color, height, hair color) is
obtained
11
Human Identity Testing
  • Forensic cases -- matching suspect with evidence
  • Paternity testing -- identifying father
  • Mass disasters -- putting pieces back together
  • Historical investigations
  • Missing persons investigations
  • Military DNA dog tag
  • Convicted felon DNA databases

Involves generation of DNA profiles usually with
the same core STR (short tandem repeat) markers
12
Steps in DNA Sample Processing
John M. Butler (2009) Fundamentals of Forensic
DNA Typing, Figure 1.2
13
Suspect developed
Crime committed
Biological material transferred
May match another (K)
Reference (Known) sample K
Evidence (Question) sample Q
Database Search
Steps Involved
Steps Involved
May be Inconclusive due to Lack of Available
Reference
Collection
Collection
Q U A L I T Y A S S U R A N C E
Q U A L I T Y A S S U R A N C E
Exclusion (no match)
Sample Storage
Sample Storage
Serology
Characterization
Q ? K
Extraction
Extraction
Q
K
DNA Profile Comparison
Quantitation
Quantitation
Biology
Amplification
Amplification
Q K
May be Inconclusive due to Forensic Issues
(degradation, mixtures, low levels)
STR Markers
STR Markers
Inclusion (match)
Separation/ Detection
Separation/ Detection
Technology
Data Interpretation
Report (with statistical weight)
Data Interpretation
Statistical Interpretation
Genetics
Court
Plea
Profile put on database
Profile put on database
John M. Butler (2009) Fundamentals of Forensic
DNA Typing, Figure 1.3
14
DNA Testing Requires a Reference Sample
A DNA profile by itself is fairly useless because
it has no context DNA analysis for identity
only works by comparison you need a reference
sample
Crime Scene Evidence compared to Suspect(s)
(Forensic Case) Child compared to Alleged Father
(Paternity Case) Victims Remains compared to
Biological Relative (Mass Disaster ID) Soldiers
Remains compared to Direct Reference Sample
(Armed Forces ID)
15
The Three Possible Outcomes of Evidence
Examination
Suspect Known (K) Sample
Evidence Question (Q) Sample
  • Exclusion (no match)
  • Non-exclusion
  • Match or inclusion
  • Inconclusive result

16
Steps in Forensic DNA Analysis
Usually 1-2 day process (a minimum of 5 hours)
Biology
If a match occurs, comparison of DNA profile to
population allele frequencies to generate a case
report with probability of a random match to an
unrelated individual
Genetics
Technology
17
The Laboratory Report
  • The end result of a forensic examination is a
    laboratory report, which represents a brief
    summary of work conducted by a forensic examiner
    (i.e., DNA analyst).
  • The work represented in a laboratory report is
    based on following standard operating procedures.
    Prior to release of a lab report, data and
    conclusions are vetted through an internal review
    process culminating with a second reviewer and/or
    the DNA technical leader approving the work.
  • A lab report is typically submitted to police
    investigators to describe DNA typing results
    obtained from evidence and reference samples
    submitted. Depending on the results, this report
    may also be used by a prosecuting attorney during
    court proceedings to illustrate that a defendant
    matches (or cannot be eliminated as a possible
    contributor to) DNA evidence from a crime scene.

