Applications and Methodology
Dept of Biological Sciences
California State University, Sacramento
ballardr@csus.edu;
Forensic Science Graduate Program
University of California, Davis
reballard@ucdavis.edu
Ruth E. Ballard, Ph.D.
Name: Ballard, Ruth
Hair: Brown
Eyes: Green
Ht: 5’ 2”
Wt: 105
Occupation: Professor and DNA/Biology
Program Advisor
Last Known Addresses:
Dept of Biological Sciences
California State University, Sacramento
ballardr@csus.edu;
Forensic Science Graduate Program
University of California, Davis
reballard@ucdavis.edu
Wanted for: Impersonating a criminalist
Why we need DNA markers
Why we need DNA markers

Definition

Applications

Short Tandem Repeat Markers

Generating a profile


CODIS
Cold Case Study: Solving the
abduction, rape, and murder of Penny
Parker

DNA profiling is a scientific technique that
exploits genetic differences among people
to distinguish them from one another


Humans share 99.9% of their DNA
On average (for unrelated individuals) 1 in
1,000 base-pairs is different
Sister chromatids
Homologues







Example: Human chromosome 1
4,220 genes (2%)
98% non-coding “junk DNA”
2.47 x 108 base-pairs
Average number of differences between
unrelated homologues: 247,000
Most differences are in non-coding fraction
DNA profiling exploits these differences
across all chromosomes

Definition

Applications

Short Tandem Repeat Markers

Generating a profile

CODIS

Cold Case Study: Solving the
abduction, rape, and murder of Penny
Parker

Solving Crimes (murder, sexual assaults,
burglaries)
Missing persons and unidentified remains


Skull found in a field in the Los
Gatos hills is identified as
belonging to missing Vallejo
child, Xiana Fairchild, 14 months
after her disappearance in
Dec,1999

Establishing Biological Relationships (child
support, visitation, immigration,
inheritance)
13

Assigning twin status
◦ Identical or fraternal?

Identifying victims of man-made disasters
◦ TWA Flight 800
◦ Exploded and crashed July 1996 in Atlantic Ocean
off New York state

Identifying victims of natural disasters
◦ “Baby 81” claimed by 9 couples after tsunami in
Southeast Asia
◦ Identity confirmed as Abilass Jevarajah and
reunited with biological parents

Definition

Applications

Short Tandem Repeat Markers

Generating a profile

CODIS

Cold Case Study: Solving the
abduction, rape, and murder of Penny
Parker

DNA profiling relies on short, tandemly
repeated sequences of DNA (STRs)
◦ Ubiquitous in the human genome
◦ Short (for DNA profiling 4 bp)
 e.g. gaca, ctat, ggca, etc.
◦ Highly polymorphic (many alleles in the population)
 “Alleles” defined by number of repeats present (e.g.
6,7,8,9,10,11,12,13,14,15, etc.)
◦ No one allele present at much higher frequencies
than others

Example: D7S820
◦ Located on chromosome 7
◦ Repeated sequence: 5’-gata-3’
◦ Alleles observed in human population:
6,7,8,9,10,11,12,13,14,15,16
aatttttgtattttttttagagacggggtttcaccatgttggtcaggctgactatggagtt
attttaaggttaatatatataaagggtatgatagaacacttgtcatagtttagaacgaac
taacgatagatagatagatagatagatagatagatagatagatagatagatagatag
atagtttttttttatctcactaaatagtctatagtaaacatttaattaccaatatttggtgca
attctgtcaatgaggataaatgtggaatcgttataattcttaagaatatatattccctctg
agtttttgatacctcagattttaaggcc

Level of discrimination rises with number of
possible alleles
# alleles in the
population (x)
# genotypes in the
population
(x2 + x)/2
1
2
3
4
5
6
7
11
1
3
6
10
15
21
28
66

Each person has only two alleles for each STR
locus
◦ Can be either heterozygous or homozygous
(4,6)
heterozygote
(5,5)
homozygote

Allele frequency tables can be used to
estimate genotype frequencies using Hardy
Weinberg statistics
ALLELE
FREQUENCY
4
5
6
7
8
9
10
11
12
13
0.001
0.018
0.162
0.130
0.262
0.250
0.128
0.045
0.003
0.001
Frequency (4,6) = 2 pq
= 2 (0.001)(0.162) = 0.000324
(or 1 in 3,086 persons)
Frequency (5,5) = p2
= (0.018)2 = 0.0262
(or 1 in 38 persons)


The scientific community has chosen 13 core STR
loci for DNA profiling
The amelogenin locus on the X and Y
chromosomes is also targeted for sex typing



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The loci are genetically unlinked
Therefore, the inheritance of each STR is an
independent event
This permits the product rule to be used
when calculating the probability of an entire
profile
The genotype frequency for each locus is
calculated and then they are multiplied
together to provide a random match
probability (RMP) for the profile
Random Match Probability (RMP)
The probability of randomly selecting an
unrelated individual from the population who
would have the same genetic profile as the
person tested

For my profile:
Locus
D8S1179
D21S11
D7S820
CSF1PO
D3S1358
THO1
D13S317
D16S539
D2S1338
D19S433
VWA
TPOX
D18S51
D5S818
FGA
RMP
Genotype
(13,13)
(29.3,33.2)
(10,12)
(10,11)
(15,18)
(6,9.3)
(11,12)
(12,12)
(16,17)
(13,14)
(17,17)
(9,11)
(12,15)
(11,11)
(20,10)
0.093025
0.000416
0.080676
0.130634
0.079648
0.170752
0.168144
0.106276
0.012012
0.186714
0.078961
0.057834
0.040386
0.130321
0.016129
8.6177E-20

The probability of
randomly selecting
an unrelated
individual from the
population with the
same genetic profile
as myself is 1 in 11
quintillion!!

