Genes TOwards Justice

lab, meaning that the laboratory can only perform diagnosing and testing of swab samples. Since the start of operations, the lab has received thousands of samples from Los Baños, and around Laguna- all directed to their facility for testing and diagnosis. Thus, it was important that the protocols and procedures of the UPLB-CMDL were up to guidelines and were strictly followed to ensure that all the samples undergo proper testing.

Showcasing some of UPLB-CMDL’s biosafety and security features

As we see in television news, the norm for healthcare workers in hospitals and laboratories includes wearing full protective equipment: isolation suits, gloves, face shields, respirators or masks, and other equipment strictly fitted to them. Aside from protective equipment, UPLB-CMDL has eleven (11) out of thirteen (13) negative pressure rooms to further ensure safety of the staff and the lab’s surroundings. The rooms possibly have contaminated air, so the negative pressure prevents the air from reaching other areas. Double high-efficiency particulate air (HEPA) filters enable the filtration of the air from the contaminated areas before flowing out of the laboratory. Each room also has CCTVs with access in the administration room. If these protective gears and systems weren’t present, what would happen? Think of the game Among Us, but COVID-19 is the impostor, and is always ready to attack.

“How does UPLB-CMDL deal with the swab samples they receive?“

Dr. Diaz stated that their workflow system resembled a factory assembly line, since different personnel carry out the tasks. However, the difference is that different rooms of isolation shelters every personnel. The workflow starts with the samples being collected from partner institutions. Then, RNA extraction using spin columnbased kits occurs. The kits isolate and aid in purifying the RNA, so that no contaminants are present. Next, they prepare the PCR mix in the reagent room. They combine the PCR mix and extracted RNA in the template room. Then, real time RT-PCR amplification allows the generation of samples, showing fluorescence, which is the basis of the test result. We might think, is the sample from swabbing enough to give us results? The answer is no, but that’s where RT-PCR comes in. Reverse Transcription Polymerase Chain Reaction (RT-PCR) amplification works by transcribing the starting material (RNA) to DNA, and then copying and multiplying it to detectable amounts and then analyzed.

“How do they diagnose which samples are positive and which samples are negative?”

Three controls accompany the PCR amplification: positive control, internal control, and no template control. According to Dr. Diaz, these function in verifying the purity of the RNA, or if the gene for the SARSCoV-2 is present (positive control), verifying the purity of the RNA and the correctness of RNA extraction, which is the internal control, and verifying the purity of the PCR mix and the correctness of the whole workflow process, that is, the absence of template control. They repeat the PCR process when the controls are faulty.

How they identify which ones are positive and negative all boils down to the cycle threshold (also called cq or ct). Dr. Diaz defined the cycle threshold as the number of cycles wherein the fluorescence curve surpasses the given threshold. Different diagnostic kits have varied ct indicated on the kits. For example, when the indicated ct of the internal control is 27, the fluorescence and ct value seen in negative samples are beyond this threshold, but only to an extent. Negative samples show no amplification curve, only following the curve of the internal control. On the other hand, the fluorescence seen in positive samples are amplified within the ct of 27, say, the ct value of the positive samples is 25. Therefore, we see that the lower the ct value of the amplified sample, the more the sample contains the specific SARS-CoV-2 gene. The fluorescence seen increases as the amplified gene for SARS-CoV-2 increases, and we say the sample is positive when the fluorescence amplification is lower than the expected cycle threshold.

Late sample amplifications are one of the challenges that Dr. Diaz and her team encounter during this process. Late amplifications are those that are not within the threshold considered positive, but still showed amplification too far into the threshold considered negative. She explained that they deal with this by repeating the run of the samples. After the second PCR run, and late amplification still ensued, they recommend re-swabbing of the individual.

Laboratories, like the UPLB-CMDL, healthcare professionals, and government aid, are critical to us during these trying times. The journey of the UPLB-CMDL was a maze of obstacles and tests; still, they continue to face these challenges head on. The UPLB-CMDL, headed by Dr. Diaz, is always ready to fight with the country in this battle against COVID-19. Suits on, ready, fight!

