fundamentals of forensic dna typing
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Chapter 12 DNA Databases. Fundamentals of Forensic DNA Typing. Slides prepared by John M. Butler June 2009. Chapter 12 – DNA Databases. Chapter Summary - PowerPoint PPT PresentationTRANSCRIPT
Fundamentals of Forensic DNA Typing
Slides prepared by John M. ButlerJune 2009
Chapter 12DNA Databases
Chapter 12 – DNA DatabasesChapter Summary
DNA databases in many cases enable successful conclusion to forensic cases without suspects and connection of serial crimes involving biological evidence. Two primary indices exist with forensic DNA databases that are searched against one another: (1) DNA profiles from offenders who have been convicted or in some cases just arrested for a crime, and (2) DNA profiles from crime scene evidence. The Combined DNA Index System (CODIS) is comprised of three levels: the Local DNA Index System (LDIS), the State DNA Index System (SDIS), and the National DNA Index System (NDIS). The U.S. CODIS system utilizes 13 core STR markers while many other national DNA databases use some of the same loci and some additional ones. Missing persons indices also exist and can be used to match unidentified human remains with personal effects or biological relatives of suspected missing persons. Missing persons analysis often involves use of lineage markers, such as Y-chromosome STRs and mitochondrial DNA, to enable expansion of possible biological relatives to serve as reference samples.
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 an accomplice)
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.
No Suspect DNA Cases
• Why look at no suspect cases to examine the value of forensic DNA?
• These cases rely on victim testimony (memory) under duress, thus the most prone to wrongful conviction
• These cases have suspect DNA present a substantial proportion of the time (seminal fluid)
• These cases make use of available tools in the forensic DNA arsenal (crime scene DNA, Y STR, DNA databases)
• No suspect cases are virtually unsolvable prior to the age of forensic DNA
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Sexual Assault Victims
• 366,460 sexual assaults are reported per year in the U.S. (1992-2000 average)
• That is 1000 per day, 42 per hour, or one sexual assault reported every 86 seconds
• Only 1/3 to 1/20 of sexual assaults are reported to police; therefore, this number is very conservative
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Sexual Assaults by Strangers
• 34% of sexual assaults are committed by a stranger (termed a “no suspect” sexual assault, therefore these cases are normally unsolved without DNA)
• Both puzzle pieces of crime scene and database DNA working together
• These are the cases where forensic DNA really shines
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Recidivism (Repeat Offenders)
• 2/3 of the offenders are repeat offenders• The same offenders are committing the
same crimes on new victims
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Number of Offenses per Offender
• The average serial rapist commits 8 sexual assaults prior to apprehension
• 7 offenses per serial sexual offender are now preventable with crime scene DNA done on every case and a current DNA database (8 offenses per serial sexual offender, minus the first offense to risk getting caught)
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Foreign DNA Profiles
• 47.58 % crime scene DNA success rate (% of cases where sperm is found and a male DNA profile is generated)
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Solving Cases
• What level of success can we expect when we put the puzzle pieces of crime scene DNA together with a DNA database?
