An investigation of 10 Y-STR loci and the detection of specific haplotype frequencies in Turkish population

Aydın Rüstemoglu, Güvem Gümüs Akay, Halil Gürhan Karabulut, Ahmet Kadıkıran, Işık Bökesoy

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DOI: 10.4236/ajmb.2011.12012                

Abstract

This study is to survey 10 Y-STR loci in 241 males from Turkey. In this study, the 241 healthy and unrelated males living in different parts of Turkey for at least three generations were included. Genomic DNAs were isolated from peripheral blood samples by standard phenol-chloroform extraction method. 10 Y-STR loci including DYS19, DYS385a/b, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, and YCAIIa/b were analyzed by using PCR and denaturing PAGE. Allele frequencies, gene diversities and haplotype frequencies were analyzed. Gene diversity per locus varied from 0.5788 (DYS388) to 0.8903 (DYS385a/b). The numbers of haplotypes in minHt recommended by YCC and Ht10 have been 208 and 186, respectively. When our minHt haplotypes frequencies compared with the other seven populations, we have found statistically significant differences between our results and other populations (P < 0.01) except that Czech population (P > 0.05). We suggest that an alternative haplotype designated as aHt maybe alternative to minHt in respect of its Y-STR content with the highest gene diversity value. The aHt haplotype has found a higher discriminatory potential than minHt haplotype with a better Pd combined value (0.9999936 vs 0.9999836) and has higher average gene diversity per locus (0.7834 vs 0.7518) in Turkish population. aHt haplotype can be proposed as an alternative to minHt in paternity testing and forensic medicine applications involving Turkish male population. This study has also provided additional information to the framework of variation involving 10 Y-STR loci as well as a further contribution to the Y-STR database for Turkish male population.

