Filipino DNA Variation at 36 Y-chromosomal Short Tandem Repeat (STR) Marker Units
Jazelyn M. Salvador1,2*, Jae Joseph Russell B. Rodriguez1,3,
Lindsay Clare D.L. Carandang1,2, Altair B. Agmata1,2, Maria Lourdes D. Honrado1,
Frederick C. Delfin1,2, and Maria Corazon A. De Ungria1,2
1DNA Analysis Laboratory, Natural Sciences Research Institute,
University of the Philippines Diliman, Quezon City 1101 Philippines
2Philippine Genome Center, University of the Philippines, Quezon City 1101 Philippines
3Genetics and Molecular Biology Division, Institute of Biological Sciences,
College of Arts and Sciences, University of the Philippines Los Baños, Laguna 4031 Philippines
*Corresponding Author: This email address is being protected from spambots. You need JavaScript enabled to view it.
ABSTRACT
Y-chromosomal short tandem repeat (Y-STR) markers are used in deficient paternity testing cases, in the detection of male DNA in vaginal smears/swabs collected during investigations of sexual assault cases, and in the identification of missing persons and disaster victims. The increasing relevance of Y-STR DNA typing to forensic practice necessitates evaluation of new markers with high gene diversity and mutation rates in the population. This study presents the work done for the Philippine population. Y-STR haplotypes composed of 36 Y-STR marker units were analyzed in a Filipino population sample of 299 individuals using the PowerPlex® Y23 (PPY23) system and protocols of the International RM Y-STR Study Group that target a set of 13 Rapidly Mutating Y-STR (RM Y-STR) comprising 15 Y-STR marker units. Concordant results were observed at two RM Y-STR marker units, namely DYS570 and DYS576, that are included in both assays. Allele frequency and gene diversity were estimated for each Y-STR marker unit, while haplotype frequency and haplotype diversity were estimated for several combinations of Y-STR marker units. The inclusion of 15 RM Y-STR marker units increased the power of the Filipino Y-STR database to differentiate paternally related males. Comparison of the Filipino Y-STR haplotype data at 36 Y-STR marker units with other populations showed the same level of substructuring for the 21 slow and moderately mutating Y-STR marker units based on geographic locations. This highlights the importance of using an appropriate population database in forensic casework. In addition, the observed high diversity of RM Y-STR haplotypes supports the need for studying diverse group of populations to characterize the extent of RM Y-STR haplotype variation. The Filipino Y-STR haplotype database reported in this study would be of great use for reliable estimation of haplotype frequency for statistical evaluation of forensic caseworks in the Philippines.
INTRODUCTION
Male-specific polymorphisms on the non-recombining region (NRY) of the Y-chromosome, specifically short tandem repeat (STR) markers, are an important tool for forensic investigations (Roewer 2009). Y-STR DNA analysis is used in sexual assault investigations because it enables targeted analysis of the DNA of male contributor/s despite the presence of abundant female DNA in intimate samples. In addition, Y-STR DNA analysis is used for missing person investigation in cases when reference DNA samples from paternal male relatives (PMR) are available for comparison. In motherless paternity testing or when father is not available (deficient paternity cases), DNA profiles of male offspring can be compared to their PMR. . . . read more
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