Challenges of Forensic DNA Testing Technology in The Philippines

The utility of forensic deoxyribonucleic acid (DNA) analysis in resolving issues involving the identification
of individuals has long been recognized and accepted worldwide. The Philippines is no exception.1
There are presently three Philippine laboratories which have the capability to do
forensic DNA work involving kinship analysis, criminal investigation, and disaster victim
identification (DVI), namely,
-the DNA Analysis Laboratory at the Natural Sciences Research Institute,
-University of the Philippines Diliman (UPD-NSRI),
-the Philippine National Police (PNP) Crime Laboratory, and the National Bureau of Investigation (NBI)
Crime Laboratory.

The first major challenge is the apparent lack of recognition of and support for the vital role of forensic
DNA in criminal investigation and DVI. This can be seen, among other things, by the fact that Congress
has not made the passing of a forensic DNA bill a priority; that hundreds of sexual assault investigation
kits collected from abused women and children remain untested; and that the government has not
released sufficient funds for laboratories to analyze samples from mass disasters such as Tropical Storm
Washi, also known as Sendong, in 2011, Typhoon Pablo in 2012, and Super Typhoon Haiyan or Yolanda
in 2013

The second major challenge that forensic DNA scientists face in the Philippines is the mishandling of
crime scene samples. Unfortunately, conducting crime scene investigations and collecting evidence in
the Philippines remain inadequate in a number of cases, even after the promulgation of the Rule on DNA
Evidence in 2007. Section 7 of the Rule adopted the ruling in the case of People v. Vallejo,38 which
outlined the requirements in assessing the probative value of DNA Evidence. These requirements
include the need for crime scene investigators and law enforcement personnel to follow “the chain of
custody, including how biological samples were collected, how they were handled, and the
possibility of contamination of samples.”

Failure to follow proper crime scene investigation procedures was evident when backhoes were used
during the retrieval of bodies in at least two relatively recent cases, namely, the Maguindanao massacre
in November 200940 and the Parojinog case in August 2017.41 In both cases, the use of backhoes
fragmented the human remains, magnified the co-mingling of body parts, and destroyed potential
evidence that could have been recovered if bodies were properly processed. Interestingly, the
Maguindanao massacre was considered as the “trial of the century” in 2009 because of the number of
victims including 32 journalists who were ambushed on the road in broad daylight and dumped in mass
graves, and the identity of the suspects who belonged to one of the powerful political clans in
Maguindanao.42 More than eight years later, the case against the perpetrators remains unresolved and
the suspects continue to be incarcerated in a detention facility, under tight security.

1
Maria Corazon A. De Ungria, et al., Overview of Forensic Services by the UPD-NSRI DNA Analysis Laboratory, ACTA
MEDICA PHILIPPINA, Volume No. 42, Issue No. 2, at 34-38.
House bill seeks creation of PH DNA Database Analysis SystemBy Newsbytes.PH on July 21, 2019
Surigao del Norte representative Robert Ace Barbers has proposed to institutionalize a national forensic
DNA database in the country through the establishment of the Philippine DNA Database Analysis System
or PDDAS.

A DNA database or DNA databank is a database of DNA profiles which can be used in the analysis of
genetic diseases, genetic fingerprinting for criminology, or genetic genealogy. DNA databases may be
public or private, the largest ones being national DNA databases.

Credit: FDA.gov
He explained that the most important function of a DNA database is to produce matches between the
suspected individual and crime scene bio-makers.

“It provides evidence to support criminal investigations which can lead to the identity of potential
suspect or suspects in criminal investigations,” Barbers said.

He further said that forensic DNA can also assist in the identification of missing persons or unidentified
human remains in times of accidents and calamities. Barbers said the DNA technology in the country is
largely used to establish paternity and other family relationships.

The bill defines the term “DNA” as a biochemical molecule found in the cells and makes each species
unique. On the other hand, the term “DNA profile” refers to the genetic information from a forensic
DNA analysis.

The measure defines DNA profiling or DNA typing as a process where a minute sample of genetic DNA
material is taken from a human tissue and is given a computerized numeric value in the form of a “bar
code.”

The bill provides that the PDDAS, which shall be the central repository of DNA profiles in the Philippines,
shall contain the forensic DNA profiles of persons classified in the following indices: crime scene index;
suspected persons index; convicted offenders index; detainee index; drugs dependent index; missing
persons index; voluntary index; uniformed personnel index; and government employees index.

As stated in the bill, the objective of the DNA Database is to establish, keep and maintain a
comprehensive National DNA database in order to perform comparative searches for the following
purposes:

To serve as a tool for crime prevention and crime solution;

To identify person who might have been involved in the commission of an offense;
exonerate a person wrongly convicted of an offense;
To prove the innocence or guilt of person allegedly involved in the commission of an offense;
To assist in the identification of missing persons or unidentified human remains; or

To establish paternity and family relations and genealogy.

