 |
| About Bioline | All Journals | Testimonials | Membership | News |
|
||||||
|
||||||
Indian Journal of Human Genetics, Vol. 11, No. 1, January-June, 2005, pp. 31-34 Original Article Heterozygosity and allele frequencies of the two VNTRs (ApoB and D1S80) in Iranian population Mahdieh Nejat, Tafsiri Elham, Karimipour Morteza, Akbari Mohammad T. Akbari Medical Genetic Laboratory, Genetic Research Center, University of Welfare and Rehabilitation Sciences, Tehran Code Number: hg05004 ABSTRACT Genetic markers are used for identity testing and paternity analysis depends on knowing the allele frequencies in the population. Minisatellites show allelic variability in the number of repeat units. We have studied the allele frequencies and heterozygosity of two VNTRs (ApoB and D1S80) in Iranian populations. A total of 96 and 82 chromosomes were analyzed by PCR and gel electrophoresis for ApoB and D1S80 respectively. In the ApoB system, allele 37 was the most common followed by allele 35 whereas allele 23 was the most common followed by allele18 at the D1S80 locus. Observed heterozygosity was relatively low in ApoB than D1S80 locus, however, no significant differences were found between observed and expected heterozygosity.Keywords: Allele frequency, heterozygosity, ApoB, D1S80, VNTR, Iranian Population INTRODUCTION The human genome contains a large amount of highly repetitive DNA sequences including many variable number of tandem repeats (VNTRs). Minisatellites are the loci composed of tandemly repeated sequences between 10 and 100 base pairs (bp)[1] and showed substantial allelic variability in the number of repeat units. The VNTR markers have been used for different applications, including linkage analysis, forensic identification, paternity testing, anthropological research and phylogenetic studies.[2],[3]One of these VNTR loci is mapped on chromosome 2 and is located 75 bp from the second polyadenylation signal at the 3 end of the apolipoprotein B gene (ApoB) and this region consists of a tandem repeat sequence, rich in A and T.[4] Higher rates of polymorphism have been found for populations of different origin and ethnicity.[2],[5],[6],[7],[8] The ApoB protein is one of the major low-density proteins and plays a central role in the metabolism of serum cholesterol. This locus is highly polymorphic and until now more than 25 alleles have been reported. Since ApoB 3 is a highly polymorphic and informative marker, it is ideal to study the genetic heterogeneity among different groups in Iranian ethnics (Kurd, Lur, Persian, etc.), similar to other allelic and loci heterogeneity such as GJB2 alleles in different populations of Iran.[9],[10] The D1S80 locus is located on chromosome 1, the largest human chromosome, and the repeating sequence at D1S80 is 16 bp in length.[11],[12] To date, 32 different alleles of D1S80 (http://www.ncbi.nlm.nih.gov/entrez/), rangeing in size from 354 bp to 850 bp have been identified. Thus, 528 different allelic combinations are theoretically possible. VNTR loci can be analysed by polymerase chain reaction (PCR) amplification and high-resolution agarose or polyacrylamide gel (PAGE) or capillary electrophoresis.[2],[3],[4],[5],[6],[7],[8],[13] There have been no studies on allele frequencies of these VNTRs in the Iranian populations. The present study was undertaken to find out the allele frequencies and heterozygosity of two VNTRs (ApoB and D1S80) locus in the Iranian populations and to compare with other Asian populations. MATERIALS AND METHODS Blood samples were collected from 48 and 41 healthy unrelated individuals for ApoB and D1S80 respectively. Genomic DNA was extracted from peripheral blood by standard methods (salting-out technique).[9] ApoB and D1S80 locus were analyzed by PCR amplification using the primers and PCR conditions as described earlier.[14],[15] The amplified product was separated on both agarose and polyacrylamide gel electrophoresis (PAGE). Following gel electrophoresis, the gels were stained using ethidium bromide and silver staining, respectively, and the repeat sizes were determined with respect to the standard Pharmacia 100-bp commercial ladder.Allele frequencies and heterozygosities were calculated using method described by Chakraborty.[16] X2 test was applied to see the association between the observed and expected heterozygosities. RESULT AND DISCUSSION Allele frequencies, observed and expected heterozygosities along with the X2 values of the two VNTRs are shown in [Table - 1]. Nine ApoB and 14 D1S80 alleles were observed. There were 31 (ApoB) and 34 (D1S80) heterozygous genotypes. The most common allele for ApoB was allele 37 and for D1S80 allele 23 which followed by allele 35 (for ApoB) and allele 18 (for D1S80). Observed heterozygosity was found to be 0.646 and 0.829 for Apob and D1S80 respectively. There was no significant differences between the observed and expected heterozygosities for both the VNTRs locus.There are many factors that suggest high heterozygosity of VNTRs loci in Iranian population, include Iran′s place on the route of the Silk Road, a history of longtime wars with foreign nations, and marked immigration from neighboring countries. On the other hand, relative ethic purity has been maintained by the natural geographic borders within Iran and by an ancient culture that encourages familiar marriages that suggest low heterozygosity. In our study, observed heterozygosity in ApoB was similar to Chinese, Malay and Indian Singaporeans, higher than Taiwanese and lower than other Asian and European populations.[3],[16],[17],[18],[19],[20],[21],[22],[23],[24],[25],[26],[27],[28] The most common alleles of D1S80 are allele 24 and 18 in the United Kingdom, USA, Canadian and Indian populations.[29],[30],[31] Although, it is rare, but in some populations such as Alaska-Inupiaq and Alaska-Yupik (USA) other alleles may be common (18 and 31 in Alaska-Inupiaq and 18 and 25 in Alaska-Yupik).[32],[33] Surprisingly, we found that alleles 23 and 18 are the most common ones. We have also compared the number of alleles and heterozygosity for ApoB in Iranian population with other world populations [Table - 2]. In our study, the number of allelea are less than the other Indian and Asian populations, however, heterozygosity is similar to the Asian populations and less than the Indian populations. Comparing Iranian populations with other world populations at the ApoB locus, provides evidence for a higher genetic diversity in Africans than non Africans. Genetic markers are used for identity testing and paternity analysis depends on knowing the allele frequencies in the population. Our preliminary results indicate that both ApoB and D1S80 are very polymorphic in the Iranian populations. However, there have been no studies on differences in allele frequencies using DNA markers in Iranian populations, and since the Iranian population is consisted of different ethnic groups hence, it will be interesting to study each group separately to look for genetic diversity. Furthermore, the number of segregating alleles and higher heterozygosity in Iranian populations further support the usefulness of ApoB and D1S80 for population genetic studies, linkage analysis and forensic purposes. ACKNOWLEDGEMENTS We are grateful of personnel of Akbari Medical Genetic Laboratory.REFERENCES
Copyright 2005 - Indian Journal of Human Genetics The following images related to this document are available:Photo images[hg05004t2.jpg] [hg05004t1.jpg] |
| |||||||||
![[Table - 1]](/showimage?hg/photo/hg05004t1.jpg){kind=link}