Keywords

Y Chromosome; Y-STR; Polymorphism; Ha- plotype; Turkey.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	de Knijff, P. (2000) Messages through bottlenecks: On the combined use of slow and fast evolving polymorphic markers on the human Y chromosome. The American Journal of Human Genetics, 67, 1055-1061.
[2]	Spurdle, A.B., Woodfield, D.G., Hammer, M.F. and Jenkins, T. (1994) The genetic affinity of Polynesians: Evidence from Y chromosome polymorphisms. Annals of Human Genetics, 58, 251-263. doi:10.1111/j.1469-1809.1994.tb01889.x
[3]	Dupuy, B.M., Stenersen, M., Egeland, T. and Ola?sen, B. (2004) Y-chromosomal microsatellite mutation rates: Differences in mutation rate between and within loci. Hum Mut, 23, 117-124. doi:10.1002/humu.10294
[4]	Gill, P., Brenner, C., Brinkmann, B., Budowle, B., Carracedo, A., Jobling, M.A., de Knijff, P., Kayser, M., Krawczak, M., Mayr, W.R., Morling, N., Olaisen, B., Pascali, V., Prinz, M., Roewer, L., Schneider, P.M., Sajantila, A. and Tyler-Smith, C. (2001) DNA Commission of the International Society of Forensic Genetics: Recommendations on forensic analysis using Y-chromosome STRs. Forensic Science International, 124, 5-10. doi:10.1016/S0379-0738(01)00498-4
[5]	Betz, A., B?bler, G., Dietl, G., Syeil, X., Weyermann, G. and Pflug, W. (2001) DYS STR analysis with epithelial cells in a rape case. Forensic Science International, 118, 126-130. doi:10.1016/S0379-0738(00)00482-5
[6]	Corach, D., Figueira, R.L., Marino, M., Penacino, G. and Sala, A. (2001) Routine Y-STR typing in forensic case-work. Forensic Science International, 118, 131-135. doi:10.1016/S0379-0738(00)00483-7
[7]	Dekairelle, A.F. and Hoste, B. (2001) Application of a Y-STR-pentaplex PCR (DYS19, DYS389I and II, DYS390 and DYS393) to sexual assault cases. Forensic Science International, 118, 122-125. doi:10.1016/S0379-0738(00)00481-3
[8]	Gill, P., Werrett, D.J., Budowle, B. and Guerrieri, R. (2004) An assessment of whether SNPs will replace STRs in national DNA databases—joint considerations of the DNA working group of the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM). Science & Justice, 44, 51-53. doi:10.1016/S1355-0306(04)71685-8
[9]	Honda, K., Tun, Z., Young, D. and Terao, T. (2001) Examination of Y-STR mutations in sex chromosomal abnormality in forensic case. Forensic Science International, 118, 136-140. doi:10.1016/S0379-0738(00)00484-9
[10]	Jobling, M.A., Pandya, A. and Tyler-Smith, C. (1997) The Y chromosome in forensic analysis and paternity testing. International Journal of Legal Medicine, 110, 118-124. doi:10.1007/s004140050050
[11]	Kayser, M. and Sajantila, A. (2001) Mutations at Y-STR loci: Implications for paternity testing and forensic analysis. Forensic Science International, 118, 116-121. doi:10.1016/S0379-0738(00)00480-1
[12]	Alaves, C., Gusmao, L., Barbosa, J. and Amorim, A. (2003) Evaluating the informative power of Y-STRs: A comparative study using European and new African haplotype data. Forensic Science International, 134, 126-133. doi:10.1016/S0379-0738(03)00127-0
[13]	Gusmao, L., Sanchez-Diz, P., Alves, C., Beleza, S., Lopes, A., Carracedo, A. and Amorim, A. (2003) Grouping of Y-STR haplotypes discloses European geografic clines. Forensic Science International, 134, 172-179. doi:10.1016/S0379-0738(03)00160-9
[14]	Koyama, H., Iwasa, M., Maeno, Y., Tsuchimochi, T., Isobe, I., Yoshimi, S.N., Jun, M.O., Matsumoto, T., Horii, T. and Nagao, M. (2001) Y-chromosomal STR haplotype in the Japanese population. Forensic Science International, 124, 221-223. doi:10.1016/S0379-0738(01)00572-2
[15]	Nakagome, Y., Young, S.R., Akane, A., Numabe, H., Jin, D.K., Yamori, Y., Seki, S., Tamura, T., Nagafuchi, S., Shiono, H. and Nakahori, Y. (1992) A Y-associated alele may be characteristic of cetain ethnic groups in Asia. Annals of Human Genetics, 56, 311-314. doi:10.1111/j.1469-1809.1992.tb01158.x
[16]	Rodig, H., Grum, M. and Grimmecke, H.-D. (2007) Population study and evaluation of 20 Y-chromosome STR loci in Germans. International Journal of Legal Medicine, 121, 24-27. doi:10.1007/s00414-005-0075-5
[17]	Rustamov, A., Gümü?, G., Karabulut, H.G., Elhan, A.H., Kad?k?ran, A. and B?kesoy, I. (2004) Y-STR polymorphism in Central Anatolian region of Turkey. Forensic Science International, 139, 227-230. doi:10.1016/j.forsciint.2003.11.009
[18]	Yan, J., Tang, H., Liu, Y., Jing, Y., Jiao, Z., Zhang, Q., Gao, J., Shang, L., Guo, H. and Yu, J. (2007) Genetic polymorphisms of 17 Y-STRs haplotypes in Chinese Han population residing in Shandong province of China. Legal Medicine, 9, 196-202. doi:10.1016/j.legalmed.2006.11.016
[19]	Park, M.J., Lee, H.Y, Chung, U., Kang, S.-C. and Shin, K.-J. (2007) Y-STR analysis of degraded DNA using reduced-size amplicons. International Journal of Legal Medicine, 121, 152-157. doi:10.1007/s00414-006-0133-7
[20]	Willuweit, S. and Roewer, L. (2007) Y chromosome haplotype reference database (YHRD): Update. Forensic Science International, 1, 83-87. doi:10.1016/j.fsigen.2007.01.017
[21]	YHRD-Y Chromosome Haplotype Reference Database. (2011). http://www.yhrd.org
[22]	Sambrook, J. and Russell, D. (2001) Molecular Cloning: A Laboratory Manual. 3rd Edition, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 543-554.
[23]	Santos, F.R., Pena, D.J. and Epplen, J.T. (1993) Genetic and population study of a Y-linked tetranucleotide repeat DNA polymorphism with a simple non-isotopic technique. Human Genetics, 90, 655-656. doi:10.1007/BF00202486
[24]	Nei, M. (1996) Phylogenetic analysis in molecular evolutionary genetics. Annual Review of Genetics, 30, 371-403. doi:10.1146/annurev.genet.30.1.371
[25]	Kimberly, A.H. (2001) Statistical analyses of STR data profiles in DNA. http://promega.de/profiles/103/Profile-sinDNA_103_14.pdf.
[26]	Ljubkovic, J., Stripisic, A., Sutlovic, D., Definis-Gojanovic, M., Bucan, K. and Andelinovic, S. (2008) Y-chromosomal short tandem repeat haplotypes in southern croatian male population defined by 17 loci. Croatian Medical Journal, 49, 201-206. doi:10.3325/cmj.2008.2.201
[27]	Ehler, E., Marvan, R. and Vanek, D. (2010) Evaluation of 14 Y chromosomal short tandem repeat haplotype with focus on DYS449, DYS456, and DYS458: Czech population sample. Croatian Medical Journal, 51, 54-60. doi:10.3325/cmj.2010.51.54
[28]	Hara, M., Kido, A., Takada, A., Adachi, N. and Saito, K. (2007) Genetic data for 16 Y-chromosomal STR loci in Japanese. Legal Medicine, 9, 161-170. doi:10.1016/j.legalmed.2006.11.002 [1] Demir?in, S. and Timur, S. (2010) Haplotype analysis of 8 Y-STR loci in the Antalya population. Romanian Journal of Legal Medicine, 18, 51-58. [2] Henke, J., Henke, L., Chatthopadhyay, P., Kayser, M., Dulmer, M., Cleef, S., Poche, H. and Felske, Z.H. (2001) Application of Y-chromosomal STR haplotypes to forensic genetics.
[29]	Demir?in, S. and Timur, S. (2010) Haplotype analysis of 8 Y-STR loci in the Antalya population. Romanian Journal of Legal Medicine, 18, 51-58.
[30]	Henke, J., Henke, L., Chatthopadhyay, P., Kayser, M., Dulmer, M., Cleef, S., Poche, H. and Felske, Z.H. (2001) Application of Y-chromosomal STR haplotypes to forensic genetics. Croatian Medical Journal, 42, 292- 297.