Fundamentals of Forensic DNA Typing Chapter 12 DNA Databases Fundamentals of Forensic DNA Typing Slides prepared by John M. Butler June 2009

Chapter 12 – DNA Databases Chapter 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 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 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 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 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 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

$111,238 cost of crime 116,183 estimated sexual assaults solved X Source: Ray Wickenheiser (AAFS 2004 talk) The Business Case for Using Forensic DNA Technology to Solve and Prevent Crime

$12.9 Billion saved cost = $12,924,000,000.00 or over 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 DNA Working through these numbers gives the following cost to crime: 366,460  34% = 124,596 reported ‘no suspect’ sexual assaults 124,596  2/3 = 83,056 of ‘no suspect’ sexual assaults are committed by repeat offenders 83,056  7 = 581,392 future sexual assaults that are preventable 58,1392  47.58% = 276,626 unnecessary victims of preventable sexual assaults 276,626  42% = 116,183 estimated sexual assaults could be solved with DNA database hits 116,183  $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. John M. Butler (2009) Fundamentals of Forensic DNA Typing, D.N.A. Box 12.1 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

No names are associated with DNA profiles uploaded to NDIS Steps in DNA Analysis Steps in DNA Analysis Collection Extraction Quantitation 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 Genotyping Interpretation of Results Database Storage & Searching 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 Database A 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 collecting specimens from known criminals or other qualifying individuals as defined by law 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

Three Tiers of the Combined DNA Index System (CODIS) National Level NDIS (FBI Laboratory) SDIS (Richmond, Virginia) (Tallahassee, Florida) LDIS (Tampa) (Orlando) (Broward County) (Roanoke) (Norfolk) (Fairfax) State Level John M. Butler (2009) Fundamentals of Forensic DNA Typing, Figure 12.1 Local Level Figure 12.1 Schematic of the three tiers in the Combined DNA Index System (CODIS). DNA profile information begins at the local level, or Local DNA Index System (LDIS), and then can be uploaded to the state level, or State DNA Index System (SDIS), and finally to the national level, or National DNA Index System (NDIS). Each local or state laboratory maintains its portion of CODIS while the FBI Laboratory maintains the national portion (NDIS). NDIS = National DNA Index System SDIS = State DNA Index System LDIS = Local DNA Index System

Primary Searches Conducted Convicted Offender Index Offenders (N) Crime Samples (C) Forensic Index Arrestee Index Arrestees (A) 1 2 3 ‘Offender Hit’ ‘Forensic Hit’ John M. Butler (2009) Fundamentals of Forensic DNA Typing, Figure 12.2 Figure 12.2 Primary searches conducted with the three largest indices of the U.S. national DNA database. (1) ‘Offender hit’ produced by conducting a search of offenders against the crime scene samples present in the forensic index. (2) ‘Forensic hit’ from searching DNA profiles in the forensic index against other crime scene profiles looking for serial crimes. (3) Arrestee search against forensic index—usually classified as ‘offender hit’.

Stages of Forensic DNA Progression Time Frame Description Beginnings, different methods tried (RFLP and early PCR) 1985-1995 Exploration Standardization to STRs, selection of core loci, implementation of Quality Assurance Standards 1995-2005 Stabilization Rapid growth of DNA databases, extended applications pursued 2005-2009 Growth Expanding tools available, confronting privacy concerns The Future Sophistication

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. States Requiring DNA Collection for Various Offenses Number of States 1999 2004 2008 Sex crimes 50 All violent crimes 36 48 Burglary 14 47 All felons 5 37 Juveniles 24 32 Arrestees/suspects 1 4 John M. Butler (2009) Fundamentals of Forensic DNA Typing, Table 12.5 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…

Growth in DNA Profiles Present in the U.S. National DNA Database various NDIS indices (cumulative totals by year) 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 6,398,874 248,943 140,719 John M. Butler (2009) Fundamentals of Forensic DNA Typing, Table 12.1 Source: CODIS brochure available at http://www.fbi.gov/hq/lab/pdf/codisbrochure2.pdf and FBI Laboratory’s CODIS Unit.