18
Example Laboratory Report from a DNA Examination
ABC Laboratory Hometown, U.S.A. Report of
Examination Date December 8, 2008 Examiner
Name Sherlock Holmes Unit Forensic Biology Case
File Number 08-3101-042 The specimens listed
below were received in the Forensic Biology unit
under cover of communication dated April 1, 2008
(080412001) and April 15, 2008 (080412312) Q1 Sw
ab from broken, bloodstained glass in window
frame (Item 2) Q2 Swab from keyboard of laptop
computer (Item 7) K1 Blood sample from SUSPECT
1 K2 Buccal swab from SUSPECT 2 This report
contains the results of the serological and
nuclear DNA analyses.
John M. Butler (2009) Fundamentals of Forensic
DNA Typing, D.N.A. Box 1.3
19
Example Laboratory Report from a DNA Examination
Results of Examinations Blood was identified on
specimen Q1. Specimen Q2 was examined for the
presence of blood however, no evidence of blood
was found. Deoxyribonucleic acid (DNA) was
isolated from specimens Q1, Q2, K1 (SUSPECT 1),
and K2 (SUSPECT 2) and subjected to DNA typing by
the polymerase chain reaction (PCR) at the
amelogenin sex typing locus and fifteen (15)
short tandem repeat (STR) loci of the AmpFlSTR
Identifiler PCR Amplification Kit. The DNA typing
results are detailed below
Specimen D8 D21 D7 CSF D3 TH01 D13 D16 D2 D19 VWA TPOX D18 AMEL D5 FGA
Q1 12,14 28,30 9,9 10,10 16,17 6,6 11,14 9,11 22,23 12,14 17,18 8,8 14,16 X,Y 12,13 21,22
Q2 12,14 28,30 9,9 10,10 16,17 6,6 11,14 9,11 22,23 12,14 17,18 8,8 14,16 X,Y 12,13 21,22
K1 12,14 28,30 9,9 10,10 16,17 6,6 11,14 9,11 22,23 12,14 17,18 8,8 14,16 X,Y 12,13 21,22
K2 13,14 30.2,32 8,12 10,12 17,17 6,9 8,12 7,8 23,25 14,14 17,20 8,10 14,17 X,X 11,13 21,25
John M. Butler (2009) Fundamentals of Forensic
DNA Typing, D.N.A. Box 1.3
Based on the typing results from the amelogenin
locus (for sex determination), male DNA is
present in the DNA obtained from specimens Q1,
Q2, and K1 (SUSPECT 1). Based on the STR typing
results and to a reasonable degree of scientific
certainty, the contributor of specimen K1
(SUSPECT 1) is the source of the DNA obtained
from specimens Q1 and Q2. The probability of
selecting an unrelated individual at random
having an STR profile matching the DNA obtained
from the questioned specimens is approximately 1
in 840 trillion from the Caucasian population, 1
in 16 quadrillion from the African American
population, and 1 in 18 quadrillion from the
Hispanic population. The STR typing results for
specimen Q1 will be entered into the Combined DNA
Index System (CODIS) and maintained by the ABC
Laboratory for future comparisons. No further
serological or nuclear DNA examinations were
conducted.
20
Applications for DNA Testing
  • Crime solving matching suspect with evidence
  • Accident victims after airplane crashes
  • Soldiers in war who is the unknown soldier
  • Paternity testing who is the father
  • Immigration testing are two people related
  • Missing persons investigations whose remains
  • Convicted felons databases cases solved

Involves generation of DNA profiles usually with
the same core STR (short tandem repeat) markers
and then MATCHING TO REFERENCE SAMPLE
21
Advantages for STR Markers
  • Small product sizes are generally compatible with
    degraded DNA and PCR enables recovery of
    information from small amounts of material
  • Numerous alleles per locus aid mixture
    interpretation
  • Multiplex amplification with fluorescence
    detection enables high power of discrimination in
    a single test
  • Commercially available in an easy to use kit
    format
  • Uniform set of core STR loci provide capability
    for national (and international) sharing of
    criminal DNA profiles