Genes Towards Justice: Outstanding Paper Progresses Filipino Forensics

Exploring genetic diversity in Filipinos has value not only in reconstructing how human pre-history unfolded in this region of the world but also in its social impact in improving forensic DNA practice in the country. by DANIEL VARIAS (Isochore)

During its 42nd Annual Scientific Meeting held on July 8-10, 2020, the National Academy of Science and Technology (NAST) awarded one of this year’s Outstanding Scientific Paper Award to the work entitled “Filipino DNA variation at 36 Y-chromosomal short tandem repeat (STR) marker units.”. The Special Genomics Issue of the Philippine Journal of Science published the paper in 2019. Researchers from the DNA Analysis Laboratory, Natural Sciences Research ...continued on page 24

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Genes Towards Justice

Institute, UP Diliman namely Jazelyn M. Salvador, GeneSoc Alumnus aProf. Jae Joseph Russell B. Rodriguez (batch Ribozymes), Lindsay Clare dL Carandang, Altair B. Agmata, Maria Lourdes D. Honrado, Frederick C. Delfin, and GeneSoc Honorary Member, Dr. Maria A. Corazon De Ungria co-authored the paper.

The DNA is one of the most powerful and objective tools in human identification and can aid in the rapid resolution of criminal cases. The most common markers used in DNA forensics are short tandem repeats (STRs) found in the autosomes and the Y-chromosome. Polymerase chain reaction (PCR) targets these STRs. Analyzed biological samples generate DNA profiles of an evidence, which enables its comparison to the reference DNA profile of a suspect. A match between these STR profiles can affirm the presence of the suspect in the crime scene, and in many cases provide support for other evidences that confirm the guilt of the accused. Autosomal STRs are highly variable and are used for direct identification and kinship comparisons. On the other hand, Y-chromosomal STRs are male-specific and can be used to identify male DNA profiles and to establish paternal relatedness. Read more about DNA profiling of Filipino men here.

In sexual assault cases, vaginal swab samples submitted for DNA testing contain a mixture of DNA coming from a female victim and the male perpetrator/s. Interpreting such male-female mixtures using autosomal STRs can be a complicated task for DNA analysts. However, the male-specificity of Y-chromosome markers enables the isolation of a male assailant’s DNA profile, thus its value in resolving sexual assault cases.

The weight of a DNA match depends on demonstrating its rarity in the population. This is made possible by establishing a database of reference DNA profiles representative of the population from which frequencies of alleles and haplotypes can be estimated. To establish such database for Filipinos, the team of scientists headed by Dr. De Ungria, invited 299 unrelated Filipino males from the Greater Manila Area. They took part in this genetic study where they consented to provide blood samples for Y-chromosome STR (Y-STR) DNA typing. The team analyzed 36 Y-STR marker units including 13 rapidly mutating (RM) Y-STRs. With the expansion of the database of the Filipino Y-STRs, the capacity to conduct forensic DNA investigation involving male comparisons is augmented. For example, the use of the RM Y-STRs will enable differentiation between paternal relatives, which was previously not possible with the slow mutating markers. This has important implications when suspects are related along the paternal line.

When compared with other populations, structuring was observed which can be explained by geographic proximity particularly for the 21 slow and moderately mutating Y-STR marker units. This reflects the distinct composition of our country’s Y-chromosome diversity. It also highlights the need for a specific Filipino DNA database when statistically evaluating the weight of DNA evidence in relation to criminal investigations and kinship tests. The database merits continuous expansion to include more samples from different groups, e.g. from other regional centers and those from specific ethno-linguistic groups, indigenous peoples/ indigenous cultural communities (IPs/ICCs) that are part of the Philippine population. “There is absolute need to further expand the database through the addition of more human samples in order to better represent the diverse communities and groups that we have in the Philippines, all of whom contribute to the Philippine identity.” Dr. De Ungria said.

“Being selected as one of the outstanding papers by NAST provides us a wonderful opportunity to talk about this aspect of our research at the DNA Analysis Laboratory, Natural Sciences Research Institute, UP Diliman. Besides being recognized for the passion in which we worked to do the science and the clarity to communicate this science to the public whilst asking vital questions about the Philippine genome highlight the value we place in studying our own genome. Our genome is like an ‘autobiography’ that contains the story of our past, the genetic signals that we have now and that we need to understand in order to survive the present, and the evolutionary mechanisms which we need to reach the future.” Dr. De Ungria stated.

Behind the success, however, are daunting challenges they have surpassed. Assistant Prof. Rodriguez mentioned that the main challenge is going through the various processes to obtain institutional approvals including the approval from an accredited ethics review committee after it has scrutinized the ethical aspect of our research, which Dr. De Ungria affirmed. “Because DNA contains the entire genetic code of an individual, there is absolute need to minimize risk and maximize the benefits from this type of research,” she ...continued on page 25

Health information cascades from one social media user to another. Each of them participates in a series of changing of profile photo frames and sharing of infographics and webinars with a healthier Philippines in mind. Such revolutionary scheme drives the First National Social Media Awareness Campaign on Preconception Health of Volunteer Youth Leaders for Health-Philippines from August 24 to 29, 2020.

