Philippine Journal of Science

132 (1): 13-19, June 2003

ISSN 0031 - 7683

Forensic DNA Analysis in Criminal

Investigations
Maria Corazon A. De Ungria

DNA Analysis Laboratory, Natural Sciences Research Institute

University of the Philippines, Diliman, Quezon City, Philippines
DNA analysis is a most powerful tool for human identification and has clear forensic
applications in identity testing (crime scene and mass disaster investigations) and parentage
determination. The development of forensic DNA technology in other countries and its
potential to improve the Philippine criminal justice system are briefly discussed. The utility
of forensic DNA testing in criminal investigations was highlighted using an actual criminal
case wherein DNA evidence played a clear role in the resolution of the case.
Keywords: Criminal investigations, DNA profiles, forensic DNA analysis
Owing to the efficacy of forensic DNA analysis in
human identification, the application of modern DNA
technology has played a crucial role in identity testing
(crime scene investigations, mass disaster 1-5 and
parentage testing6-10.
This paper reviews the basic background of the
science behind forensic DNA analysis and presents
its utility in criminal cases, with particular focus on the
use of STR methods in sexual assault cases in the
Philippines.

isolated from both living and deceased persons as

long as biological samples are not exposed to adverse
environmental conditions and/or microbial contaminants
that can degrade them.
The method of fingerprinting using an individuals

DNA-based methods of identification

DNA, or deoxyribonucleic acid, is the fundamental
building block of a persons entire genetic makeup.
DNA is present in all human cells and is the same in
every cell (Figure 1). It is composed of sugar, phosphate
and nitrogen bases namely Adenine (A), Guanine (G),
Cytosine (C) and Thymine (T). The order of the nitrogen
bases determines the so-called DNA sequence.
Several DNA molecules make up a gene. Humans
have 22 pairs of body chromosomes (autosomes) and
1 pair of sex chromosomes per body cell.
The genetic make-up of each individual is unique
(except for identical twins) and may be used to
identify a person. DNA is also very stable and can be

Figure 1. Diagram of DNA strand, gene and chromosome.

Several DNA molecules make up a gene, and genes are
located in chromosomes (nuclear DNA) or mitochondrion
(mitochondrial DNA).

*Corresponding author: [email protected]

13

De Ungria, Maria Corazn A.

DNA (DNA fingerprinting) was invented by Alec Jeffreys

in 1984 at the University of Leicester while studying the
human myoglobin gene11. The technique developed,
called Restriction Fragment Length Polymorphism
(RFLP), utilizes a special class of enzymes (restriction
enzymes) to cut human DNA into smaller fragments
that can be visualized as distinct banding patterns
(Figure 2).
Since then, other techniques have been developed.
These include the use of the reverse dot blot methods
for the characterization of the human leukocyte
antigen DQ a (HLA-DQa) and other Polymarkers
(Figure 3), sequencing of mitochondrial DNA (Figure
4), and the amplification of non-coding regions of the
human chromosome with variable number of tandem
repeats (VNTR) or short tandem repeats (STR) via
the Polymerase Chain Reaction or PCR (Figure 5).
STR markers are short DNA regions characterized by
repeated sequences. Individuals may possess different
numbers of repeats per copy of the STR marker (known
as allele) without affecting their overall metabolism.
PCR-based methods that target highly polymorphic
STR markers are currently the most prevalent procedures
worldwide. This technology is preferred by many
laboratories due to the extensive genetic variability of
STR markers, the high success rate in generating DNA
profiles with small quantities of DNA, the availability of
standard kits and protocols, and the relative ease of DNA
analysis12. The UK, US, Australia and New Zealand
use 6-20 STR markers for routine casework analysis.
In the Philippines, the DNA laboratories of the National

Figure 2. DNA patterns observed in RFLP analysis.