The proposal provides for the establishment of the Philippine DNA Database Office (PDDO) which shall
manage the Philippine DNA Database Analysis System (PDDAS).
The PDDO shall be responsible for the general conduct, administration, and management of the PDDAS
and other functions.
It shall be composed of three organic personnel each from the Philippine National Police (PNP), National
Bureau of Investigation (NBI), Philippine Drug Enforcement Agency (PDEA) and the Armed Forces of the
Philippines.

The PDDAS and any information contained therein shall only be accessed by the Philippine DNA
Database Office. They shall only access the same purposes of administering the database and comparing
DNA profiles or information in the course of an investigation conducted by any law enforcement agency.

Any other law enforcement agencies who may wish to access information in the PDDAS shall get prior
clearance from the PDDO.

The bill also provides for the establishment of a Philippine DNA Database System Scientific Advisory
Committee for the purposes of developing DNA testing database quality assurance standards for DNA
testing and databasing, including standards for testing the proficiency of forensic laboratories and
forensic analysts conducting forensic DNA analysis.

The PDDAS Scientific Advisory Committee shall be composed of a maximum of 10 individuals

scientifically qualified to understand, develop and adopt DNA quality assurance standards, with
representatives from the University of the Philippines –Philippine General Hospital (UP-PGH) as chair
and other government entities and institutions actively engaged in forensic DNA testing and analysis as
members.

The bill imposes the penalty of 12 years and one day imprisonment or a fine of not less that P600,00, or
both, at the discretion of the court for any person found guilty of tampering of DNA samples and
records. — Ma. Victoria Palomar (HoR)

Database abroad

The Israel Police DNA database, also known as IPDIS (Israel Police DNA Index System), has been
operating since February 2007. During that time more than 135,000 reference samples have been
uploaded and more than 2000 hits reported. We have developed an effective semi-automated system
that includes two automated punchers, three liquid handler robots and four genetic analyzers. An
inhouse LIMS program enables full tracking of every sample through the entire process of registration,
pre-PCR handling, analysis of profiles, uploading to the database, hit reports and ultimately storage. The
LIMS is also responsible for the future tracking of samples and their profiles to be expunged from the
database according to the Israeli DNA legislation. The database is administered by an in-house
developed software program, where reference and evidentiary profiles are uploaded, stored, searched
and matched. The DNA database has proven to be an effective investigative tool which has gained the
confidence of the Israeli public and on which the Israel National Police force has grown to rely.

Break Through Of Technology

Forensics 2.0 comes to the Philippines
January 12, 2018 | Written by Andre DP Encarnacion

In 2016, National Geographic ran a story on the case of Sierra Bouzigard, a 19-year-old from Louisiana,
USA who was found beaten to death seven years prior. Although in the fatal struggle Bouzigard
managed to get some of her attacker’s tissue under her nails, traditional methods of matching DNA to
suspect failed to yield any result. Policemen were stumped.
With the collected DNA their only lead, the case analyst decided to take a chance and send the evidence
to Parabon Nanolabs, a company specializing in “DNA phenotyping.” Using so-called single nucleotide
polymorphisms (SNPs, pronounced “snips”), which are variations in a single building block of DNA,
Parabon promised to conjure a rough likeness of the sample’s owner that would include certain physical
features and probable ethno-geographic ancestry.

While the analysis of these characteristics is in its relative infancy and not without controversy, its use in
the Bouzigard case highlighted the question of how much more science could contribute in the pursuit
of justice. If a broader variety of DNA markers could be simultaneously analyzed to build on what
current methods can accomplish, how much more sophisticated could our power to discriminate and
investigate become?

That question is one of many that the DNA Analysis Laboratory, Natural Sciences Research Institute, UP
Diliman (DNA Analysis Laboratory, NSRI-UPD) is currently trying to address. Using breakthrough
technology called “Next Generation Sequencing” (NGS), University research associates Jazelyn M.
Salvador and Dame Loveliness T. Apaga are now getting a first-hand glimpse of the answers.

The gold standard

The laboratory, headed overall by Dr. Maria Corazon A. De Ungria, is no stranger to breakthrough
contributions. Its work was a major driver behind the approval by the Supreme Court of the 2007 Rules
on DNA Evidence that set terms and guidelines for the conduct of DNA testing and its specific
applications in Philippine courts.

The technology behind much of the team’s success to date is called capillary electrophoresis (CE). In
creating a DNA profile for any individual using this method, members of the team look at what they call
“short tandem repeats” (STRs). These are areas in the genome with sequences of nucleotides, made up
of combinations of nitrogen bases: (G)uanine, (T)hymine, (A)denine and (C)ytosine. True to their name,
STRs are sequences of these bases that repeat a certain number of times with successive repeats being
located next to each other (i.e., TCGA-TCGA-TCGA…).