• 42% DNA database success rate (% of cases where a hit is made to a known offender) and 69% if case to case hits are included (Forensic Science Service – Britain)
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Cost of Crime
• $111,238 cost of crime per offense committed, adjusted from 1995 study to 2003 dollars
• This figure includes the physical injury, hospitalization, lost time at work, counseling, and “pain and suffering”
• No amount has been added for the cost of investigation, prosecution, the justice system, or incarceration
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Let’s put all these pieces together
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
• 366,460 U.S. annual reported sexual assaults
• X
• 34% of sexual assaults are committed by a stranger
• = 124,596 reported “no suspect” sexual assaults
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
• 124,596 reported “no suspect” sexual assaults
• X
• 2/3 of the offenders are repeat offenders
• = 83,056 of no suspect sexual assaults are committed by repeat offenders
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
• 83,056 of no suspect sexual assaults are committed by repeat offenders
• X
• 7 offenses per serial sexual offender are now preventable)
• = 581,392 future sexual assaults that are preventable
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
• 581,392 future sexual assaults that are preventable
• X
• 47.58 % crime scene DNA success rate
• = 276,626 unnecessary victims of preventable sexual assaults
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
• 276,626 unnecessary victims of preventable sexual assaults
• X
• 42% DNA database success rate
• = 116,183 estimated sexual assaults solved
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
• 116,183 estimated sexual assaults solved • X
• $111,238 cost of crime
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
= $12,924,000,000.00 or over
$12.9 Billion saved cost
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Expense to Do Cases
• 366,460 sexual assaults are reported per year in the U.S. (1992-2000 average)
• X• $1000 per case
• = $366 Million
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Return on Investment (ROI)
• $12,924,000,000.00 or over $12.9 Billion saved cost
• $366 Million in annual expense to conduct testing on every reported sexual assault
• Database cost is a “one time cost” in establishing, as we only need one sample per suspect per lifetime
• Annual cost of database aside, the ROI is:
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
Over $35 saved for every $1 expended
That’s a 3500% Return on Investment!
Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime
The Business Case for Using Forensic DNAWorking through these numbers gives the following cost to crime:
366,460 34% = 124,596 reported ‘no suspect’ sexual assaults124,596 2/3 = 83,056 of ‘no suspect’ sexual assaults are committed by repeat offenders83,056 7 = 581,392 future sexual assaults that are preventable58,1392 47.58% = 276,626 unnecessary victims of preventable sexual assaults276,626 42% = 116,183 estimated sexual assaults could be solved with DNA database hits116,183 $111,238 = $12.9 billion saved in terms of costs from prevented crimes
The cost to perform sexual assault testing in every case is approximately $366 million assuming a cost of $1000 per case and working all 366,460 sexual assaults. Thus, the return on investment is over 3500%. For every dollar invested in forensic DNA testing, this analysis shows over $35 would be saved in terms of expense to victims and society.Jo
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Published in Wickenheiser, R.A. (2004) The business case for using forensic DNA technology to solve and prevent crime. J. Biolaw Business 7(3): 34–50
Steps in DNA Analysis
Collection
Extraction
Quantitation
Genotyping
Interpretation of Results
Database Storage & Searching
Steps in DNA Analysis
Combined DNA Index System (CODIS)•Used for linking serial crimes and unsolved cases with repeat offenders
•Convicted offender and forensic case samples
•Launched October 1998
•Requires 13 core STR markers
•Annual Results with NIST SRM required for submission of data to CODIS
No names are associated with DNA profiles uploaded to NDIS An example profile entered for searching:
16,17-17,18-21,22-12,14-28,30-14,16-12,13-11,14-9,9-9,11-6,6-8,8-10,10
Database vs. Databank
• A database is a collection of computer files containing entries of DNA profiles that can be searched to look for potential matches.
• A databank is a collection of the actual samples – usually in the form of a blood sample or buccal swab or their DNA extracts.
Sample Retention
• Most jurisdictions permit the retention of the biological specimen even after the STR typing results have been obtained and the DNA profile entered into the database.
• This sample retention is for quality control purposes (including hit confirmation) and enables testing of additional STRs or other genetic loci should a new technology be developed in the future.
Aspects of a National DNA DatabaseA number of components must be in place before the database can be
established and actually be effective. These include:
• A commitment on the part of each state (and local) government to provide samples for the DNA database – both offender and crime scene samples;
• A common set of DNA markers or standard core set so that results can be compared between all samples entered into the database;
• Standard software and computer formats so that data can be transferred between laboratories and a secure computer network to connect the various sites involved in the database (if more than one laboratory is submitting data);
• Quality standards so that everyone can rely on results from each laboratory.