Each column represents the DNA profile (DNA
print) of a person (C: Control DNA; S1: Suspect 1;
S2: Suspect 2; E: DNA from evidence). The DNA
profiles of the two suspects S1 and S2 do not match
E, hence are not the source of the DNA isolated

Figure 3. Result of DNA analysis using Five Polymarker genes of the Amplitype PM Typing Kit. The genes tested
include 1: Low density lipoprotein or LDLR; 2: GypA or Glycophorin A; 3: HBGG or hemoglobin G gammaglobulin; 4:
D7S8 and 5: group specific component C or GC. In this instance, eight individuals possess different DNA profiles in
the five genes tested as shown by the variations in the colorimetric pattern per individual. The method used is called
reverse dot blot hybridization. Notably, this technology is no longer used by many laboratories and the production of
the Amplitype PM Typing Kit by Applied Biosystems Inc. has been discontinued.

14

Forensic DNA Analysis

Figure 4. DNA sequencing results. Sequencing refers to the determination of the order of nitrogen bases
A, C, G and T of DNA molecules in a prescribed region.

Bureau of Investigations (NBI), the Philippine National

Police (PNP), St Lukes Medical Center (SLMC) and the
Natural Sciences Research Institute (NSRI), University
of the Philippines routinely use 9-15 STR markers, albeit
laboratories differ in the actual markers used. Some
common STR markers used are listed in Table 1.
DNA-based methods of identification
The use of RFLP testing in human DNA identification
was pioneered by Alec Jeffreys 11 and was first
used in the investigation of the rape/murder of two
British schoolgirls in November 1986. In the initial

investigations, semen samples isolated from the

victims bodies did not match the suspects DNA. To
find individuals with the same DNA pattern as that
of the semen sample, police investigators requested
17 34 year old males living in the area to voluntarily
submit blood samples. Over 4000 reference samples
were processed and compared with the DNA pattern of
the semen samples. Eventually, the DNA profile from
the semen samples matched the DNA profile of a man
named Collin Pitchfork. Pitchfork later confessed to the
crime and was subsequently convicted for the rape and
murder of the two schoolgirls. In this instance, DNA

Table 1. Common STR markers used in forensic DNA testing.

15

De Ungria, Maria Corazn A.

custodian and lawyers. Notably, false positive reactions

do not occur when common non-human sources of
contamination, e.g. dog, cat, bacteria, dirt, soil, grass or
other plants, and water are mixed with human biological
samples. For this reason, meticulous documentation
of the chain of custody of samples listing the identities
and extent of handling of all personnel, starting from the
crime scene to the court, is required if physical evidence
is to be made admissible 2. To date, DNA has been
successfully isolated from diverse types of biological
samples such as blood and bloodstains, saliva, semen
and seminal stains, vaginal smears/swabs, tissues and
organs, bones and hair with follicles in varying states
of degradation.
Figure 5. DNA typing using Short Tandem Repeat markers.
In this case, the STR gene known as HUMvWA was used
wherein individuals are known to have 14 to 19 repeats per
allele (as shown in Control DNA). Each individual has two
copies of a marker which can be identical copies (hence the
individual is homozygous for that marker: Person B is 16 and
16) or different copies (hence the individual is heterozygous
for that marker: Person A is 16 and 18; and Person C is 16
and 18). Since Persons A and C have similar DNA profiles
at HUMvWA, additional STR markers must be tested to
distinguish Person A and Person C.

evidence played an important role in excluding the first

suspect and in identifying a second suspect who turned
out to be the real perpetrator of the crime 13.
The initial success of DNA fingerprinting in resolving
the rape/murder case of the two British schoolgirls in 1986
helped to promote the use of forensic DNA technology by
law enforcement agencies. Since then, use of forensic DNA
analysis to assist in criminal investigations has become
routine in many countries such as the United Kingdom14,15,
United States 16, Canada 17, Germany 18, Japan 19,
Australia20 and New Zealand21.
The use of forensic DNA analysis in criminal
investigations depends on the availability and the
proper processing of biological samples from crime
scenes. Properly collected samples contain biological
material that may lead to criminal identification. In the
process of collecting and processing samples, great
attention must be paid to issues of proper handling,
contamination, and storage/preservation because of
the minute amounts of DNA being handled. Reactions
used in forensic DNA analysis are specific for humans,
although in some instances, may also have positive
reactions for DNA of non-human primates, e.g.
chimpanzee, orangutan and gorilla22. Due to the general
specificity of the reactions used in forensic DNA analysis
for human DNA, the common sources of false positive
reactions are contaminations from human handlers, e.g.
curious bystanders at the crime scene, investigators,
medico-legal examiners, forensic analysts, evidence