The laboratory typically examines a person’s DNA profile in 20 of these STR regions that are found
across 22 so-called “autosomal” chromosomes, as well as in the X and Y, or human sex chromosomes. In
a sample like blood or saliva, which has sufficient amounts of DNA, these pre-selected DNA regions or
markers are amplified or “photocopied” via a process called the Polymerase Chain Reaction or PCR.

“After amplification,” Jazelyn says, “fragments of DNA are separated by length via CE, where they
migrate along an electric field through a tube separating anode from cathode. Because of their size,
smaller fragments can migrate from start to end much faster.

Fragments, distinguished by the number of repeats using a reference set, are then detected by a laser
via fluorescent tags. The result of this process is a person’s DNA profile. As more STR regions are
analyzed, the probability that two unrelated individuals would have the same DNA profile on each DNA
marker becomes increasingly remote.
Dame also spoke about how CE continues to be the gold standard for human identification. “The system
is stable and accurate, and is relatively easy to use for forensic applications.” The technique, however,
has its limits. Because of the relative length of STRs, creating a suitable profile may not always be
possible, especially with degraded DNA. The latter situation is unfortunately all too common in disaster
areas and in many crime scenes.

Next Generation Sequencing

“That’s the advantage of Next Generation Sequencing (NGS), also known as Massively Parallel
Sequencing,” Dame continues, referring to the newest technology being validated by the laboratory.
“This technology enables a researcher to study and sequence several markers simultaneously, thereby
significantly increasing the amount of information that can be mined from the sample.” In fact, NGS can
be used to sequence an entire genome at a relatively shorter time compared to more traditional
procedures.

The NGS project by the Laboratory funded by DOST-PCHRD has for the most part used Illumina’s MiSeq
FGx Forensic Genomics System. Using this platform, billions of short, single-stranded templates of DNA
are attached to a slide. Fluorescently-labeled nucleotides are added one by one to the templates, after
which a photo is taken that captures light from color-coded bases. The process is repeated with these
bases added one at a time until sequencing is complete.

Jazelyn says this technique allowed the team to simultaneously analyze not only STRs, but also SNPs. In a
paper published earlier this year, the team analyzed more than 200 markers from 143 unrelated
Filipinos who volunteered to provide samples. These DNA markers included 28 autosomal STRs, 24 STRs
from the Y chromosome and 7 from the X chromosome, providing supplementary information that can
be vital in resolving complex kinship cases.

Moreover, they were also able to analyze 173 SNPs, including 22 phenotypic informative SNPs and 56
ancestry informative SNPs. “The purpose of ancestry SNPs is to determine the bio-geographic lineage of
individuals,” explains Dame. “If you test an individual, these markers can predict whether one is likely to
be Caucasian, East Asian, or from another group based on reference population datasets.”

“Phenotypic SNPs, on the other hand determine externally visible characteristics. These characteristics
include eye color, skin color, and hair color,” Dame adds. Both SNPs, they say, might be extremely
important in cases that involve people that have crossed national boundaries, as in the 2004 Madrid
Bombing, and those who commit international crimes like human trafficking. In these situations, DNA
may provide the lead to aid investigation in the absence of other clues.

Asian-specific markers

Despite these findings, much work remains to be done before the technology can be used routinely in
the Philippines. Since many of the markers used to create DNA panels originated from research that
involved Europe and the US, the project aims to generate the “Southeast Asian reference population
database” that will be more useful for local law enforcement agencies.

“We might find that many of the current DNA markers included in the panel are not useful for the
Philippine population,” Jazelyn said. Citing the case of China, which manufactures DNA kits that better
discriminate among the local population, she mentioned the possibility of creating kits that are both
cheaper and better suited to the region. “What our population-based studies can do is maybe select the
most useful markers and come up with something more applicable to the country.”

With the use of NGS, Jazelyn foresees an even larger role for DNA in forensic investigations. “Usually,”
she said, “we use DNA to answer: Whom does this belong to? But with the discovery and existence of
these SNPs, we can use Asian-specific ones to narrow the field, prior to pinpointing identities.”

Just a year after the Sierra Bouzigard story ran on National Geographic, officers arrested a suspect based
on Parabon Nanolabs’ profile. As the DNA suggested (and contrary to police speculation), the man was
not Hispanic, but Caucasian. He had fair skin and blue-green eyes. DNA later taken from an item he
discarded finally matched the sample from under Bouzigard’s nails. Police believe they have their man.

Does this case represent the future of forensic analysis in the country? With a little more work, the
answer seems to be “Yes.”