KENYATTA UNIVERSITY

SBC 235: Forensic biology 2

Department of Biochemistry, Microbiology

& Biotechnology
Ojolapatrick@[Link]
Semester-Ii 2023/2024
 Examples of DNA in the News
• Saddam Hussein Identification
• Source of Cow with “Mad cow” Disease
• Scot Peterson Murder Trial
• Identification of WTC Victims
• “Thomas Jefferson fathered slave’s children”
 December 14, 2003

“We got him!”

DNA Profile

Saddam Hussein’s
capture verified with
DNA testing

Source: [Link]; The Scientist Dec 19, 2003

 “A Forensic Paternity Test”
Captured December 13, 2003

Y-chromosome tests were also

used to verify male lineage…

Portion of DNA Profile

Suspected
Saddam

From Son #1
Killed
July 22, 2003 From Son #2

DNA Used as the Ultimate Biometric

for Confirming Saddam’s Identity
Source: [Link] Uday and Qusay Hussein
 Our DNA Comes from our Parents

Father’s Mother’s
Sperm Egg

Child’s Cell
Genetic Inheritance Pattern of
DNA Profiles

DAD

CHILD

MOM
 PATERNITY TESTING
Family Inheritance of STR Alleles (D13S317)
PCR product size (bp)

11 14
Results Father
Me
Resultsof
ofDNA
DNATests
Tests
Impact
ImpactFamilies
Families
12 14
Child #1

8 14
Child #2

11 12
Child #3

8 12
Mother
 PATERNITY TESTING
Family Inheritance of STR Alleles (D13S317)
PCR product size (bp)

11 14
Father
Me

12 14
Amanda
Child #1

8 14
Child
Marshall
#2

11 12
Child
Katy#3

8 12
Mother
My Wife
 Historical Investigation DNA Study
(Matching Relatives to Remains or Relatives to Relatives)
Thomas Jefferson Failure
Failure to to
II Exclude
Exclude Jefferson
Jefferson
Field Jefferson Peter Jefferson as
as Eston
Eston Hemings’
Hemings’
Father
Father
President Thomas Woodson

Thomas
?
Jefferson
Eston Hemings

Genetic Genealogy Companies

Different Y
Haplotype
Same Y
Jefferson Haplotype
Jefferson Y Haplotype
Nature article (Nov
Y Haplotype 1998)
Butler, J.M. (2001) Forensic DNA Typing, Figure 17.4, ©Academic Press
 Methods for Human Identification

Fingerprints have been used since 1901 DNA since 1986

 Forensic DNA Testing
The genome of each individual is unique (with the
exception of identical twins)

Probe subsets of genetic variation in order to

differentiate between individuals

DNA typing must be done efficiently and reproducibly

(information must hold up in court)

Typically, we are not looking at genes – little/no

information about race, predisposal to disease, or
phenotypical information (eye color, height, hair color) is
obtained
 Law Judicial
Enforcement

Laboratory
 Applications for Human Identity Testing

Forensic cases - matching suspect with evidence

Paternity testing - identifying father
Historical investigations
Missing persons investigations
Mass disasters - putting pieces back together
Military DNA “dog tag”
Convicted felon DNA databases
As
AsDNA
DNAanalysis
analysishas
hasshown
shownits
itsusefulness,
usefulness,the
thenumber
numberof
ofsamples
samples
gathered
gatheredfor
fortesting
testingpurposes
purposeshas
hasgone
goneupupdramatically…
dramatically…
 Armed Forces DNA Repository

>4.5 million blood cards on

file from members of U.S.
military

Are being used to identify

remains in case of combat
casualties in Iraq

Located in Gaithersburg,
Maryland
Tomb of Unknown Soldier
Armed Forces DNA
Identification Laboratory
(Rockville, MD)

Identification of Skeletal Remains from

Previous Military Conflicts

Identification of
Michael J. Blassie - Vietnam Tomb of the
Unknown

>2100 Unaccounted for

from Southeast Asia
>8000 Unaccounted for
from Korea
>75,000 Unaccounted for
from WWII
Roles of Biological Evidence in
Criminal Investigation
Identify a person
Exclude a suspect
Link suspect, victim and crime scene
Link weapon to victim
Link witness to scene
Prove or disprove an alibi Post-conviction DNA testing is
used to exonerate falsely
Reconstruct the scene incarcerated individuals
(143 so far)
Provide investigative leads
Sources of Biological Evidence
• Blood
• Semen
• Saliva
• Urine
• Hair
• Teeth
• Bone
• Tissue
Blood stain
Only a very small
amount of blood is
needed to obtain a
DNA profile
 Steps in DNA Analysis
Slot Blot
1 ng
0.3 ng
Collection No DNA
0.5 ng
0.5 ng

