DNA profiling of Filipino men: Why the Y?

Y-chromosome DNA typing is the most useful test for male identification since this chromosome is found only in males, and is passed from fathers to sons. Hence, paternal grandfathers, fathers, sons and their male relatives along an uninterrupted paternal line share the same Y chromosome. In fact, one can trace one’s paternal ancestors through many generations using Y chromosome data. Results of Y chromosome studies of different populations are consistent with the identified African origin of humankind. The question of human origin has been the subject of many studies and featured in many exhibits such as those found at the Cradle of Humankind Museum, a UNESCO World Heritage Site located in the Gauteng province in South Africa (http://www.gauteng.net/cradleofhumankind). Y-DNA typing data, consistent with archaeological evidence, has contributed to the concept of the “African Adam,” and show that all anatomically modern humans originated from a common ancestor that lived in Africa.

Besides the utility of using Y data in tracing paternal histories, Y-DNA profiling is also used in characterizing forensic samples and in identifying human remains. In forensics, Y-chromosome DNA typing involves the use of Short Tandem Repeat (STR) markers. STRs are short sequences of DNA that are repeated adjacent to each other. The number of times STRs are repeated in the DNA of a person may be different with that of another person. However, all males who are descendants from the same paternal line will have similar Y-chromosome STR (Y-STR) DNA profiles. A Y-STR DNA profile is generated via capillary gel electrophoresis and consists of a single copy of each STR marker per person. Since these markers are all located in the one chromosome, the Y-STR DNA profile is referred to as a haplotype. Y-STR DNA profiles are then compared to global reference databases (http://www.yhrd.org/) to determine the frequency of a Y haplotype profile in a population. The frequency value of a Y-haplotype is needed in calculating the likelihood ratio (LR) that a sample is from an individual over a random match in a given population. Higher LR values indicate a greater probability that the suspect is the source of the male DNA contained in the crime scene sample.

Initially, Y DNA profiling included a minimal Y haplotype with nine STR markers, namely DYSI9, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 and DYS385a and DYS385b. Subsequently, commercial kits that involve the simultaneous genotyping or multiplexing of 11 up to 23 Y-STR markers were made available. Increasing the number of Y-STR markers increases the capacity of the DNA test to distinguish two persons. In environmentally challenged samples where the amount of DNA is limited, multiplexing results in the generation of more genetic information per given amount of sample. In 2003 and 2008, the DNA Analysis Laboratory of the Natural Sciences Research Institute (UP-NSRI DAL; www.dnaforensic.org) reported the establishment of a Y-STR Philippine database using seven and 10 Y-STR DNA markers, respectively. In 2013, the laboratory expanded the database to include up to 23 Y-STR markers which it now uses for routine casework and population genetic studies. The most notable use of the Y-STR database was in the identification of child victims of the fire in Paco that ravaged the Assosacion de Damas de Filipinas social welfare institution in 1998. Because the children were buried without proper identification, the UP-NSRI DAL assisted the UP College of Medicine and the Department of Dentistry in processing human remains that were exhumed following the request of the families who lost their children in the fire. Another important use of Y-STR profiling is the identification of male DNA in intimate samples collected from sexual assault victims. The fact that Y-DNA is found in the samples, especially from minors, supports a victim’s allegation of rape. Work to validate an effective investigative system of rape cases that includes the routine collection of biological samples from victims for DNA profiling, is underway at UP-NSRI DAL (http://www.philstar.com/science-and-technology/2013/02/21/911156/dna-testing-sexual-assault-cases-surmounting-challenges).

In 2011, a set of Y-STR markers termed as “rapidly mutating (RM) Y-STRs” were found to mutate faster compared to conventional markers in European populations. Unlike conventional Y-STRs, the high mutation rate of RM YSTRs has the potential to distinguish fathers and sons as well as other paternally related individuals. This is important in population evolutionary genetics when there is a need to distinguish paternally related males in small communities where most men are related to each other; and in forensic investigations which require the individuation of the actual source of sample. To evaluate the utility of RM-YSTRs in the Philippines, the UP-NSRI DAL and the Program on Forensics and Ethnicity, Philippine Genome Center (PGC-PFE) received financing from the Philippine Health Research and Development of the Department of Science and Technology (DOST-PCHRD) in 2013. The study involves the Y-DNA profiling of 150 males and two of their paternally related relatives using conventional and RM YSTR genetic markers. Results to be generated in this new initiative are expected to further increase the utility of Y-DNA profiling in answering questions of our genetic past, in assisting to solve current problems and in looking forward to a more genetically informed future.

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This ongoing study that is funded by the Philippine Council for Health Research and Development (PCHRD) of the Department of Science and Technology (DOST) is looking for males with two paternal relatives who are equally willing  to volunteer. For more information, the authors may be contacted via phone (925-2965), text (09064058783 or 09155327264) or e-mail (rm.ystr@gmail.com). Volunteers will be provided with their Y-DNA profile once the study is completed.

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JM Salvador is a BS Biology and MSc Microbiology graduate of UP Manila and UP Diliman, respectively. She is a university research associate at the DNA Analysis Laboratory, Natural Sciences Research Institute of UP Diliman since 2002. She received the UP Diliman Gawad Chancellor para sa Natatanging Research, Extension and Professional Staff (Research Category) in 2009. 

MCA De Ungria is the current head of the DNA Analysis Laboratory and the director of the Program on Forensic and Ethnicity of the Philippine Genome Center. The UP-NSRI DNA Laboratory offers its parentage testing and DNA profiling expertise as part of its commitment to serve the community. The laboratory may be contacted at 632 925-2965 and updnalab@gmail.com.