Definition

Applications

Short Tandem Repeat Markers

Generating a profile

CODIS

Cold Case Study: Solving the
abduction, rape, and murder of Penny
Parker

DNA Profiling always starts with a biological
sample
◦ Cigarette butt a suspect smoked during
questioning (cheek cells in suspect’s saliva)
◦ A bloody knife found in a suspect’s car (blood
cells - possibly from the victim)
◦ A hair found in a ski mask left at the site of an
armed robbery (hair root cells, possibly from the
suspect)
◦ Human femur bone found in a dumpster (bone
cell DNA, possibly from the victim of a homicide)
◦ A reference buccal swab from an alleged father for
paternity testing

Lyse open cells and extract DNA
◦ PCA (organic method)
◦ Spin columns
◦ Robots (e.g. EZ1)

Quantify the amount of human DNA present
◦ quantitative PCR (qPCR)

Amplify 13-15 STR loci in one PCR reaction
◦ Multiplex
◦ PCR primers are fluorescently-labeled
◦ Amplicons differ by length depending on the
number of repeats present

Separate and resolve amplicons by gel
electrophoresis
CHROMOSOME 7 received from mother
carrying 9 repeats of GATA
Primer A (forward primer)
Primer B (reverse primer)
CHROMOSOME 7 received from father
carrying 12 repeats of GATA
Amplicon from chromosome carrying 9 repeats
Amplicon from chromosome carrying 12 repeats
12 base pairs
(-)
PCR sample loaded
into capillary
Allele 14 at D7S820
Allele 14 at D7S820
Allele 11 at TPOX
Samples run through capillary
according to size
Allele 9 atTPOX
Allele 7 atD7S820
As PCR products pass capillary
window, a laser excites the
fluorescent tag and the tag
emits a signal
detector
The signal is sent to a
computer for
interpretation and
analysis
(+)
Y axis = Amplitude
of fluorescent signal
Blue
Green
Yellow
Red
X axis = Time since injection = size of amplicon

Definition

Applications

Short Tandem Repeat Markers

Generating a profile

CODIS

Cold Case Study: Solving the
abduction, rape, and murder of Penny
Parker

Established in 1994
◦ Director of FBI established a DNA Advisory Board
◦ Defined and developed standards for DNA typing
◦ Defined Indices for sample data banking

Fully operational in 1998
◦ Stores DNA profiles from in:





Convicted Offenders Index
Forensic Index
Missing persons Index
Missing persons reference Index
Arrestee Index
◦ Allows law enforcement agencies to share
information across all 50 states
Reference sample from victim
DNA profile of victim
BIOLOGICAL EVIDENCE AT CRIME SCENE
Match?
DNA Profile from evidence
Match?
DNA Profile from suspect(s)
If suspect(s) eliminated
(or no suspects)
Suspect(s)
Search Convicted Offender or Arrestee Indexes in CODIS
NO “HIT”
“HIT”
Repeat search
every 7 days
Prosecute
• National (2008)
• Convicted Offender profiles: 7,940,321
• Forensic profiles: 306,028
• “Hits”: 107,600
• California (2008)
• Convicted Offender profiles: 1,251,307
• Forensic profiles: 25,323
• “Hits”: 12, 412

Definition

Applications

Short Tandem Repeat Markers

Generating a profile

CODIS

Cold Case Study: Solving the
abduction, rape, and murder of Penny
Parker
May 1977: Penny Parker, 15,
disappeared while out
collecting money for her
Sacramento Bee paper route
 Found dead three days later,
stabbed and sexually assaulted
 At the time, the analysis of
biological evidence was in its
infancy
 Suspect identified but
insufficient evidence to charge





DNA typing methods introduced in 1986 and rapidly
improved in 1990’s
Parker case reopened in
2001
Semen stain found on
panties and DNA profile
obtained
Profile entered into the
FBI’s national CODIS
database; no match
42



December 2002, samples submitted from the exwife and biological daughter of suspect Don
Jennings.
Relationship DNA profiling showed that it was
10,000 times more likely that Mr. Jennings was the
source of the semen on Penny Parker’s panties than
a random, unrelated man
Judge ordered Mr. Jennings to provide DNA
reference sample for comparison to DNA from
semen stain on panties




January 2003, Sacramento Police Department
detectives traveled to Arkansas to obtain a
reference sample from Mr. Jennings.
Sample profiled and found to match the profile of
the semen donor.
Mr. Jennings committed suicide in February 2003,
when officers returned to Arkansas and attempted
to arrest him for the rape/homicide of Parker.
Demonstrates power of biological evidence to solve
crimes, even “cold” ones

American Academy of Forensic Sciences

U.S. Bureau of Labor Statistics

California Association of Criminalists


http://www.aafs.org/
http://www.aafs.org/
http://www.cacnews.org/
STRbase (http://www.cstl.nist.gov/strbase/)
U.C. Davis Forensic Science Graduate Program
http://forensicscience.ucdavis.edu/