Specimen Storage 0.7 ng

1 ng
Blood Stain Buccal swab 1 ng

Extraction Sample Collection DNA DNA

& Storage Extraction Quantitation
Quantitation

Genotyping Multiplex PCR Amplification

Interpretation
of Results
STR Typing
Database Male: 13,14-15,16-12,13-10,13-15,16
Storage & Searching
Interpretation of Results DNA Database
 DNA in the Cell
chromosome 22 pairs + XX or XY

cell nucleus

Double stranded
DNA molecule Target Region for PCR

~3 billion total base pairs

Individual
nucleotides
What Type of Genetic Variation?
•Length Variation
short tandem repeats (STRs)
CTAGTCGT(GATA)(GATA)(GATA)GCGATCGT

•Sequence Variation
single nucleotide polymorphisms (SNPs)
insertions/deletions
GCTAGTCGATGCTC(G/A)GCGTATGCTGTAGC
 Basic Concepts
PCR polymerase chain reaction – method of
amplifying a specific region of the genome – go from 1 to
over a billion copies in about 2 hours

Locus region of the genome being examined

Allele the state of the genetic variation being examined

(STRs = number of repeat units)
(SNPs = base sequence at the site)

Chromosomes are paired so…

Homozygous – Alleles are identical on each chromosome
Heterozygous - Alleles differ on each on each chromosome
 Short Tandem Repeats (STRs)
Fluorescent
Fluorescentdye
dyecreates
creates
Fluorescent
aalabeled
labeledPCR
PCRproduct
product
dye label AATG AATG
primer1

7 repeats primer2
primer1

8 repeats primer2

the repeat region is variable between samples while the

flanking regions where PCR primers bind are constant
Homozygote = both alleles are the same length
Heterozygote = alleles differ and can be resolved from one another

Primer positions define PCR product size

 Position of Forensic STR Markers on
Human Chromosomes
TPOX 13 CODIS Core STR Loci
D3S1358

TH01
D8S1179
D5S818 VWA
FGA D7S820
CSF1PO

AMEL
Sex-typing
D13S317
D16S539 D18S51 D21S11 AMEL
 Labeled DNA fragments
(PCR products) Principles of Sample
Capillary Separation and Detection
or Gel
Lane Sample Detection

CCD Panel
Size Ar+
Separation LASER
(488 nm)

Detection Color
region Separation

Fluorescence ABI Prism

spectrograph

Butler, J.M. (2001) Forensic DNA Typing, Figure 10.8, ©Academic Press
Capillary Electrophoresis Instrumentation
ABI 310 ABI 3100
single capillary 16-capillary array
Scanned
Gel
Image

8
repeats
9
repeats

Capillary Electropherogram
 PCR Product Size (bp)

loci
Allelic 8 11 14
Ladders

Sample
#1

All heterozygous

Sample
#2
 PCR Product Size (bp)

loci
Allelic 8 11 14
Ladders

Sample alleles
#1

All heterozygous

Sample
#2
 Crime Scene - Two Suspects

Suspect 1

D3 vWA FGA
S1 14,15 17,18 23,24
S2 15,18 17,19 23.2,24
Suspect 2
E 15,18 17,19 23.2,24

Evidence
Methods for Parallel Sample Processing
Multiplex
Multiplexby
bySize
Size Multiplex
Multiplexby
byDye
DyeColor
Color
Blue

Green

Yellow

Internal sizing standard in red Combined

Multiplex
Multiplexby
byNumber
Numberof
of Capillaries
Capillaries
 Information is tied together with multiplex PCR and data analysis

AmpFlSTR® Identifiler™ (Applied Biosystems)

D8S1179 D21S11 D7S820 CSF1PO

TH01 D13S317
D3S1358 D16S539 D2S1338

D19S433 VWA TPOX D18S51

D5S818
AMEL FGA
11 integrated
integrated analysis
analysis
vs.
vs. 16
16 separate
separate runs
runs
High-Throughput STR Typing on the ABI 3100 (16-capillary array)

256 data points in 45 minutes with

STR 16plex and 16 capillaries
 DNA Statistics
For heterozygous loci
P = 2pq
P = probability; p and q are frequencies of allele
in a given population