Three Parts to Forensic DNA Databases
(1) collecting specimens from known criminals or other qualifying individuals as defined by law
(2) analyzing those specimens and placing their DNA profiles in a computer database, and
(3) comparing unknown or ‘Q’ profiles obtained from crime scene evidence with the known or ‘K’ profiles in the computer database
National Level
NDIS(FBI Laboratory)
SDIS(Richmond, Virginia)
SDIS(Tallahassee, Florida)
LDIS(Tampa)
LDIS(Orlando)
LDIS(Broward County)
LDIS(Roanoke)
LDIS(Norfolk)
LDIS(Fairfax)
State Level
Local Level
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Three Tiers of the Combined DNA Index System (CODIS)
NDIS = National DNA Index SystemSDIS = State DNA Index SystemLDIS = Local DNA Index System
Convicted Offender Index
Offenders (N) Crime Samples (C)Forensic Index Arrestee Index
Arrestees (A)
1
2
3
‘Offender Hit’
‘Forensic Hit’
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Primary Searches Conducted
Stages of Forensic DNA ProgressionDescriptionTime FrameStages
Beginnings, different methods tried (RFLP and early PCR)
1985-1995Exploration
Standardization to STRs, selection of core loci, implementation of Quality Assurance Standards
1995-2005Stabilization
Rapid growth of DNA databases, extended applications pursued
2005-2009Growth
Expanding tools available, confronting privacy concerns
The FutureSophistication
Growth of DNA Databases
• Have benefited from significant federal funding over the past five years
• Expanded laws now enable more offenders to be included
• Have effectively locked technology with core STR markers used to generate DNA profiles that now number in the millions
Growth in Numbers of U.S. StatesRequiring DNA Collection for Various Offenses
Offenses Number of States1999 2004 2008
Sex crimes 50 50 50All violent crimes 36 48 50Burglary 14 47 50All felons 5 37 47Juveniles 24 32 32Arrestees/suspects 1 4 14
Sources: http://www.dnaresource.com and http://www.ncsl.org/programs/cj/dnadatabanks.htm
Starting initially with sex crimes, each category has grown in the past decade… burglary, all felons, arrestees…
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Growth in DNA Profiles Present in the U.S. National DNA Database
Year ending Dec 31
Convicted Offender Forensic Arrestee
2000 460,365 22,484 --
2001 750,929 27,897 --
2002 1,247,163 46,177 --
2003 1,493,536 70,931 --
2004 2,038,514 93,956 --
2005 2,826,505 126,315 --
2006 3,977,433 160,582 54,313
2007 5,287,505 203,401 85,072
2008 6,398,874 248,943 140,719Source: CODIS brochure available at http://www.fbi.gov/hq/lab/pdf/codisbrochure2.pdf and FBI Laboratory’s CODIS Unit.
various NDIS indices (cumulative totals by year)
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Hit Counting Statistics (cumulative totals by year)
2000 1,573 507 731 705 (97%) 262001 3,635 1,031 2,371 2,204 (93%) 1672002 6,670 1,832 5,032 4,394 (87%) 6382003 11,220 3,004 8,269 7,118 (86%) 1,1512004 20,788 5,147 13,855 11,991 (87%) 1,8642005 30,455 7,071 21,519 18,664 (87%) 2,8552006 43,156 9,529 32,439 28,163 (87%) 4,2762007 62,059 11,750 49,813 43,305 (87%) 6,5082008 80,948 14,122 66,783 58,304 (87%) 8,479
Year ending Dec 31
Investigations Aided
Forensic Hits
Offender Hits
Within state hits (~87%)
National offender hits
Source: CODIS brochure available at http://www.fbi.gov/hq/lab/pdf/codisbrochure2.pdf and FBI Laboratory’s CODIS Unit.
