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

Fundamentals of Forensic DNA Typing

Slides prepared by John M. Butler

June 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.

http://www.amazon.com/exec/obidos/tg/stores/detail/-/books/0553282816/reader/2/104-0432528-1560754

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


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


Recidivism (Repeat Offenders)

• 2/3 of the offenders are repeat offenders• The same offenders are committing the

same crimes on new victims


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)


Foreign DNA Profiles

• 47.58 % crime scene DNA success rate (% of cases where sperm is found and a male DNA profile is generated)


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)


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


Let’s put all these pieces together


• 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


• 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


• 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


• 581,392 future sexual assaults that are preventable

• X

• 47.58 % crime scene DNA success rate

• = 276,626 unnecessary victims of preventable sexual assaults


• 276,626 unnecessary victims of preventable sexual assaults

• X

• 42% DNA database success rate

• = 116,183 estimated sexual assaults solved


• 116,183 estimated sexual assaults solved

• X

• $111,238 cost of crime


= $12,924,000,000.00 or over

$12.9 Billion saved cost


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


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:


Over $35 saved for every $1 expended

That’s a 3500% Return on Investment!


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 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 States

1999 2004 2008

Sex crimes 50 50 50

All violent crimes 36 48 50

Burglary 14 47 50

All felons 5 37 47

Juveniles 24 32 32

Arrestees/suspects 1 4 14Sources: 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 6,398,874 248,943 140,719

Source: 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%) 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

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



Numbers of Offenders & Arrestees in U.S. National DNA Database

460,365750,929

1,247,1631,493,536

2,038,514

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



Numbers of Forensic Samples in U.S. National DNA Database

22,484 27,89746,177

70,931

93,956

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



CSF1PO

D5S818

D21S11

TH01

TPOX

D13S317

D7S820

D16S539 D18S51

D8S1179

D3S1358

FGA

VWA

13 CODIS Core STR Loci

AMEL

AMEL

Sex-typing

Position of Forensic STR Markers on Human Chromosomes

Core

STR

Loci

for

the U

nit

ed S

tate

s

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 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

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

0

200

400

600

800

1000

1200

1400

1600

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 CASES

57,800 OFFENDERS


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


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

Conclusions

STR 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?

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

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