[Informativeness of D7S2456 marker for molecular diagnosis of autosomal recessive non syndromic hearing loss in five Iranian ethnic groups]

SLC26A4 gene mutations after GJB2 mutations are the second currently identifiable genetic cause of autosomal recessive non syndromic hearing loss [ARNSHL] which currently is used in molecular diagnosis of ARNSHL. Several potential STR markers related to this region have been reported .This study was carried out to identity the informativeness of D7S2456 CA repeat STR marker in SLC26A4 gene region in five ethnic groups of the Iranian population. In this descriptive study, The locus was genotyped in 165 unrelated healthy individuals of five different ethnics including Fars, Azari, Turkmen, Gilaki and Arabs ethnic groups using polymerase chain reaction [PCR] followed by polyacrylamide gel electrophoresis [PAGE] and fluorescent capillary electrophoresis. Data was analyzed by Gene Marker HID Human STR Identity software, Gene Pop program and Microsatellite Tools software. Analysis of the allelic frequency revealed the presence of 9 alleles for D7S2456 marker in the Iranian population, which allele 5 at the D7S2456 locus with 55% frequency was the most frequent. The most frequent heterozygosity with rate of 81.8% belongs to Azari ethnic group. Analysis of deviations from Hardy-Weinberg equilibrium demonstrated that all the ethnics except Fars were in equilibrium for D7S2456 locus. D7S2456 marker is a moderately informative marker in Iranian ethnic population [PIC value within 0.44 and 0.7]. D7S2456 is a moderately informative marker in diagnosis of SLC26A4 based autosomal recessive non syndromic hearing loss in Iranian population by linkage analysis

Genetic diversity and balancing selection within the human phenylalanine hydroxylase [PAH] gene region in Iranian population

Genetic diversity of three polymorphic markers in the phenylalanine hydroxylase [PAH] gene region including PvuII [a], PAHSTR and MspI were investigated. Unrelated individuals [n=139] from the Iranian populations were genotyped using primers specific to PAH gene markers including PvuII[a], MspI and PAHSTR. The amplified products for PvuII[a], MspI were digested using the appropriate restriction enzymes and separated on 1.5% agarose. The PAHSTR alleles were identified using polyacrylamide gel electrophoresis followed by silver staining. The exact size of the STR alleles was determined by sequencing. The allele frequency and population status of the alleles were estimated using PHASE, FBAT and GENEPOP software. The estimated degree of heterozygosity for PAHSTR, MspI and PvuII [a] was 66%, 56% and 58%, respectively. The haplotype estimation analysis of the markers resulted in nine informative haplotypes with frequencies >/=5%. Moreover, the results obtained from Ewens-Watterson test for neutrality suggested that the markers were under balancing selection in the Iranian population. These findings suggested the presence of genetic diversity at these three markers in the PAH gene region. Therefore, the markers could be considered as functional markers for linkage analysis of the PAH gene mutations in the Iranian families with the PKU disease

investigation of haplotype phasing efficiency at the PAH gene region in Iranian family trios

The haplotype phasing is more useful than genotyping markers independently at carrier detection and prenatal diagnosis of diseases. The PAH gene region contains several markers used in detection of PKU disease. In the present study, the efficiency of BglII-EcoRI-VNTR haplotype phasing in Iranian family trios was investigated. Then, this information was compared with those obtained for unrelated individuals. Blood samples were collected from 20 healthy family trios and 60 unrelated individuals. The genomic DNA was extracted by use of salting-out procedure. The two markers BglII and EcoRI were genotyped by use of PCR-RFLP. The genotype of VNTR marker was identified by use of PCR and electrophoresis. The genotyping data obtained from family trios was used to infer haplotype phase. We also compared this data with results obtained from a widely used method for haplotype frequency inference from unrelated individuals, the PHASE program. The haplotype phase of all members was only ascertained at eight family trios. The comparison of this data with the results obtained by use of PHASE program showed that eight haplotypes [211, 221, 215, 216, 214, 121, 225 and 111] were informative haplotypes in Iranian population. Since diversity of BglII-EcoRI-VNTR haplotypes was high in Iranian population, haplotype phasing at family trios was difficult. The results of this study showed that the genotyping data obtained from family trios could not provide enough information for BglII-EcoRI-VNTR haplotype phasing at Iranian PKU families and the genotyping of other family members was necessary at most cases