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

2. 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.

3. 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.

4. 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

5. Sexual Assault Victims
366,460 sexual assaults are reported per year in the U.S. ( 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. $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

19. $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

20. Expense to Do Cases
366,460 sexual assaults are reported per year in the U.S. ( 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

21. Return on Investment (ROI)
$12,924,000, 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

22. 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

23. 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

24. 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

25. 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.

26. 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.

27. 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.

28. 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

29. 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

30. 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’.

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

32. 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

33. 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: and
Starting initially with sex crimes, each category has grown in the past decade… burglary, all felons, arrestees…

34. 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 and FBI Laboratory’s CODIS Unit.

35. 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 and FBI Laboratory’s CODIS Unit.

36. 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

37. 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

38. 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

39. 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

40. 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

41. 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)

42. 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)

43. 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
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

44. 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
Feb. 14, Prince George's police receive word that there was a hit and that the person with the matching DNA was already in jail.

45. 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:

46. 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:

47. Issues and Concerns with DNA Databases
Privacy concerns
Sample collection from convicted offenders
Sample retention

48. 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:

49. 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

50. 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”

51. 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:

52. 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, ,
Profile 2: 8, ,
Profile 3: 10, ,
Profile 4: 15, ,
Evidence Profile (Q): 8, ,
Profile 5: 9, ,
Profile 6: 8, ,
Profile 7: 9, ,
Profile 8: 7, ,
Questions Posed
Is this person in the database?
Is a relative of this person in the database?
Profile 9: 9, ,
What if poor quality references are loaded on the database?
Successfulness of Search Depends on Data Quality from Q and K

53. 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)

54. 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:

55. 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

56. 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?