Example: For the locus D3S1358 and individual

is 16,17 with frequencies of 0.2315 and 0.2118
respectively

P = 2(0.2315)(0.2118) = 0.0981 or 1 in 10.2

For independent loci, the genotype frequencies can

be combined through multiplication…
Profile Probability = (P1)(P2)…(Pn)
= 1 in a very large number…
 DNA Profile Frequency with all 13 CODIS STR loci
TH01 TPOX D7 CSF
AmpFlSTR® Identifiler™
D13 D16
What
would
(Applied Biosystems) D19 be
D3 entered into a D21
D8 VWA
DNA database for searching:
D18 D2
AMEL D5
16,17-17,18-21,22-12,14-28,30-14,16-12,13-11,14-9,9-11,13-6,6-8,8-10,10
FGA

Locus allele value allele value frequency, 1 in

D3S1358 16 0.2315 17 0.2118 10.20
VWA 17 0.2628 18 0.2219 8.57
FGA 21 0.1735 22 0.1888 15.26
D8S1179 12 0.1454 14 0.2015 17.07
D21S11 28 0.1658 30 0.2321 12.99
D18S51 14 0.1735 16 0.1071 26.91
D5S818 12 0.3539 13 0.1462 9.66
D13S317 11 0.3189 14 0.0357 43.92
D7S820 9 0.1478 43.28
D16S539 11 0.2723 13 0.1634 11.24
THO1 6 0.2266 18.83
TPOX 8 0.5443 3.35
CSF1PO 10 0.2537 15.09

The Random Match Probability for this profile in the FBI Caucasian population
is 1 in 1.56 quadrillion (1015)
 CODIS DNA Database

Combined DNA Index System

Used for linking serial crimes and unsolved cases with
repeat offenders
Convicted offender and forensic case samples
Launched October 1998 and links all 50 states
Requires 13 core STR markers
Current backlog of >750,000 samples (millions of dollars
are spent each year to reduce backlog)
 All 50 states now require convicted offenders
to submit a sample for DNA testing purposes

16,160 Investigations Aided

as of March 2004

As of March 2004 the profile composition of the National DNA Index

System (NDIS) is as follows:

Total number of profiles: 1,719,551

Total Forensic profiles: 78,475
Total Convicted Offender Profiles: 1,641,076

[Link]
1,641,076 offenders National DNA Database
78,475 forensic
102 missing persons
175 CODIS labs in 50 states, FBI, US Army Crime Lab & Puerto Rico
16,160 investigations aided
Results from Virginia

Statistical Information Total

Offender Profiles 185,387
Forensic Samples 3,068
Number of CODIS Labs 4
NDIS Participating Labs 4
Investigations Aided 1,773
[Link]
Our Human Identification Project Team
• Prepares Standard Reference Materials (SRMs)
– SRM 2391b PCR-based DNA Profiling Standard
– SRM 2395 Human Y-Chromosome DNA Profiling Standard
• Creates databases with useful information
– STRBase ([Link]
• Evaluates and develops new technologies
• Conducts interlaboratory testing
• Performs quality control testing for labs & companies
Ensuring Accurate Forensic DNA Results
ASCLD-LAB Proficiency
Accreditation Testing of
Analysts

Inspections/
DAB Audits
Standards- NIST Standard
SWGDAM (SRMs)
Guidelines
 STRBase
Short Tandem Repeat DNA
Internet Database
General Information Forensic Interest Data Supplemental Info
•Intro to STRs •FBI CODIS Core Loci •Reference List
(downloadable PowerPoint) •DAB Standards •Technology Review
•STR Fact Sheets
•NIST SRM 2391 •Addresses for Scientists
•Sequence Information
•Published PCR Primers •Links to Other Web Sites
•Multiplex STR Kits
•Y-Chromosome STRs
•Variant Allele Reports Standardized
•Population Data Standardized
information
informationformats
formats
•Validation Studies

[Link]
New DNA Test for Cats Developed in Our Lab
(the “MeowPlex”)

male

Different peak patterns between samples

female
Telling Cats Apart…

“Kitty Biometrics”
 DNA within the Biometric Model
Deny Entry
Creating the reference sample…
“Exonerated”

Testing the “evidence”…

“Implicated”
[Link]
Permit Entry

Match of 13 points (each with 2 variable alleles) within DNA

String of 26 numbers (order of listing DNA results would have to be
standardized)
16,17-17,18-21,22-12,14-28,30-14,16-12,13-11,14-9,9-11,13-6,6-8,8-10,10
 Issues with DNA as a Biometric
Tool
Individualization of everyone except identical twins
• Invasive collection of test sample (swab of cheek cells or finger prick for
blood)
• Concern over genetic privacy if sample is stored (would or could sample
ever be used for other purposes?)
• Expense for testing (>$20 per sample; forensic testing is >$500)
• Time required for testing (minimum 4-5 hours with forensic markers)