22
The Future of Forensic DNA Testing
  • Report published in Nov 2000
  • Asked to estimate where DNA testing would be 2,
    5, and 10 years into the future
  • Conclusions
  • STR typing is here to stay for a few years
    because of DNA databases that have grown to
    contain millions of profiles

http//www.ojp.usdoj.gov/nij/pubs-sum/183697.htm
23
Major Historical Events in Forensic DNA Compared
to Timeline for Microsoft Corporation
Year Forensic DNA Science Application Parallel Developments in Biotechnology Microsoft Corporation Chronology
1985 Alec Jeffreys develops multi-locus RFLP probes PCR process first described First version of Windows shipped
1986 DNA testing goes public with Cellmark and Lifecodes in United States automated DNA sequencing with 4-colors first described Microsoft goes public
1988 FBI begins DNA casework with single locus RFLP probes
1989 TWGDAM established NY v. Castro case raises issues over quality assurance of laboratories DNA detection by gel silver-staining, slot blot, and reverse dot blots first described
1990 Population statistics used with RFLP methods are questioned PCR methods start with DQA1 Human Genome Project begins with goal to map all human genes Windows 3.0 released (quality problems) exceeds 1 billion in sales
1991 fluorescent STR markers first described Chelex extraction Windows 3.1 released
John M. Butler (2009) Fundamentals of Forensic
DNA Typing, Table 1.1
24
Major Historical Events in Forensic DNA Compared
to Timeline for Microsoft Corporation
Year Forensic DNA Science Application Parallel Developments in Biotechnology Microsoft Corporation Chronology
1992 NRC I Report FBI starts casework with PCR-DQA1 capillary arrays first described
1993 first STR kit available sex-typing (amelogenin) developed first STR results with CE
1994 Congress authorizes money for upgrading state forensic labs DNA wars declared over FBI starts casework with PCR-PM Hitachi FMBIO and Molecular Dynamics gel scanners first DNA results on microchip CE
1995 O.J. Simpson saga makes public more aware of DNA DNA Advisory Board setup UK DNA Database established FBI starts using D1S80/amelogenin ABI 310 Genetic Analyzer and TaqGold DNA polymerase introduced Windows 95 released
1996 NRC II Report FBI starts mtDNA testing first multiplex STR kits become available STR results with MALDI-TOF and GeneChip mtDNA results demonstrated
1997 13 core STR loci defined Y-chromosome STRs described Internet Explorer begins overtaking Netscape
John M. Butler (2009) Fundamentals of Forensic
DNA Typing, Table 1.1
25
Major Historical Events in Forensic DNA Compared
to Timeline for Microsoft Corporation
Year Forensic DNA Science Application Parallel Developments in Biotechnology Microsoft Corporation Chronology
1998 FBI launches national Combined DNA Index System Thomas Jefferson and Bill Clinton implicated with DNA 2000 SNP hybridization chip described Windows 98 released anti-trust trial with U.S. Justice Department begins
1999 Multiplex STR kits are validated in numerous labs FBI stops testing DQA1/PM/D1S80 ABI 3700 96-capillary array for high-throughput DNA analysis chromosome 22 fully sequenced
2000 FBI and other labs stop running RFLP cases and convert to multiplex STRs PowerPlex 16 kit enables first single amplification of CODIS STRs First copy of human genome completed Bill Gates steps down as Microsoft CEO Windows 2000 released
2001 Identifiler STR kit released with 5-dye chemistry first Y-STR kit becomes available ABI 3100 Genetic Analyzer introduced Windows XP released
2002 FBI mtDNA population database released Y-STR 20plex published Windows XP Tablet PC Edition released
2003 U.S. DNA database (NDIS) exceeds 1 million convicted offender profiles the U.K. National DNA Database passes the 2 million sample mark Human Genome Project completed with the final sequence coinciding with 50th anniversary of Watson-Crick DNA discovery Windows Server 2003 released 64-Bit Operating Systems expand capabilities of software
John M. Butler (2009) Fundamentals of Forensic
DNA Typing, Table 1.1
26
Chapter 1 Points for Discussion
  • What role does a forensic laboratory play in the
    criminal justice system?
  • What are some ways that DNA testing has impacted
    forensic science and the criminal justice system?
  • Discuss some communication skills that might be
    beneficial for a forensic DNA scientist to have
    in interacting with law enforcement and the legal
    community
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