Genotyping of 25 highly informative autosomal SNPs in population of Khuzestan province using the SNaPshot method

Subject Areas : biology

payam hajibabaei ¹ (Department of Genetics & Biotechnology, School of Biological Science, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran)
mahmoud tavalaei ² (Human Genetic Research Center, Baqiyatallah University of Medical Science, Tehran, Iran)
shohreh zare karizi ³ (Department of Genetics & Biotechnology, School of Biological Science, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran)

Received: 2017-08-13 Accepted : 2017-12-09 Published : 2017-12-21

Keywords: Khuzestan, Autosomal SNPs, SNPforID, SnapShot,

Abstract :

Single nucleotide polymorphisms (SNPs) are being increasingly used by forensic laboratories. In Iranian population, few studies have been reported with aim to investigation allelic frequencies and determination of genetic variation of SNPs based on SNP for ID database. The goal of this study was to evaluate of population genetic diversity by genotyping of 25 informative autosomal single nucleotide polymorphisms residing in Khuzestan province by using the SNaPshot assay. The cross-sectional study, the results of bioinformatics analysis indicated that at least 25 autosomal loci SNPs had the power to discriminate between the Iranian Ethnicity. A total of 53 unrelated individuals from Arab ethnicity group were extracted genomic DNA from blood samples. Genotyping 25 selected SNPs by using SNapShot method on the 3110xl Genetic Analyzer were performed. Statistical analysis was calculated using the Arlequin 3.5 & Gene Alex 6.5 soft wares. The mean heterozygosity was calculated 0.428, also the minimum heterozygosity was observed 0.190 that relate to rs938283.  Minor allele frequency (MAF) for rs938283 was 0.105. There was significant deviation in allelic frequencies from Hardy-Weinberg equilibrium for all the studied SNPs except rs1382387. The calculated FST values and Evaluation of the 25 autosomal SNPs simultaneously, presented that among Arabs and three Iranian ethnic groups including Kurd, Persian and Lurs were not significantly genetic different and thay are similar to each other. Finally, it is obvious that this 25 autosomal SNPs enable to discriminate between ethnic groups within the population. The SnapShot method has appropriate sensitivity and specificity in order to simultaneously SNP genotyping.

References:

1. Cheung, K. H., Osier, M. V., Kidd, J. R., Pakstis, A. J., Miller, P. L., Kidd, K. K., Alfered. H., 2000. An allele frequency database for diverse populations and DNA polymorphisms. Nucleic Acids Research 28(1): 361-3.


2. http://www.nationsencyclopedia.com/Asia-and-Oceania/Iran-ETHNIC- GROUPS.html.


3. Goodwin, W., Linacre, A., Hadi, S., 2011. An introduction to forensic genetics. second edition, John Wiley & Sons. UK, pp. 38-220.


4. Sunnucks, P., 2000. Efficient genetic markers for population biology. Trends in Ecology & Evolution 15(5):199-203.


5. Butler, J. M., 2005. Forensic DNA typing: biology, technology, and genetics of STR markers. second edition, Academic Press. USA, pp.220-310.


6. Butler, J. M., Coble, M. D., Vallone, P. M., 2007. STRs vs. SNPs: thoughts on the future of forensic DNA testing. Forensic Science, Medicine and Pathology 3(3): 200-5.


7. Sanchez, J. J., Phillips, C., Børsting, C., Balogh, K., Bogus, M., Fondevila, M., 2006. A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27(9): 1713.


8. Amigo, J., Phillips, C., Lareu, M., Carracedo, Á., 2008. The SNP for ID browser: an online tool for query and display of frequency data from the SNPforID project. International Journal of Legal Medicine 122(5): 435-40.


9. Coble, M. D., Just, R. S., O’Callaghan, J. E., Letmanyi, I. H., Peterson, C. T., Irwin, J. A., 2004. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. International Journal of Legal Medicine 118(3): 137-46.


10. Phillips, C., Salas, A., Sanchez, J., Fondevila, M., Gomez-Tato, A., Alvarez-Dios, J., 2007. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Science International Genetics 1(3): 273-80.  


11. Walsh, S., Liu, F., Ballantyne, K. N., Van-Oven, M., Lao, O., Kayser, M., 2011. Iris Plex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic Science International Genetics 5(3): 170-80.


12. Drobnic, K., Borsting, C., Rockenbauer, E., Tomas, C.., Morling, N., 2010. Typing of 49 autosomal SNPs by SNaPshot in the Slovenian population. Forensic Science International Genetics 4(5): e125-7.


13. Tomas, C., Diez, I. E., Moncada, E., Borsting, C., Morling, N., 2013. Analysis of 49 autosomal SNPs in an Iraqi population. Forensic Science International Genetics 7(1): 198-9.


14. Sharafi, F. M., Tomas, C., Borsting, C., Zeinali, Z., Malekdoost, M., Zeinali, S., 2013. Analysis of 49 autosomal SNPs in three ethnic groups from Iran: Persians, Lurs and Kurds. Forensic Science International Genetics 7(4): 471-3.


15. Ali, S. M., Mahnaz, S., Mahmood, T., 2008. Rapid genomic DNA extraction (RGDE). Forensic Science International Genetics Supplement Series 1(1): 63-5.


16. Budowle, B., Van-Daal, A., 2008. Forensically relevant SNP classes. Biotechniques: The International Journal of Life Science Methods 44(5): 603.


17.  Daniel, R., Santos, C., Phillips, C., Fondevila, M., Van-Oorschot, R., Carracedo, A., 2015. A SNaPshot of next generation sequencing for forensic SNP analysis. Forensic Science International Genetics 14: 50-60.


18. Waples, R. S., Gaggiotti, O., 2006. Invited review: What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15(6): 1419-39.


19. Phillips, M. L., 2008. Crime scene genetics: transforming forensic science through molecular technologies. BioScience 58(6): 484-9.


20. Børsting, C., Sanchez, J. J., Hansen, H. E., Hansen, A. J., Bruun, H. Q., Morling, N., 2008. Performance of the SNP for ID 52 SNP-plex assay in paternity testing. Forensic Science International Genetics 2(4): 292-300.