Hit Counting Statistics (cumulative totals by year) Year ending Dec 31 Investigations Aided Forensic Hits Offender Hits Within state hits (~87%) National offender hits 2000 1,573 507 731 705 (97%) 26 2001 3,635 1,031 2,371 2,204 (93%) 167 2002 6,670 1,832 5,032 4,394 (87%) 638 2003 11,220 3,004 8,269 7,118 (86%) 1,151 2004 20,788 5,147 13,855 11,991 (87%) 1,864 2005 30,455 7,071 21,519 18,664 (87%) 2,855 2006 43,156 9,529 32,439 28,163 (87%) 4,276 2007 62,059 11,750 49,813 43,305 (87%) 6,508 2008 80,948 14,122 66,783 58,304 (87%) 8,479 John M. Butler (2009) Fundamentals of Forensic DNA Typing, Table 12.3 Source: CODIS brochure available at http://www.fbi.gov/hq/lab/pdf/codisbrochure2.pdf and FBI Laboratory’s CODIS Unit.

Numbers of Investigations Aided with U.S. National DNA Database (NDIS) Growth due to funding from the President’s DNA Initiative Source: FBI Laboratory’s CODIS Unit

Numbers of Offenders in U.S. National DNA Database 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 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 Growth due to funding from the President’s DNA Initiative Source: FBI Laboratory’s CODIS Unit

Position of Forensic STR Markers on Human Chromosomes 13 CODIS Core STR Loci TPOX 1997 D3S1358 TH01 D8S1179 D5S818 VWA FGA Core STR Loci for the United States D7S820 CSF1PO AMEL Sex-typing D13S317 D16S539 D18S51 D21S11

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)

Possible scenarios for extending sets of genetic markers to be used in national DNA databases Core set of markers (e.g., CODIS 13 STRs) (a) Past and Present John M. Butler (2009) Fundamentals of Forensic DNA Typing, Figure 18.1 (b) Future (c) Figure 18.1 Possible scenarios for extending sets of genetic markers to be used in national DNA databases. (a) A core set of markers have been established for past and present DNA profiles now numbering in some cases in the millions of profiles (e.g., in the U.S., 13 CODIS core STR loci). Three future scenarios exist: (b) keep all of the current core loci and add some additional supplemental loci (e.g., Identifiler or PowerPlex 16 add two additional STRs), (c) only retain some of the current core loci and add more additional supplemental loci, or (d) abandon the previous genetic markers and have no overlap with current core loci. (d)

National DNA Index System (NDIS) 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 http://www.fbi.gov/hq/lab/codis/index1.htm Combined DNA Index System (CODIS) Launched in October 1998 and now links all 50 states Used for linking serial crimes and unsolved cases with repeat offenders Convicted offender and forensic case samples along with a missing persons index Requires 13 core STR markers >85,000 investigations aided nationwide as of early 2009 Contains more than 7 million DNA profiles

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 as of 4/30/2007 356 2716 253 671 113 155 2516 378 606 655 161 Types of Crimes Solved Previous Criminal Conviction of Offender Identified Source: http://www.dnaresource.com/presentations.html

Oregon DNA Program Growth Casework Submissions Annual Growth Offender Sample Submissions Annual Growth Pre-Expansion 1,650 CASES 12,000 OFFENDERS Post-Expansion 6,008 CASES 69,800 OFFENDERS Difference 4,358 CASES 57,800 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 John M. Butler (2009) Fundamentals of Forensic DNA Typing, Table 12.4

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 Reference Profiles (K1 to Kn) 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 - .. Evidence Profile (Q): 8,14 - 10,13 - .. Profile 5: 9,10 - 10,10 - .. Profile 6: 8,14 - 10,13 - .. Profile 7: 9,12 - 10,11 - .. Profile 8: 7,15 - 10,12 - .. Questions Posed Is this person in the database? Is a relative of this person in the database? Profile 9: 9,13 - 11,11 - .. What if poor quality references are loaded on the database? Successfulness of Search Depends on Data Quality from Q and K

Why Y-STRs Are Needed for Familial Searching Autosomal STRs Y-Chromosome STRs 8,10 8,10 8,8 10,10 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.

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

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?