16

Analysis of DNA evidence

Once samples are processed, possible sources of
DNA profile/s are evaluated. Sources may be a) the victim;
b) human handlers such as crime scene investigators,
medico-legal officers, forensic analysts and lawyers; c) the
perpetrator of the crime.
Suspect is excluded as source of evidence
The presence of two or more mismatches between
the evidentiary stain and suspects reference sample
necessarily excludes him as the source of the evidentiary
sample. Notably, mismatches do not necessarily equate
with innocence, but merely show that the suspect is not the
source of the evidentiary sample. Other evidence collected
from the crime scene may still contain the suspects DNA or
that the suspect did not leave sufficient DNA, if he is indeed
the real perpetrator of the crime. Alternatively, the suspect
may not have left sufficient DNA at the crime scene and
other physical evidence (e.g. ballistics, shoeprint evidence)
and information, (e.g. eyewitness testimony) must be used
to further the case.
Nonetheless, the exclusion of a suspect as possible
source of non-victim DNA that is not that of any known
human handler is crucial in criminal investigations since this
indicates the presence of another individual at the crime
scene who remains unaccounted for.
Suspect as possible source of evidence
If a suspects reference sample is consistent with the
DNA profile of the evidentiary sample, then the suspect
remains as a candidate source of the sample. Since
only a selected set of STR markers are analyzed, there
remains a probability that another individual has the same
DNA profile. If the alleles comprising the DNA profile
are rare, then this profile may be attributed to only a few
persons in a given population, and the likelihood of the
suspect being the source of evidence is higher. Hence it
is essential that the significance of matching profiles must
be estimated using established statistical principles23. In
addition, match probability estimates and/or likelihood
ratios must accompany all DNA reports submitted to

Forensic DNA Analysis

courts to assist in the proper evaluation of the weight

of DNA evidence24.
The inclusion or exclusion of a suspect greatly
contributes to the reconstruction of events that
transpired and the progress of criminal investigations. In
this manner, DNA evidence is objective and irrevocable,
unlike some witness statements that may be partial or
subject to various psychosocial influences.
Forensic DNA technology in the Philippines
Empirical examination of archived trial court records
in the Supreme Court of affirmed Death Row inmates
revealed the unavailability of physical evidence in many
cases. For example, of the 58 Death Row cases (52
involving rape, two for robbery homicide, two kidnap for
ransom, one for drug possession and one for multiple
murder) reviewed by the UP DNA Analysis Laboratory in
the first quarter of 2002, samples for only two cases are
still available for DNA testing. Apparently many victims
especially minors, do not immediately report the rape
out of fear and shame. This was further compounded by
the absence of guidelines for the proper collection and
storage of collected evidence in local health and police
units. Attempts to locate samples were unsuccessful
because many samples were not stored or could not
be located.
Theoretically, the chance of isolating biological
material is much higher in sexual assault cases
compared to other crimes due to the direct physical
contact; hence transfer of biological material, between
assailant and victim. In fact, the best biological samples
that may be used as DNA evidence are those obtained
from the victim and her clothing worn at the time of the
assault. Sperm DNA is generally stable up to 72 hours in
the female reproductive organs, provided that the victim
does not bathe or wash during this time period. In the
US, DNA testing is mostly used in rape and homicide
prosecutions 25.
The unrealized potential of using forensic DNA
technology in accelerating criminal investigations in
the Philippines is great. Medical records at the National
Bureau of Investigations (NBI) and the Philippine
National Police (PNP) from August to November 2000
contained 780 sexual assault cases (366 cases in NBI
and 414 cases in PNP). Within this period, the PNP
Crime Laboratory examined 174 victims (42%) <72
hours after the commission of the crime compared to
106 NBI cases (29%). In theory, the proper collection and
subsequent laboratory analysis of samples, in particular
vaginal swabs, should facilitate the identification of
the real offenders in these cases. Clearly, if DNA
analysis was conducted on all these samples, then the
identification of real suspects or exclusion of individuals
would have undoubtedly accelerated the criminal
investigations of these cases.