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Numbers of Investigations Aided with U.S. National DNA Database (NDIS)
1,573 3,6356,670
11,220
20,788
30,455
43,156
62,059
80,948
0
10,000
20,000
30,000
40,000
50,000
60,000
70,000
80,000
90,000
1999 2001 2003 2005 2007 2009
Growth due to funding from the President’s DNA Initiative
Source: FBI Laboratory’s CODIS Unit
Numbers of Offendersin U.S. National DNA Database
460,365750,929
1,247,1631,493,536
2,038,514
2,826,505
3,977,433
5,287,505
6,398,874
0
1,000,000
2,000,000
3,000,000
4,000,000
5,000,000
6,000,000
7,000,000
1999 2001 2003 2005 2007 2009
Growth due to funding from the President’s DNA Initiative
Source: FBI Laboratory’s CODIS Unit
Numbers of Offenders & Arrestees in U.S. National DNA Database
460,365750,929
1,247,1631,493,5362,038,514
2,826,505
4,031,746
5,372,577
6,539,593
0
1,000,000
2,000,000
3,000,000
4,000,000
5,000,000
6,000,000
7,000,000
1999 2001 2003 2005 2007 2009
Growth due to funding from the President’s DNA Initiative
Source: FBI Laboratory’s CODIS Unit
Numbers of Forensic Samples in U.S. National DNA Database
22,484 27,89746,177
70,93193,956
126,315
160,582
203,401
248,943
0
50,000
100,000
150,000
200,000
250,000
300,000
1999 2001 2003 2005 2007 2009
Growth due to funding from the President’s DNA Initiative
Source: FBI Laboratory’s CODIS Unit
CSF1PO
D5S818
D21S11
TH01
TPOX
D13S317
D7S820
D16S539 D18S51
D8S1179
D3S1358
FGAVWA
13 CODIS Core STR Loci
AMEL
AMEL
Sex-typing
Position of Forensic STR Markers on Human Chromosomes
Core
STR
Loc
i for
the
Unite
d St
ates
1997
Additional STR Loci in the Future?
• Will be needed for more complex kinship analyses and extended applications
• Example: Y-STRs needed for familial searching
• Immigration testing often needs more than 13 STRs (25 STRs have been recommended)
Core set of markers(e.g., CODIS 13 STRs)
Past and Present
Future
(a)
(b)
(c)
(d)
Possible scenarios for extending sets of genetic markers to be used in national DNA databases
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Combined DNA Index System (CODIS)
Launched in October 1998 and now links all 50 statesUsed for linking serial crimes and unsolved cases with repeat offendersConvicted offender and forensic case samples along with a missing
persons indexRequires 13 core STR markers>85,000 investigations aided nationwide as of early 2009
Contains more than 7 million DNA profiles
National DNA Index System (NDIS)
http://www.fbi.gov/hq/lab/codis/index1.htm
No names are associated with DNA profiles uploaded to NDIS An example profile entered for searching:
16,17-17,18-21,22-12,14-28,30-14,16-12,13-11,14-9,9-9,11-6,6-8,8-10,10
CODIS DNA Database “Cold Hit”
Mary Frances McDonald, 76, and Madeline "Mattie" Thompson, 73 were violently murdered in McDonald’s flower shop in Suitland (Sept. 2003)
during a robbery/homicide for $60.
No Suspects/Witnesses (DNA evidence from a discarded shirt was taken).
Adam I. Neal, 24 is arrested in Alexandria, VA in the Spring of 2005 for stealing two cars and burglarizing a home… pled guilty in Nov. 2005.
Feb. 14, 2006 - Prince George's police receive word that there was a hit and that the person with the matching DNA was already in jail.