• Database search/storage of DNA profile (who controls access?; would it ever

be used for criminal investigations?)
• Development of reference databases for terrorists, etc. (how would a match
be used?)
• Chance for falsifying your sample (e.g., movie GATTACA)
 Collection of Test Sample

• Buccal (cheek cell)

swab is not as
invasive as a finger
prick to draw
blood

Used routinely in Virginia for • DNA can be

felon arrestee DNA collection
with 99.5% success (only 23
reliably extracted
failures in first 6 months of use) off of the paper or
 Genetic Privacy Concerns
• The DNA profile itself is neutral (and uninformative)—just
a string of numbers like a Social Security Number

• DNA markers used in forensics were selected to be neutral

and are located away from or between genes rather than
being part of gene products and therefore are not
generally thought to be associated with any genetic
disease

• Concern is really with the DNA sample collected—would it

be retained and used for any other type of testing? (e.g.,
Armed Forces DNA Repository can only be used for
identifying combat casualties)
 Time Required for Testing
Now typically a minimum of 4-5 hours
Collection

Extraction Could be <5

minutes
Not necessary if samples
Quantitation are uniform in amount Biggest problem is
Rapid thermal cycling to-date done length of time for PCR
Amplification with singleplexes; typically 2-3 (with multiplex amplification)
hours
Genotyping DNA separations (STR analysis) of <5
minutes have been demonstrated; typically
~30 minutes
Currently performed manually in most
Interpretation
labs; expert systems are under
of Results
development to enable rapid
interpretation
Database Search could be similar to
Storage & Searching fingerprint search in terms of speed

Comparison a DNA profile to a reference or database

Male: 13,14-15,16-12,13-10,13-15,16-…..
 Possible Ways DNA Could Be Used Now
As part of check before issuing visa for foreign visitors wanting to visit U.S.
– DNA samples could be shipped from each embassy to U.S.-based lab for
testing
– Visa would not be issued until DNA profile was generated and searched
against a national/international database
– DNA profile would be included in biometric passport for future confirmation of
identity as needed

Confirming identity upon entry into the U.S.

while the plane is in the air
– Would require DNA labs operating in
foreign airports
– 200+ DNA profiles would be generated in ~8
hours (before a plane coming from Europe
landed)

In FY2003, 7,300,667 U.S. passports were issued

[Link]
 How close are we to GATTACA?
Gattaca Corp. is an aerospace firm in the future. During
this time society analyzes your DNA and determines where
you belong in life.

Ethan Hawke's character was born with a congenital heart

condition which would cast him out of getting a chance to
travel in space. So in turn he assumes the identity of an
athlete named Jerome who has genes that would allow him
to achieve his dream of space travel.

Hawke’s character Vincent constantly passes genetic tests

by diligently using samples of Jerome's hair, skin, blood
and urine.

Entry to secure locations controlled by

rapid genetic profiling

Ability to predict future health risks

based on genetic testing
[Link]

1997 movie with a futuristic story of a

genetically imperfect man and his NOT THERE YET!
seemingly unobtainable goal to travel in
From Richard Mathies presentation at 14 th International Symposium on Human Identification, Oct 2003
 Lagally et al., Lab-on-a-Chip, 1, 102 (2001)

15 minutes for PCR amplification and detection

From Richard Mathies presentation at 14 th International Symposium on Human Identification, Oct 2003
 Virginia DNA Testing of Felon Arrestees
As of January 1, 2003, any individual arrested for a violent felony crime (Code of Virginia §
19.2-310.2:1) must provide a buccal sample for DNA analysis, with the resultant profile
incorporated into the Virginia DNA Data Bank (Code of Virginia § 19.2-310.5).

Since January 2003

• Buccal swab collected upon arrest
• DNA sample processed within 72 hours
• DNA profile searched against state database (national
database does not currently allow searches for individuals
prior to conviction)
• If a match results, then arrestee is detained and later
prosecuted
• From Jan 2003 – Dec 2003, VA processed 7,836 arrestee
samples (not all analyzed) and scored 63 hits against their
state database (Profiles in DNA, 2004, 7(1):3-5)
 If you want to know more…
• Forensic DNA Typing: Biology and Technology behind STR
Markers
• NIST website: [Link]
• John Butler email: [Link]@[Link]

STRBase