Written by Jazelyn M. Salvador, MSc; Ma. Corazon de Ungria, PhD
STAR SCIENCE, Philippine Star
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).
***
JM Salvador (MSc Microbiology) is a university research
associate at the DNA Analysis Laboratory, Natural Sciences Research
Institute of UP Diliman since 2002.
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.
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