About the Advocacy

VYLH-Philippines conducts the social media campaign to conceive more advocates for their fourth and latest advocacy: preconception health, i.e. the health and wellness of people within their reproductive years. The need to advocate preconception health arises as birth defects and preterm births annually afflict 23 million babies worldwide, with emphasized incumbrance towards low- and middle-income countries (LMICs) like the Philippines. Thus, the advocacy is an effort to prevent deaths of newborns and children below the age of five by 2030, which is part third Sustainable Development Goal of the United Nations: Good Health and Well-Being.

The inequalities in survival rates of premature infants are alarming, especially in low-income countries, where half of the babies born two months early die due to the absence of feasible and cost-effective care such as incubation, breastfeeding, and infection and respiration management. Those who survive, however, are at risk of facing lifelong learning disabilities and/or audiovisual impairments. Multiple pregnancies, infections, and chronic illnesses of the parents commonly cause preterm births, where mothers give birth to infants before 37 weeks of pregnancy, though currents

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Genes Towards Justice

“Because DNA contains the entire genetic code of an individual, there is absolute need to minimize risk and maximize the benefits from this type of research,” she said.

Amongst the many challenges faced in forensic genomics research is working to balance the need for openness in sharing scientific discovery and protecting the genetic privacy of the individuals who generously contribute their own samples to advance Philippine genomic science for the common good of this and future generations.

#PreconceptionHealthPH—Rippling Awareness Across Social Media

by DANIEL VARIAS (Isochore)

studies could not conclude a specific cause.

Another cause of newborn and children impairment and death are congenital anomalies, i.e. commonly notorious for the term “birth defects.” These are functional anomalies occurring while the fetus resides in the womb. However, it is concerning that 94% of congenital anomalies occur in LMICs, and survivors of these defects often face deficient access to support services amid social stigma, discrimination, and distance from community interaction. Some birth defects, on the other hand, are preventable through screening, vaccination, medical care during pregnancy, and adequate supplementation of nutrients such as folic acid and iodine.

With preconception health catering the health of people within the reproductive age to ensure healthy newborns, the advocacy shines the most not only in reducing preterm births and birth defects, but also in promoting the overall health of the community throughout age brackets: from neonatal to adulthood.

L.I.N.C. Framework—Link to Preconception Health

Promoting preconception health utilizes the Lifestyle, Infection, Nutrition, and Contraception (L.I.N.C.) framework to address the risk factors associated with birth defects and preterm birth. In 2006, the Global Report on Birth Defects identified these risk factors. Six years later, Born Too Soon: The Global Action Reports on Preterm Births followed up in identifying the factors. Through the framework, people within the reproductive age achieve physical, social, and psychological health to keep diseases at bay, thus sparing future newborns from the perils or congenital anomalies and preterm births.

The L.I.N.C. framework fosters a checklist for everyone monitoring their health for conception. Under the Lifestyle component, the framework implores us to refrain from alcohol consumption, smoking, illegal drug usage, exposure to harmful chemicals, seeking medical advice for chronic illnesses, and medication intake. It also encourages 150 minutes of weekly exercise, stress management, and mental healthcare.

Under the Infection component, the framework urges every person to avoid contacting infectious diseases through vaccination, proper hygiene, sanitation, and food preparation. The framework also promotes safe sex to avoid Sexually Transmitted Diseases (STDs) along with STD screening.

Moving on to the Nutrition component, the framework reminds everyone to combat malnutrition by maintaining a balanced, nutrient-packed diet and being knowledgeable of the “10 Kumainments” and “Pinggang Pinoy.” Lastly, the Contraception component of the framework promotes family planning to future parents through information dissemination on the right age of pregnancy, proper time it takes before the next pregnancy, planned number of children in the family, the importance of family history regarding genetic diseases, intake of dietary supplements especially folic acid, and vaccination advice upon preconception.

Heeding the Advocacy

Amid the COVID-19 pandemic, VYLH-Philippines and their partner organizations promote preconception health through initiatives that utilize social media. They released publicity materials that inform the public about preconception health and the L.I.N.C. framework through infographics posted and shareable on Facebook pages and profiles. Social media users are also able to set up frames on their profile pictures with captions on advocating about preconception health. They also organized a webinar on preconception health to be held on August 29, 2020, 7 PM.