In order to implant DNA typing methods into the Pakistani medico legal system it was necessary to study the genetic structure of the Pakistani populations. For this purpose seven hundred and sixty fresh blood and buccal swab samples were collected from seven ethnic groups the Punjabi, Pushtoon, Sindhi, Baluchi, Makrani, Brosho & Kalash. DNA extraction from the samples was performed using the PuregeneRTM kit and ChelexRTM extraction methods. The populations were profiled for three autosomal STR loci D3S1358, vWA and FGA for which modified primers were designed and allelic ladders prepared. Some of the samples were profiled using the AmpFlSTRRTM Blue kit. A database of the allele/genotype frequencies was established and the structure of the population was studied. It was established that the allele and genotype frequencies differ significantly among the Pakistani populations. In the Punjabi and Sindhi populations the exact test p value was 0.05. Substructure was detected in these populations and the FST values of 0.01-0.04 were determined between different populations in pairwise comparisons. Using a simulation study it was shown that incorporation of the substructure in the calculation of allele and genotype frequencies results in conservative estimates of the likelihood ratio of match. The analyses favoured the generation of separate databases for sub populations even if they are as closely related as are the Pakistani populations. The second part of the project was to study the populations using the Y chromosome specific STR systems. For this purpose seven Y STRs (DYS19, 3891, 389II, 390, 391, 392 & 393) were selected which define the haplotype Yh1 (Y chromosome haplotype I). Sequenced allelic ladders were prepared for all the loci. The different ethnic groups of Pakistan were profiled for these loci in two multiplex reactions and 564 complete haplotypes generated. The individual locus and haplotype frequencies were calculated for all the populations. Yh1 had a high diversity and discrimination capacity for the Pakistani populations when these populations were compared to other populations. The diversity within and between populations was determined by AMOVA. It was established that diversity for Y STRs within the populations was greater than between populations. AMOVA also revealed that there was much less diversity between the three major populations of Pakistan pointing to closer male lineage relationship between these populations. Two smaller ethnic groups the Brosho and the Kalash generated higher diversity when compared to the major populations of Pakistan. Phylogenetic trees (UPGMA & NJ) were constructed using the phylogenetic software PHYLIP. The phylogenetic analysis of the Pakistani populations suggested that the Punjabi and the Sindhi populations are closest to each other as are the Baluchi and the Makrani populations while the positions of the Kalash and Brosho populations were mostly distant from those of the other Pakistani populations
