"دراســة جزيئية حيوية على التتابعــات القصيــرة في الحــمض النـــووي دى أوكسى ريبوزي في المجتمع المصري

Ahmed Mohamed Refaat El Sayed"  

Biomolecular study on the short tandem repeat loci of Deoxyribo Nucleic Acid

in the Egyptian population"         Ain Shams   Science      Biochemistry Ph. D 2009             "Prof. Ahmed M. Salem        Prof. Mostafa K. El-Awady

   Prof. of Biochemistry                Prof. of Molecular Genetics

      Faculty of Science                 Biomedical Technology Dept.

   Ain Shams University                 National Research Centre

  Dr. Wael Tharwat Elgarf        Dr. Walid El Sayed Zahran

Assit. Prof. of Molecular Genetics             Lecturer of Biochemistry

Biomedical Technology Dept.                Faculty of Science

National Research Centre                  Ain Shams University"                 "Short Tandem Repeat (STR) technology is currently the method of choice in all forensic investigations.  This DNA typing technique utilizes STRs that occur in non-coding regions of the human genome as these loci are highly polymorphic in human populations.  In other words, they occur in different lengths in different individuals according to how many times the nucleotide base pattern is repeated.  PCR based STR loci have several advantages over conventional southern blotting techniques of the larger VNTRs.  Where STRs differ from VNTRs in having smaller repeat units (from 2 to 7 basepairs) and the total size of a STR is smaller, usually less than 500 bases.  The smaller size means that the PCR can be used to amplify very small amounts, less than 1 ng of DNA.  It also permits analysis of degraded DNA that can not be analyzed by southern blot analysis of VNTRs, which require larger DNA fragments.

The selection of specific STR loci has produced a move toward standardization.  The Federal Bureau of Investigation (FBI) announced the selection of 13 STR loci to constitute the core of the United States national database, CODIS (Combined DNA Index System).  The European Network of Forensic Science Institutes (ENFSI) and the European DNA Profiling Group (EDNAP) has worked collaboratively to achieve standardization of DNA profiling throughout Europe.  In succession, studies were made in several populations from all different ethnic groups all over the world aiming to build a concrete idea about the heterogeneity of each STR locus inside each population.  This is done in order to evaluate the ideal DNA profiling system for each population that employs the least number of STR loci achieving the highest possible genetic variability.

The present study was conducted on 420 unrelated individuals (from both sexes, from different ages and from different parts of Egypt), using seventeen somatic STR loci: CSF1PO, THO1, TPOX, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, vWA, PentaD, and PentaE.  These loci comprise the two major DNA profiling kits;

1) AmpFlSTRÒ Identifilerä (PE Applied Biosystems).

2) PowerPlexä 16 (Promega).

It was planned to achieve a national objective to construct a genetic database for Egyptian population and putting the ideal DNA profiling system for the Egyptian population that will be applied in all DNA profiling laboratories working on Egyptian samples.

Experiments were performed on whole blood and forensic casework samples from a variety of geographical and social backgrounds.  Frequencies for each allele in STR loci were calculated and then used to evaluate the heterogeneity of each STR genetic locus using two software programs; the first is a home made Microsoft Excel program that calculates three forensic statistical parameters for each STR locus;

1.       Matching Probability (MP).

2.       Power of Discrimination (PD).

3.       Polymorphism Information Content (PIC).

And two paternity statistical parameters for each STR locus;

1.       Power of Exclusion (PE).

2.       Typical Paternity Index (PI).

This program is valuable to assess the most variant STR loci in the Egyptian population.  The second program is called STRLab software and computes for each DNA profile, two forensic statistical parameters;

1.       DNA profile matching probability.

2.       DNA profile exclusion percent.

And two paternity statistical parameters;

1.       DNA profile combined paternity index.

2.       DNA profile probability of paternity.

In order to assess the least number of the most variant STR loci and finally compose an ideal system for DNA profiling for Egyptian population.  The last step in the study is to subject all data to analysis via Arlequin Software ver. 3.1 (Excoffier et. al., 2005) to test whether each STR locus obeys or deviates from Hardy-Weinberg Equilibrium (HWE).  Arlequin software computes for every STR locus, three major statistical parameters;

1.       Observed Heterozygosity.

2.       Expected Heterozygosity.

3.       P-Value.

The current study has set the scientific basis for the ideal DNA profiling system that will be applied in Egypt and was given the name: ‘‘Egyptian DNA Index System’’ and abbreviated (EGYDIS).  This system utilizes a group of ten autosomal STR loci besides Amelogenin (as a gender- determining locus) for all applications.

It is recommended that the present study should be applied in all DNA profiling laboratories working on Egyptian individuals, to create genotype probabilities special for the Egyptian population according to the statistics made in the study.

It is also recommended that the group of STR loci chosen by the (EGYDIS) will be assembled in a commercial kit and utilized by all Egyptian DNA profiling laboratories, therefore, saving money spent in other DNA profiling kits possessing larger number of STR loci, unifying and standardizing the profiling results so that no mistrust in the legal arena."