Virginia DNA Database Hits Virginia DNA Database Hits as of 4/30/2007
Types of Crimes Solved Previous Criminal Conviction of Offender Identified
2516
356
671
378
155
655161
606
2716
113253
Source: http://www.dnaresource.com/presentations.html
Post-Expansion
6,008 CASES
69,800 OFFENDERS
Pre-Expansion
1,650 CASES
12,000 OFFENDERS
Oregon DNA Program Growth
0200400600800
1000120014001600
1997 1998 1999 2000 2001 2002 2003 2004 2005
Casework Submissions Annual Growth
0
5000
10000
15000
20000
25000
30000
35000
1997 1988 1999 2000 2001 2002 2003 2004 2005
Offender Sample Submissions Annual Growth
Difference
4,358 CASES57,800 OFFENDERS
Source: http://www.dnaresource.com/presentations.html
Issues and Concerns with DNA Databases
• Privacy concerns
• Sample collection from convicted offenders
• Sample retention
Privacy Protections
• Victim samples not permitted on the national index
• Offender profiles uploaded with state record locater, ONLY
• Offender database access limited to state CODIS Administrator
• FBI encryption and security protections
• States maintain control of all samples and identifying data
• Federal laws and state laws harshly penalize and criminalize improper use of DNA samples
Source: http://www.dnaresource.com/presentations.html
History of Federal U.S. Laws on DNA Databases
Legislation What was Authorized
DNA Identification Act of 1994
FBI receives authority to establish a National DNA Index System (NDIS); NDIS becomes operational in Oct 1998 with 9 states participating
DNA Analysis Backlog Elimination Act of 2000
Authorizes collection of DNA samples from federal convicted offenders
Justice for All Act of 2004
Indicted persons permitted at NDIS, one-time ‘keyboard’ search authorized; accreditation and audit for labs required; expansion to all felonies for federal convicted offenders; requires notification of Congress if new core loci desired
DNA Fingerprint Act of 2005
Arrestees and legally collected samples permitted at NDIS; elimination of one-time ‘keyboard’ search; expansion to arrestees and detainees for federal offenders
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Three Approaches That Have Been Taken When Initial DNA Database Search Failed
• John Doe Warrant – To “stop the clock” on statute of limitations and enable
prosecution when a DNA match is found at a later date
• Familial Searching – Has been used in the UK with some success– A lower stringency search is conducted enabling
close relatives to potentially hit to evidence profile• DNA Dragnets
– Collecting DNA samples from all individuals in a local area through “mass screens”
Partial Matching/Familial Searching
• Current CODIS searching software not designed for partial matches
• Need Y-STRs along with autosomal STR information to help sort through false positive matches obtained with single allele sharing hits
• See Bieber et al. (2006) Finding criminals through DNA of their relatives. Science 312:1315-1316
Comparisons of Q and K DNA Profiles
What if poor quality evidence data is used?
DNA Database Query
Profile 1: 9,13 - 10,11 - ..
Profile 2: 8,11 - 10,12 - ..
Profile 3: 10,11 - 11,12 - ..
Profile 4: 15,16 - 13,13 - ..
Profile 5: 9,10 - 10,10 - ..
Profile 6: 8,14 - 10,13 - ..
Profile 7: 9,12 - 10,11 - ..
Profile 8: 7,15 - 10,12 - ..
Profile 9: 9,13 - 11,11 - ..
Successfulness of Search Depends on Data Quality from Q and K
Evidence Profile (Q): 8,14 - 10,13 - ..
Reference Profiles (K1 to Kn)
What if poor quality references are loaded
on the database?
Questions Posed1) Is this person in the database?2) Is a relative of this person in the database?
Why Y-STRs Are Needed for Familial Searching
8,8 10,10
Autosomal STRs Y-Chromosome STRs
8,108,10
Y-STRs match
For brothers, autosomal STRs may not match at a locus (or even share a single allele)
STRs vs SNPs Article
• Describes challenges with SNPs in terms of mixture detection and interpretation
• Most likely use of SNPs is as ancestry-informative markers (AIMs)
Butler et al. (2007) STRs vs SNPs: thoughts on the future of forensic DNA testing. Forensic Science, Medicine and Pathology 3:200-205.
http://www.ojp.usdoj.gov/nij/pubs-sum/183697.htm
•Report published in Nov 2000
•Asked to estimate where DNA testing would be 2, 5, and 10 years into the future
ConclusionsSTR typing is here to stay for a few years because of DNA databases that have grown to contain millions of profiles
Chapter 12 – Points for Discussion
• What is a cold hit and what steps are needed to follow up on one?
• Why is it important for the CODIS matching algorithm to permit low and moderate stringency matches?