Figure 6. Microscopic preparation of sperm cells (Eosin stain).

Sperm cells have a characteristic cellular morphology: head
with a long tail. This morphology is easily distinguished by
visual inspection under a microscope, but is vulnerable to
cellular disruption. The tail region is mainly used for motility
whereas sperm DNA is located at the head region. Sperm cells
are may be disrupted thus characteristic cell morphology is
destroyed, releasing sperm DNA. In this instance, sperm cells
are not detected but sperm DNA may have been transferred to
the victim, which may be amplified at prescribed STR markers
to generate a DNA profile of the perpetrator.

DNA evidence in Philippine courts: A case report

To demonstrate the role of DNA evidence in criminal
courts and in resolving a disputed paternity case, the
case of People of the Philippines vs. Victoriano Paras
(Criminal case nos. 85974-85978 Regional Trial Court,
Branch 163 Pasig City) is discussed. This case was
selected because it involved a man charged with sexual
assault resulting in the victims pregnancy and birth of
a child. DNA evidence was obtained by conducting a
simple paternity test on the DNA of the suspect, the
victim and the child.
The accused was charged with five counts of rape
committed on various dates, namely: December 31,
1989, the first, second and fourth weeks of January
1990, and first week of February 1990 leading to the
birth of a child on November 8, 1990. The case was
filed on March 31, 1991. However inconsistencies
were detected in the testimony and subsequent cross
examination of the victim. In addition, the defense
presented evidence that showed the accused was not
in Pasig during the period covered by the charges. The
defense also argued that the child was born 10 months
after the last incident of the supposed rapes.
Hence, to determine whether the accused was
indeed the father of Joanna Ocray, the Court ordered
the UP-NSRI DNA Analysis Laboratory to conduct
DNA tests on the child, the victim and the accused.
Two weeks later, on the basis of mismatching DNA
profiles at four out of five STR markers tested, the

17

De Ungria, Maria Corazn A.

accused was excluded from being the father of the

child26.
The results of the laboratory examination, the
inconsistencies of the victims testimony as well as
other evidences presented by the defense in Court on
the whereabouts of the accused during the stated time
and dates of the incidences of rape cast a very serious
doubt in the mind of the court as to the guilt of the
accused on the five incidences of rape filed against him
(Judge Aurelio C. Trampe, 5 May 1999). The accused
was subsequently acquitted and released.
Nonetheless, the accused was imprisoned and his
petition for bail was denied whilst the case was being
tried in court. Thus, prior to acquittal, the accused had
already been incarcerated for six years. In contrast,
DNA analysis that provided key evidence in this case
was conducted within two weeks. Consideration of
these facts highlights the need to incorporate forensic
DNA testing in routine criminal investigations to
decrease the possibility of erroneous convictions as
well as to accelerate the progress of pending cases
that clog Philippine courts.

Conclusion
The strength of DNA evidence to resolve crimes is
well established in the US, Germany, Australia, New
Zealand, Japan, the UK and other countries. However,
the routine use of DNA evidence in criminal cases has
yet to be adopted in the Philippines. The development
of DNA testing and forensic science overseas has
provided us a remarkable opportunity to improve our
criminal justice system. Further, the availability of
forensic DNA technology in the Philippines necessitates
the amendment of current rules of evidence to
incorporate scientific advances which enables the
judiciary to better appreciate the value of physical
evidence in criminal courts.

Acknowledgments
This study was made possible through the
assistance of the European Commission. The views
expressed herein do not necessarily represent the
official view of the European Community. The author
would like to acknowledge Chrisgel Cruz, Celeste
Jumadla, Abelardo Maglanque, Paul Pineda and Neil
Yabut for their work on Death Row cases during the
summer of 2002.

References
Asplen CH. From crime scene to courtroom: integrating

18

DNA technology into the criminal justice system.

Judicature 1999;83(3):144-149.
Ayres KL, Chaseling J, Balding DJ. Implications for DNA
identification arising from an analysis of Australian
forensic databases. Forensic Sci Int 2002;129:9098.
Ban JD. Operating and managing a statewide DNA
program. Croat Med J 2001;42(3):281-284.
Brenner C. A note on paternity computation in cases
lacking a mother. Transfusion 1993;33(1):51-54.
Budowle B, Chakraborty R, Carmody G, Monson KL.
Source attribution of a forensic DNA profile. Forensic
Sci Communic 2000;2:1-5.
Butler JM. Forensic DNA Typing: Biology and
Technology Behind STR Markers. San Diego:
Academic Press; 2001. 322 p.
Chakraborty R, Stivers DN. Paternity exclusion by DNA
markers: effects of paternal mutations. J Forensic
Sci 1996;41(4):671-677.
Corach D, Sala A, Penacino G, Sotelo A. Mass
disasters: rapid molecular screening of human
remains by means of short tandem repeats typing.
Electrophoresis 1998;16:1617-1623.
Crouse CA, Schumm J. Investigation of species
specificity using nine PCR-based human STR
systems. J Forensic Sci 1995;40(6):952-956.
De Ungria MCA, Calacal GC, Magno MMF, Delfin FC,
Tabbada KA, Frani AM. DNA evidence in Philippine
courts: a case report. Philippine Law Gazette
2001;13(3):46-49.
De Ungria MCA, Frani AM, Magno MMF, Tabbada KA,
Calacal GC, Delfin FC, Halos SC. Evaluating DNA
tests of motherless cases using a Philippine genetic
database. Transfusion 2002;42:954-957.
Evett IW, Weir BS. Interpreting DNA Evidence: Statistical
Genetics for Forensic Scientists. Sunderland:
Sinauer Associates Inc; 1998. 278 p.
Franklin-Barbajosa C. DNA profiling: the new science of
identity. National Geographic 1992;181(5):112-123.
Furbish LK. Paternity establishment law in 1988 and
today. http:www/ojp/usdoj.gov/nij/ 1997.
Gill P, Evett I. Population genetics of short tandem
repeat (STR) loci. Genetica 1995;96:69-87.
Gill P, Jeffreys AJ, Werrett DJ. Forensic application of
DNA fingerprints. Nature 1985;318:577-581.
Harbison SA, Buckleton JS. Applications and extensions
of subpopulation theory: a caseworkers guide.
Science and Justice 1998;38:249-254.

Forensic DNA Analysis

Honda K, Roewer L, de Knijff P. Male DNA typing from

25-year old vaginal swabs using Y chromosomal
STR polymorphisms in a retrial request case. J
Forensic Sci 1999;44(4):868-872.
Hou Y, Song Z, Wu J, Zhang J. How many STR markers
are enough for paternity identification? Prog Forensic
Genetics 2000;8:384-386.
Jeffreys AJ, Wilson AV, Thein SL. Individual-specific
fingerprints; of human DNA. Nature 1985;316:7679.
Mukaida M, Kimura H, Takada Y, Masuda T, Nakata
Y. The personal identification of many samples
recovered from under the sea. Forensic Sci Int
2000;113:79-85.
Schneider PM, Martin PD. Criminal DNA databases: the
European situation. Forensic Sci Int 2001;119:232238.
Travis J, Asplen C. Postconviction DNA testing:
recommendations for handling requests. Washington,
D.C.: US Department of Justice; 1999. 118 p.
Weir BS. Genetic Data Analysis II: Method of discrete
population genetic data. Sunderland, Massachussets:
Sinauer Associates Inc.; 1996. 445 p.
Whitaker JP, Clayton TM, Urquhart AJ, Millican ES,
Downes TJ, Kimpton CP, Gill P. Short tandem repeat
typing of bodies from a mass disaster: high success
rate and characteristic amplification patterns in highly
degraded samples. BioTechniques 1995;18(4):670677.
Word CJ, Sawosik TM, Bing DH. Summary of validation
studies from twenty six forensic laboratories in
the United States and Canada on the use of the
Amplitype PM PCR amplification and typing kit. J
Forensic Sci 1997;42(1):39-48.

19